Title of Invention

ORDERED MOLECULAR PRESENTATION OF ANTIGENS, METHOD OF PREPARATION AND USE .

Abstract The invention provides compositions and processes for the production of ordered and repetitive antigen or antigenic determinant arrays. The compositions of the invention are useful for the production of vaccines for the prevention of infectious diseases, the treatment of allergies and the treatment of cancers. Various embodiments of the invention provide for a virus, virus-like particle, viral capsid particle, phage or recombinant form thereof coated with any desired antigen in a highly ordered and repetitive fashion as the result of specific interactions. In one specific embodiment, a versatile new technology based on a cassette-type system (Alpha Vaccine Technology) allows production of antigen coated viral particles. Other specific embodiments allow the production of antigen coated hepatitis B virus-like particles or antigen coated Measles virus-like particles.
Full Text Field of the Invention
The present invention is related to the fields of molecular biology,
virology, immunology and medicine. The invention provides a composition
comprising in ordered and repetitive antigen or antigenic determinant array. The
invention also provides a process for producing an antigen or antigenic
determinant in an ordered and repetitive array. The ordered and repetitive antigen
or antigenic determinant is useful in the production of vaccines for the treatment
of infectious diseases, the treatment of allergies and as a pharmaccine to prevent
or cure cancer and to generate defined self-specific antibodies.
RelatedArt
Vaccine development for the prevention of infectious disease has had the
greatest impact on human health of any medical invention. It is estimated that
three million deaths per year are prevented worldwide by vaccination (Hillemann,
Nature Medicine 4:507 (1998)). The most common vaccination strategy, the use
of attenuated (i.e. less virulent) pathogens or closely related organisms, was first
demonstrated by Edward Jenner in 1796, who vaccinated against smallpox by the
administration of a less dangerous cowpox virus. Although a number of live
attenuated viruses (e. g. measles, mumps, rubella, varicella, adenovirus, polio,
influenza) and bacteria (e. g. bacille Calmette-Guerin (BCG) against tuberculosis)
are successfully administered for vaccination, there is a risk for the development
of serious complications related to a reversion to virulence and infection by the
'vaccine' organism, in particular in immunocompromised individuals.

The specific design of attenuated viruses is now enabled by recombinant
DNA technology (i.e., genetic engineering) through the generation of deletion or
mutation variants. For example, the administration of an engineered Simian
Immunodeficiency Virus (SIV) with a deletion within the nef'gene was shown to
protect macaques from subsequent infection with a pathogenic SIV strain (Daniel
et al, Science 255:1938-1941 (1992)). However, the progression of acquired
immunodeficiency syndrome (AIDS)-like symptoms in animals administered
attenuated SIV raises safety concerns (Baba et al., Science 267:1820-1825
((1995)).
As an alternative approach, attenuated viruses or bacteria may be used as
carriers for the antigen-encoding genes of a pathogen that is considered too unsafe
to be administered in an attenuated form (e.g., Human Immunodeficiency Virus
(HIV)). Upon delivery of the antigen-encoding gene to the host, the antigen is
synthesized in situ. Vaccinia and related avipox viruses have been used as such
carriers for various genes in preclinical and clinical studies for a variety of
diseases (e.g., Shen et al, Science 252:440 (1991)). One disadvantage of this
vaccination strategy is that it does not mimic the virion surface, because the
recombinant protein is expressed on the surface of the host cell. Additionally,
complications may develop in immunocompromised individuals, as evidenced by
life-threatening disseminated vaccinia infections (Redfield. N. Eng. J. Med.
316:673 ((1998)).
A fourth vaccination approach involves the use of isolated components of
a pathogen, either purified from the pathogen grown in vitro (e.g. influenza
hemagglutinin or neuraminidase) or after heterologous expression of a single viral
protein (e.g. hepatitis B surface antigen). For example, recombinant, mutated
toxins (detoxified) are used for vaccination against diphtheria, tetanus, cholera
and pertussis toxins (Levine et al, New generation vaccines. 2nd edn., Marcel
Dekker, Inc., New York 1997), and recombinant proteins of HI V (gp 120 and full-
length gpl 60) were evaluated as a means to induce neutralizing antibodies against
HIV with disappointing results (Connor et al, J. Virol. 72:1552 (1998)).

Recently, promising results were obtained with soluble oligomeric gpl60, that
can induce CTL response and elicit antibodies with neutralizing activity against
HIV-1 isolates (Van Cortt et al, J. Virol. 71:4319(1997)). In addition, peptide
vaccines may be used in which known B- or T-cell epitopes of an antigen are
coupled to a carrier molecule designed to increase the immunogenicity of the
epitope by stimulating T-cell help. However, one significant problem with this
approach is that it provides a limited immune response to the protein as a whole.
Moreover, vaccines have to be individually designed for different MHC
haplotypes. The most serious concern for this type of vaccine is that protective
antiviral antibodies recognize complex, three-dimensional structures that cannot
be mimicked by peptides.
A more novel vaccination strategy is the use of DNA vaccines (Donnelly
et al, Ann. Rev. Immunol. 15:617 (1997)), which may generate MHC Class I-
restricted CTL responses (without the use of a live vector). This may provide
broader protection against different strains of a virus by targeting epitopes from
conserved internal proteins pertinent to many strains of the same virus. Since the
antigen is produced with mammalian post-translational modification,
conformation and oligomerization, it is more likely to be similar or identical to
the wild-type protein produced by viral infection than recombinant or chemically
modified proteins. However, this distinction may turn out to be a disadvantage
for the application of bacterial antigens, since non-native post-translational
modification may result in reduced immunogenicity. In addition, viral surface
proteins are not highly organized in the absence of matrix proteins.
In addition to applications for the prevention of infectious disease, vaccine
technology is now being utilized to address immune problems associated with
allergies. In allergic individuals, antibodies of the IgE isotype are produced in an
inappropriate humoral immune response towards particular antigens (allergens).
The treatment of allergies by allergy immunotherapy requires weekly
administration of successively increasing doses of the particular allergen over a
period of up to 3-5 years. Presumably, 'blocking' IgG antibodies are generated

that intercept allergens in nasal or respiratory secretions or in membranes before
they react with IgE antibodies on mast cells. However, no constant relationship
exists between IgG titers and symptom relief. Presently, this is an extremely
time- and cost-consuming process, to be considered only for patients with severe
symptoms over an extended period each year.
It is well established that the administration of purified proteins alone is
usually not sufficient to elicit a strong immune response; isolated antigen
generally must be given together withhelper substances called adjuvants. Within
these adjuvants, the administered antigen is protected against rapid degradation,
and the adjuvant provides an extended release of a low level of antigen.
Unlike isolated proteins, viruses induce prompt and efficient immune
responses in the absence of any adjuvants both with and without T-cell help
(Bachmann & Zinkernagel, Ann. Rev. Immunol. 15:235-270(1997)). Although
viruses often consist of few proteins, they are able to trigger much stronger
immune responses than their isolated components. For B cell responses, it is
known that one crucial factor for the immunogenicity of viruses is the
repetitiveness and order of surface epitopes. Many viruses exhibit a quasi-
crystalline surface that displays a regular array of epitopes which efficiently
crosslinks epitope-specific immunoglobulins on B cells (Bachmann &
Zinkernagel, Immunol. Today 77:553-558 (1996)). This crosslinking of surface
immunoglobulins on B cells is a strong activation signal that directly induces cell-
cycle progression and the production of IgM antibodies. Further, such triggered
B cells are able to activate T helper cells, which in turn induce a switch from IgM
to IgG antibody production in B cells and the generation of long-lived B cell
memory - the goal of any vaccination (Bachmann & Zinkernagel, Ann. Rev.
Immunol. 75:235-270 (1997)). Viral structure is even linked to the generation of
anti-antibodies in autoimmune disease and as a part of the natural response to
pathogens (see Fehr, T., el al, J. Exp. Med. 7(55:1785-1792 (1997)). Thus,
antigens on viral particles that are organized in an ordered and repetitive array are
highly immunogenic since they can directly activate B cells.

In addition to strong B cell responses, viral particles are also able to
induce the generation of a cytotoxic T cell response, another crucial arm of the
immune system. These cytotoxic T cells are particularly important for the
elimination of non-cytopathic viruses such as HIV or hepatitis B virus and for the
eradication of tumors. Cytotoxic T cells do not recognize native antigens but
rather recognize their degradation products in association with MHC class I
molecules (Townsend & Bodmer, Ann. Rev. Immunol. 7:601-624 (1989)).
Macrophages and dendritic cells are able to take up and process exogenous viral
particles (but not their soluble, isolated components) and present the generated
degradation product to cytotoxic T cells, leading to their activation and
proliferation (Kovacsovics-Bankowski et al., Proc. Nad. Acad. Sci. USA
90:4942-4946 (1993); Bachmann et al., Eur. J. Immunol. 26:2595-2600 (1996)).
Viral particles as antigens exhibit two advantages over their isolated
components: (1) Due to their highly repetitive surface structure, they are able to
directly activate B cells, leading to high antibody titers and long-lasting B cell
memory; and (2) Viral particles but not soluble proteins are able to induce a
cytotoxic T cell response, even if the viruses are non-infectious and adjuvants are
absent.
Several new vaccine strategies exploit the inherent immunogenicity of
viruses. Some of these approaches focus on the particulate nature of the virus
particle; for example see Harding, C.V. and Song, R., (J. Immunology 153:4925
(1994)), which discloses a vaccine consisting of latex beads and antigen;
Kovacsovics-Bankowski, ML, et al. (Proc. Natl. Acad. Sci. USA 90:4942-4946
(1993)), which discloses a vaccine consisting of iron oxide beads and antigen;
U.S. Patent No: 5,334.394 to Kossovsky, N., et al., which discloses core particles
coated with antigen; U.S. Patent No. 5,871,747. which discloses synthetic
polymer particles carrying on the surface one or more proteins covalently bonded
thereto; and a core particle with a non-covalently bound coating, which at least
partially covers the surface of said core particle, and at least one biologically
active agent in contact with said coated core particle (see. e.g., WO/94/15585).

However, a disadvantage of these viral mimicry systems is that they are
not able to recreate the ordered presentation of antigen found on the viral surface.
Antigens coupled to a surface in a random orientation are found to induce CTL
response and no or only weak B-cell response. For an efficient vaccine, both
arms of the immune system have to be strongly activated, as described above and
in Bachmann & Zinkernagel, Ann. Rev. Immunol. J5:235 (1997).
In another example, recombinant viruses are being utilized for antigen
delivery. Filamentous phage virus containing an antigen fused to a capsid protein
has been found to be highly immunogenic (see Perham R.N., et al, FEMS
Microbiol. Rev. 77:25-31 (1995); Willis et al, Gene 725:85-88 (1993);
Minenkova et al, Gene 725:85-88 (1993)). However, this system is limited to
very small peptides (5 or 6 amino acid residues) when the fusion protein is
expressed at a high level (Iannolo et al, J. Mol. Biol 2^5:835-844 (1995)) or
limited to the low level expression of larger proteins (de la Cruz et al, J. Biol
Chem. 263:4318-4322 (1988)). For small peptides, so far only the CTL response
is observed and no or only weak B-cell response.
In yet another system, recombinant alphaviruses are proposed as a means
of antigen delivery (see U.S. Patent Nos. 5,766,602; 5,792,462; 5,739,026;
5;789,245 and 5,814,482). Problems with the recombinant virus systems
described so far include a low density expression of the heterologous protein on
the viral surface and/or the difficulty of successfully and repeatedly creating a
new and different recombinant viruses for different applications.
In a further development, virus-like particles (VLPs) are being exploited
in the area of vaccine production because of both their structural properties and
their non-infectious nature. VLPs are supermolecular structures built in a
symmetric manner from many protein molecules of one or more types. They lack
the viral genome and, therefore, are noninfectious. VLPs can often be produced
in large quantities by heterologous expression and can be easily be purified.
Examples of VLPs include the capsid proteins of hepatitis B virus (Ulrich,
et al. Virus Res. 50:141-182 (1998)), measles virus (Warnes, et al, Gene

160:173-178 (1995)), Sindbis virus, rotavirus (US Patent Nos. 5.071,651 and
5,374,426), foot-and-mouth-disease virus (Twomey, et al., Vaccine 13:
1603-1610, (1995)), Norwalk virus (Jiang, X., et al., Science 250:1580-1583
(1990);Matsui, S.M.,et al.,J. Clin. Invest. 87:1456-1461 (1991)), the retro viral
GAG protein (PCT Patent Appl. No. WO 96/30523), the retrotransposon Ty
protein p1, the surface protein of Hepatitis B virus (WO 92/11291) and human
papilloma virus (WO 98/15631). In some instances, recombinant DNA
technology may be utilized to fuse a heterologous protein to a VLP protein
(Kratz, P.A., et al, Proc. Natl Acad. Sci. USA 96: 19151920 (1999)).
Thus, there is a need in the art for the development of new and improved
vaccines that promote a strong CTL and B-cell immune response as efficiently as
natural pathogens.
Summary of the Invention
The invention provides a versatile new technology that allows production
of particles coated with any desired antigen. The technology allows the creation
of highly efficient vaccines against infectious diseases and for the creation of
vaccines for the treatment of allergies and cancers.
In a first embodiment, the invention provides a novel composition
comprising (A) a non-natural molecular scaffold and (B) an antigen or antigenic
determinant.
The non-natural molecular scaffold comprises (i) a core particle selected
from the group consisting of (1) a core particle of non-natural origin and (2) a
core particle of natural origin; and (ii) an organizer comprising at least one first
attachment site, wherein said organizer is connected to said core particle by at
least one covalent bond.
The antigen or antigenic determinant has at least one second attachment
site which is selected from the group consisting of (i) an attachment site not

naturally occurring with said antigen or antigenic determinant; and (ii) an
attachment site naturally occurring with said antigen or antigenic determinant.
The invention provides for an ordered and repetitive antigen array through
an association of the second attachment site to the first attachment site by way of
at least one non-peptide bond. Thus, the antigen or antigenic determinant and the
non-natural molecular scaffold are brought together through this association of
the first and the second attachment site to form an ordered and repetitive antigen
array.
In another embodiment, the core particle of the aforementioned
composition comprises a virus, a virus-like particle, a bacteriophage, a viral
capsid particle or a recombinant form thereof. Alternatively, the core particle
may be a synthetic polymer or a metal.
In a particular embodiment, the organizer may comprise at least one first
attachment site. The first and the second attachment sites are particularly
important elements of the composition of the invention. In various embodiments
of the invention, the first and/or the second attachment site may be an antigen and
an antibody or antibody fragment thereto; biotin and avidin; strepavidin and
biotin; a receptor and its ligand; a ligand-binding protein and its ligand;
interacting leucine zipper polypeptides; an amino group and a chemical group
reactive thereto; a carboxyl group and a chemical group reactive thereto; a
sulfhydryl group and a chemical group reactive thereto; or a combination thereof.
In a more preferred embodiment, the invention provides the coupling of
almost any antigen of choice to the surface of a virus, bacteriophage, virus-like
particle or viral capsid particle. By bringing an antigen into a quasi-crystalline
"virus-like' structure, the invention exploits the strong antiviral immune reaction
of a host for the production of a highly efficient immune response, i.e., a
vaccination, against the displayed antigen.
In one preferred embodiment, the core particle may be selected from the
group consisting of: recombinant proteins of Rotavirus, recombinant proteins of
Norwalkvirus, recombinant proteins of Alphavirus, recombinant proteins of Foot

and Mouth Disease virus, recombinant proteins of Retrovirus, recombinant
proteins of Hepatitis B virus, recombinant proteins of Tobacco mosaic virus,
recombinant proteins of Flock House Virus, and recombinant proteins of human
Papilomavirus.
In another preferred embodiment, the antigen may be selected from the
group consisting of: (1) a protein suited to induce an immune response against
cancer cells; (2) a protein suited to induce an immune response against infectious
diseases; (3) a protein suited to induce an immune response against allergens; and
(4) a protein suited to induce an immune response in farm animals.
In a particularly preferred embodiment of the invention, the first
attachment site and/or the second attachment site comprise an interacting leucine
zipper polypeptide. In most preferred embodiment, the first attachment site
and/or the second attachment site are selected from the group comprising: (1) the
JUN leucine zipper protein domain; and (2) the FOS leucine zipper protein
domain.
In another preferred embodiment, the first attachment site and/or the
second attachment site are selected from the group comprising: (1) a genetically
engineered lysine residue and (2) a genetically engineered cysteine residue, two
residues that may be chemically linked together.
Other embodiments of the invention include processes for the production
of the compositions of the invention and a methods of medical treatment using
said compositions.
It is to be understood that both the foregoing general description and the
following detailed description are exemplary and explanatory only and are
intended to provide further explanation of the invention as claimed.

Brief Description of the Drawings
Figure 1 Western blot demonstrating the production of viral particles
containing the E2-JUN fusion protein using the pCYTts::E2JUN expression
vector.
Figure 2 Western blot demonstrating the production of viral particles
containing the E2-JUN fusion protein expressed from pTE5'2J::E2JUN
expression vector.
Figure 3 Western dot blot demonstrating bacterial and eukaryotic
expression of the FOS-hgh. antigen.
Figure 4 Expression of HBcAg-JUN in E. coli cells.
Figure 5 Western blot demonstrating that HBcAg-JUN is soluble in
E. colilysates.
Figure 6 SDS-PAGE analysis of enrichment of HBcAg-JUN capsid
particles on a sucrose density gradient.
Figure 7 Non-reducing SDS-PAGE analysis of the coupling of hGH-FOS
and HBcAg-JUN particles.
Detailed Description of the Preferred Embodiments
1. Definitions
The following definitions are provided to clarify the subj ect matter which
the inventors consider to be the present invention.
Alphavirus: As used herein, the term "alphavirus" refers to any of the
RNA viruses included within the genus Alphavirus. Descriptions of the members
of this genus are contained in Strauss and Strauss. Microbiol. Rev., 55:491-562
(1994). Examples of alphaviruses include Aura virus, Bebaru virus, Cabassou
virus, Chikungunya virus, Easter equine encephalomyelitis virus, Fort morgan
virus, Getah virus, Kyzylagach virus, Mayoaro virus. Middleburg virus.

Mucambo virus, Ndumu virus, Pixuna virus, Tonate virus, Triniti virus, Una
virus, Western equine encephalomyelitis virus, Whataroa virus, Sindbis virus
•SIN), Semliki forest virus (SFV), Venezuelan equine encephalomyelitis virus
(VEE), and Ross River virus.
Antigen: As used herein, the term "antigen" is a molecule capable of
being bound by an antibody. An antigen is additionally capable of inducing a
humoral immune response and/or cellular immune response leading to the
production of B- and/or T-lymphocytes. An antigen may have one or more
epitopes (B- and T- epitopes). The specific reaction referred to above is meant
to indicate that the antigen will react, in a highly selective manner, with its
corresponding antibody and not with the multitude of other antibodies which may
be evoked by other antigens.
Antigenic determinant: As used herein, the term"antigenic determinant"
is meant to refer to that portion of an antigen that is specifically recognized by
either B- or T-lymphocytes. B-lymphocytes respond to foreign antigenic
determinants via antibody production, whereas T-lymphocytes are the mediator
of cellular immunity. Thus, antigenic determinants or epitopes are those parts of
an antigen that are recognized by antibodies, or in the context of an MHC, by T-
cell receptors.
Association: As used herein, the term "association" as it applies to the
first and second attachment sites, is used to refer to at least one non-peptide bond.
The nature of the association may be covalent, ionic, hydrophobic, polar or any
combination thereof.
Attachment Site, First: As used herein, the phrase "first attachment site"
refers to an element of the "organizer", itself bound to the core particle in a non-
random fashion, to which the second attachment site located on the antigen or
antigenic determinant may associate. The first attachment site may be a protein,
a polypeptide, a peptide, a sugar, a polynucleotide, a natural or synthetic polymer,
a secondary metabolite or compound (biotin, fluorescein, retinol, digoxigenin,
metal ions, phenylmethylsulfonylfluoride), or a combination thereof, or a

chemically reactive group thereof. Multiple first attachment sites are present on
the surface of the non-natural molecular scaffold in a repetitive configuration.
Attachment Site, Second: As used herein, the phrase "second attachment
site" refers to an element associated with the antigen or antigenic determinant to
which the first attachment site of the "organizer" located on the surface of the
non-natural molecular scaffold may associate. The second attachment site of the
antigen or antigenic determinant may be a protein, a polypeptide, a peptide, a
sugar, a polynucleotide, a natural or synthetic polymer, a secondary metabolite or
compound (biotin, fluorescein, retinol, digoxigenin, metal ions,
phenylmethylsulfonylfluoride), or a combination thereof, or a chemically reactive
group thereof. At least one second attachment site is present on the antigen or
antigenic determinant.
Core particle: As used herein, the term "core particle" refers to a rigid
structure with an inherent repetitive organization that provides a foundation for
attachment of an "organizer". A core particle as used herein may be the product
of a synthetic process or the product of a biological process.
Cis-acting: As used herein, the phrase "Cis-acting" sequence refers to
nucleic acid sequences to which a replicase binds to catalyze the RNA-dependent
replication of RNA molecules. These replication events result in the replication
of the full-length and partial RNA molecules and, thus, the alpahvirus
subgenomic promoter is also a "Cis-acting" sequence. Cis-acting sequences may
be located at or near the 5' end, 3' end, or both ends of a nucleic acid molecule,
as well as internally.
Fusion: As used herein, the term "fusion" refers to the combination of
amino acid sequences of different origin in one polypeptide chain by in-frame
combination of their coding nucleotide sequences. The term "fusion" explicitly
encompasses internal fusions, i.e., insertion of sequences of different origin
within a polypeptide chain, in addition to fusion to one of its termini.
Heterologous sequence: As used herein, the term "heterologous
sequence" refers to a second nucleotide sequence present in a vector of the

invention. The term "heterologous sequence" also refers to any amino acid or
RNA sequence encoded by a heterologous DNA sequence contained in a vector
of the invention. Heterologous nucleotide sequences can encode proteins or RNA
molecules normally expressed in the cell type in which they are present or
molecules not normally expressed therein (e.g., Sindbis structural proteins).
Isolated: As used herein, when the term "isolated" is used in reference to
a molecule, the term means that the molecule has been removed from its native
environment. For example, a polynucleotide or a polypeptide naturally present
in a living animal is not "isolated," but the same polynucleotide or polypeptide
separated from the coexisting materials of its natural state is "isolated." Further,
recombinant DNA molecules contained in a vector are considered isolated for the
purposes of the present invention. Isolated RNA molecules include in vivo or in
vitro RNA replication products of DNA and RNA molecules. Isolated nucleic
acid molecules further include synthetically produced molecules. Additionally,
vector molecules contained in recombinant host cells are also isolated. Thus, not
all "isolated" molecules need be "purified."
Immunotherapeutic: As used herein, the term "immunotherapeutic" is
a composition for the treatment of diseases or disorders.. More specifically, the
term is used to refer to a method of treatment for allergies or a method of
treatment for cancer.
Individual: As used herein, the term "individual" refers to multicellular
organisms and includes both plants and animals. Preferred multicellular
organisms are animals, more preferred are vertebrates, even more preferred are
mammals, and most preferred are humans.
Low or undetectable: As used herein, the phrase "low or undetectable,"
when used in reference to gene expression level, refers to a level of expression
which is either significantly lower than that seen when the gene is maximally
induced (e.g.. at least five fold lower) or is not readily detectable by the methods
used in the following examples section.

Lectin: As used herein, proteins obtained particularly from the seeds of
leguminous plants, but also from many other plant and animal sources, that have
binding sites for specific mono- or oligosaccharides. Examples include
concanavalin A and wheat-germ agglutinin, which are widely used as analytical
and preparative agents in the study of glycopfoteins.
Natural origin: As used herein, the term "natural origin" means that the
whole or parts thereof are not synthetic and exist or are produced in nature.
Non-natural: As used herein, the term generally means not from nature,
more specifically, the term means from the hand of man.
Non-natural origin: As used herein, the term "non-natural origin"
generally means synthetic or not from nature; more specifically, the term means
from the hand of man.
Non-natural molecular scaffold: As used herein, the phrase "non-natural
molecular scaffold" refers to any product made by the hand of man that may serve
to provide a rigid and repetitive array of first attachment sites. Ideally but not
necessarily, these first attachment sites are in a geometric order. The non-natural
molecular scaffold may be organic or non-organic and may be synthesized
chemically or through a biological process, in part or in whole. The non-natural
molecular scaffold is comprised of: (a) a core particle, either of natural or non-
natural origin; and (b) an organizer, which itself comprises at least one first
attachment site and is connected to a core particle by at least one covalent bond.
In a particular embodiment, the non-natural molecular scaffold may be a virus,
virus-like particle, a virus capsid particle, a phage, a recombmant form thereof,
or synthetic particle.
Ordered and repetitive antigen or antigenic determinant array: As
used herein, the term "ordered and repetitive antigen or antigenic determinant
array" generally refers to a repeating pattern of antigen or antigenic determinant,
characterized by a uniform spacial arrangement of the antigens or antigenic
determinants with respect to the scaffold. In one embodiment of the invention,
the repeating pattern may be a geometric pattern. An ideal ordered and repetitive

antigen or antigenic determinant array will possess a strictly repetitive
paracrystalline order of antigen or antigenic determinant with a spacing of 5 to 15
. nanometers.
Organizer: As used herein, the term "organizer" is used to refer to an
element bound to a core particle in a non-random fashion that provides a
nucleation site for creating an ordered and repetitive antigen array. An organizer
is any element comprising at least one first attachment site that is bound to a core
particle by at least one covalent bond. An organizer may be a protein, a
polypeptide, a peptide, an amino acid (i.e., a residue of a protein, a polypeptide
or peptide), a sugar, a polynucleotide, a natural or synthetic polymer, a secondary
metabolite or compound (biotin, fluorescein, retinol, digoxigenin, metal ions,
phenylmethylsulfonylfluoride), or a combination thereof, or a chemically reactive
group thereof.
Permissive temperature: As used herein, the phrase "permissive
temperature" refers to temperatures at which an enzyme has relatively high levels
of catalytic activity.
Purified: As used herein, when the term "purified" is used in reference to
a molecule, it means that the concentration of the molecule being purified has
been increased relative to molecules associated with it in its natural environment.
Naturally associated molecules include proteins, nucleic acids, lipids and sugars
but generally do not include water, buffers, and reagents added to maintain the
integrity or facilitate the purification of the molecule being purified. For
example, even if mRNA is diluted with an aqueous solvent during oligo dT
column chromatography, mRNA molecules are purified by this chromatography
if naturally associated nucleic acids and other biological molecules do not bind
to the column and are separated from the subject mRNA molecules.
Receptor: As used herein, the term "receptor" refers to proteins or
glycoproteins or fragments thereof capable of interacting with another molecule,
called the ligand. The ligand may belong to any class of biochemical or chemical
compounds. The receptor need not necessarily be a membrane-bound protein.

Soluble protein, like e.g. maltose binding protein or retinol binding protein are
receptors as well.
Residue. As used herein, the term "residue" is meant to mean a specific
amino acid in a polypeptide backbone or side chain.
Temperature-sensitive: As used herein, the phrase "temperature-
sensitive" refers to an enzyme which readily catalyzes a reaction at one
temperature but catalyzes the same reaction slowly or not at all at another
temperature. An example of a temperature-sensitive enzyme is the replicase
protein encoded by the pCYTts vector, which has readily detectable replicase
activity at temperatures below 34 °C and has low or undetectable activity at 37 °C.
Transcription: As used herein, the term "transcription" refers to the
production of RNA molecules from DNA templates catalyzed by RNA
polymerases.
Recombinant host cell: As used herein, the term "recombinant host cell"
refers to a host cell into which one ore more nucleic acid molecules of the
invention have been introduced.
Recombinant virus: As used herein, the phrase "recombinant virus"
refers to a virus that is genetically modified by the hand of man. The phrase
covers any virus known in the art. More specifically, the phrase refers to a an
alphavirus genetically modified by the hand of man, and most specifically, the
phrase refers to a Sinbis virus genetically modified by the hand of man.
Restrictive temperature: As used herein, the phrase "restrictive
temperature" refers to temperatures at which an enzyme has low or undetectable
levels of catalytic activity. Both "hot" and "cold" sensitive mutants are known
and, thus, a restrictive temperature may be higher or lower than a permissive
temperature.
RNA-dependent RNA replication event: As used herein, the phrase
"RNA-dependent RNA replication event" refers to processes which result in the
formation of an RNA molecule using an RNA molecule as a template.

RNA-Dependent RNA polymerase: As used herein, the phrase "RNA-
Dependent RNA polymerase" refers to a polymerase which catalyzes the
production of an RNA molecule from another RNA molecule. This term is used
herein synonymously with the term "replicase."
Untranslated RNA: As used herein, the phrase "untranslated RNA" refers
to an RNA sequence or molecule which does not encode an open reading frame
or encodes an open reading frame, or portion thereof, but in a format in which an
amino acid sequence will not be produced (e.g., no initiation codon is present).
Examples of such molecules are tRNA molecules, rRNA molecules, and
ribozymes.
Vector: As used herein, the term "vector" refers to an agent {e.g., a
plasmid or virus) used to transmit genetic material to a host cell. A vector may
be composed of either DNA or RNA.
one, a, or an: When the terms "one," "a," or "an" are used in this
disclosure, they mean "at least one" or "one or more," unless otherwise indicated.
2. Compositions of Ordered and Repetitive Antigen or Antigenic
Determinant Arrays and Methods to Make the Same
The disclosed invention provides compositions comprising an ordered and
repetitive antigen or antigenic determinant. Furthermore, the invention
conveniently enables the practitioner to construct ordered and repetitive antigen
or antigenic determinant arrays for various treatment purposes, which includes the
prevention of infectious diseases, the treatment of allergies and the treatment of
cancers.
Compositions of the invention essentially comprise two elements: (1) a
non-natural molecular scaffold; and (2) an antigen or antigenic determinant with
at least one second attachment site capable of association through at least one
non-peptide bond to said first attachment site.
The non-natural molecular scaffold comprises (a) a core particle selected
from the group consisting of (1) a core particle of non-natural origin and (2) a

core particle of natural origin; and (b) an organizer comprising at least one first
attachment site, wherein said organizer is connected to said core particle by at
least one covalent bond.
The antigen or antigenic determinant has at least one second attachment
site which is selected from the group consisting of (a) an attachment site not
naturally occurring with said antigen or antigenic determinant; and (b) an
attachment site naturally occurring with said antigen or antigenic determinant.
The invention provides for an ordered and repetitive antigen array through
an association of the second attachment site to the first attachment site by way of
at least one non-peptide bond. Thus, the antigen or antigenic determinant and the
non-natural molecular scaffold are brought together through this association of
the first and the second attachment site to form an ordered and repetitive antigen
array.
The practioner may specifically design the antigen or antigenic
determinant and the second attachment site such that the arrangement of all the
antigens or antigenic determinants bound to the non-natural molecular scaffold
will be uniform. For example, one may place a single second attachment site on
the antigen or antigenic determinant at the carboxyl or amino terminus, thereby
ensuring through design that all antigen or antigenic determinant molecules that
are attached to the non-natural molecular scaffold are positioned in a uniform
way. Thus, the invention provides a convenient means of placing any antigen or
antigenic determinant onto a non-natural molecular scaffold in a defined order
and repetition.
As will be clear to those skilled in the art, certain embodiments of the
invention involve the use of recombinant nucleic acid technologies such as
cloning, polymerase chain reaction, the purification of DNA and RNA, the
expression of recombinant proteins in prokaryotic and eukaryotic cells, etc. Such
methodologies are well known to those skilled in the art and may be conveniently
found in published laboratory methods manuals (e.g., Sambrook, J. et al, eds.,
MOLECULAR CLONING, A LABORATORY MANUAL, 2nd. edition, Cold Spring

Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989): Ausubel, F. el al.,
eds., CURRENTPROTOCOLS IN MOLECULAR BIOLOGY, John H. Wiley & Sons, Inc.
(1997)). Fundamental laboratory techniques for working with tissue culture cell
lines (Celis, J., ed., CELL BIOLOGY, Academic Press, 2nd edition, (1998)) and
antibody-based technologies (Harlow, E. and Lane, D., "Antibodies: A Laboratory
Manual," Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1988);
Deutscher, M.P., "Guide to Protein Purification," Meth. Enzymol. 128, Academic
Press San Diego (1990); Scopes, R.K., "Protein Purification Principles and
Practice," 3rd ed., Springer-Verlag, New York (1994)) are also adequately
described in the literature, all of which are incorporated herein by reference.
A. Construction of a Non-natural Molecular Scaffold
One element in the composition of the invention is a non-natural,
molecular scaffold comprising a core particle and an organizer. As used herein,
the phrase "non-natural molecular scaffold" refers to any product made by the
hand of man that may serve to provide a rigid and repetitive array of first
attachment sites. More specifically, the non-natural molecular scaffold comprises
(a) a core particle selected from the group consisting of (1) a core particle of non-
natural origin and (2) a core particle of natural origin; and (b) an organizer
comprising at least one first attachment site, wherein said organizer is connected
to said core particle by at least one covalent bond.
As will be readily apparent to those skilled in the art. the core particle of
the non-natural molecular scaffold of the invention is not limited to any specific
form. The core particle may be organic or non-organic and may be synthesized
chemically or through a biological process.
In one embodiment, a non-natural core particle may be a synthetic
polymer, a lipid micelle or a metal. Such core particles are known in the art,
providing a basis from which to build the novel non-natural molecular scaffold
of the invention. By way of example, synthetic polymer or metal core particles

are described in U.S. Patent No. 5,770,380, which discloses the use of a
calixarene organic scaffold to which is attached a plurality of peptide loops in the
creation of an 'antibody mimic', and U.S. Patent No. 5,334,394 describes
nanocrystalline particles used as a viral decoy that are composed of a wide variety
of inorganic materials, including metals or ceramics. Preferred metals in this
embodiment include chromium, rubidium, iron, zinc, selenium, nickel, goldj
silver, platinum. Preferred ceramic materials in this embodiment include silicon
dioxide, titanium dioxide, aluminum oxide, ruthenium oxide and tin oxide. The
core particles of this embodiment may be made from organic materials including
carbon (diamond). Preferred polymers include polystyrene, nylon and
nitrocellulose. For this type of nanocrystalline particle, panicles made from tin
oxide, titanium dioxide or carbon (diamond) are particularly preferred. A lipid
micelle may be prepared by any means known in the art. For example micelles
may be prepared according to the procedure of Baiselle and Millar (Baiselle, C. J.
and Millar, D.B., Biophys. Chem. 4:355-361 (1975)) or Corti et al. (Corti, M.,
Degriorgio, V., Sonnino, S., Ghidoni R., Masserini, M. and Tettamanti, G.,
Chem. Phys. Lipids 38: 197-214 (1981)) or Lopez et al. (Lopez, O. de la Maza,
A., Coderch, L., Lopez-Iglesias, C, Wehrli, E. and Parra, J.L., FEBS Lett. 426:
314-318 (1998)) or Topchieva and Karezin (Topchieva, I. and Karaezin, K., J.
Colloid Interface Sci. 213: 29-35 (1999)) or Morein et al, (Morein, B.,
Sundquist, B., Hoglund, S., Dalsgaard K. and Osterhaus, A.. Nature 308: 457-60
(1984)), which are all incorporated herein by reference.
The core particle may also be produced through a biological process,
which may be natural or non-natural. By way of example, this type of
embodiment may includes a core particle comprising a virus, virus-like particle,
a phage, a viral capsid particle or a recombinant form thereof. In a more specific
embodiment, the core particle may comprise recombinant proteins of Rotavirus,
recombinant proteins of Norwalkvirus, recombinant proteins of Alphavirus,
recombinant proteins of Foot and Mouth Disease virus, recombinant proteins of
Retrovirus, recombinant proteins of Hepatitis B virus, recombinant proteins of

Tobacco mosaic virus, recombinant proteins of Flock House Virus, and
recombinant proteins of human Papilomavirus.
Whether natural or non-natural, the core particle of the invention is
characterized by comprising organizer that is attached to the natural or non-
natural core particle by at least one covalent bond. The organizer is an element
bound to a core particle in a non-random fashion that provides a nucleation site
for creating an ordered and repetitive antigen array. Ideally, but not necessarily,
the organizer is associated with the core particle in a geometric order. Minimally,
the organizer comprises a first attachment site.
As previously stated, the organizer may be any element comprising at
least one first attachment site that is bound to a core particle by at least one
covalent bond. An organizer may be a protein, a polypeptide, a peptide, an
amino acid (i.e., a residue of a protein, a polypeptide or peptide), a sugar, a
"polynucleotide, a natural or synthetic polymer, a secondary metabolite or
compound (biotin, fluorescein, retinol, digoxigenin, metal ions,
phenylmethylsulfonylfluoride), or a combination thereof, or a chemically reactive
group thereof. In a more specific embodiment, the organizer may comprise a first
attachment site comprising an antigen, an antibody or antibody fragment, biotin,
avidin, strepavidin, a receptor, a receptor ligand, a Iigand. a ligand-binding
protein, an interacting leucine zipper polypeptide, an amino group, a chemical
group reactive to an amino group; a carboxyl group, chemical group reactive to
a carboxyl group, a sulfhydryl group, a chemical group reactive to a sulfhydryl
group, or a combination thereof.
In a preferred embodiment, the core particle of the non-natural molecular
scaffold comprises a virus, a bacteriophage, a virus-like panicle, a viral capsid
particle or a recombinant form thereof. Any virus known in the art having an
ordered and repetitive coat and/or core protein structure may be selected as a non-
naiural molecular scaffold of the invention; examples of suitable viruses include:
sindbis and other alphaviruses; vesicular somatitis virus; rhabdo-, (e.g. vesicular
stomatitis virus), picorna-, toga-, orthomyxo-, polyoma-, parvovirus, rotavirus,

norwalkvirus, foot and mouth disease virus, a retrovirus. hepatitis B virus,
tobacco mosaic virus, flock house virus, human papilomavirus (for example, see
Table 1 in Bachman, M.F. and Zinkernagel, R.M., Immunol. Today 77:553-558
(1996)).
In one embodiment, the invention utilizes genetic engineering of a virus
to create a fusion between an ordered and repetitive viral envelope protein and an
organizer comprising a heterologous protein, peptide, antigenic determinant or a
reactive amino acid residue of choice. Other genetic manipulations known to
those in the art may be included in the construction of the non-natural molecular
scaffold; for example, it may be desirable to restrict the replication ability of the
recombinant virus through genetic mutation. The viral protein selected for fusion
to the organizer (i.e., first attachment site) protein should have an organized and
repetitive structure, more preferably a paracrystalline organization optimally with
a spacing of 5-15nm on the surface of the virus. The creation of this type of
fusion protein will result in multiple, ordered and repetitive organizers on the
surface of the virus. Thus, the ordered and repetitive organization of the first
attachment sites resulting therefrom will reflect the normal organization of the
native viral protein.
As will be discussed in more detail herein, in a preferred embodiment of
the invention, the scaffold is a recombinant alphavirus, and more specifically, a
recombinant Sinbis virus. Alphaviruses are positive stranded RNA viruses that
replicate their genomic RNA entirely in the cytoplasm of the infected cell and
without a DNA intermediate (Strauss, J. and Strauss, E., Microbiol. Rev. JS:491 -
562 (1994)). Several members of the alphavirus family, Sindbis (Xiong, C. et al,
Science 243:1188-1191 (1989); Schlesinger, S., Trends Biotechnol. 77:18-22
(! 993)), Semliki Forest Virus (SFV) (Liljestrom, P. & Garoff. H., Bio/Technology
P:1356-1361 (1991)) and others (Davis, N.L. et al. Virology 777:189-204
(1989)), have received considerable attention for use as virus-based expression
vectors for a variety of different proteins (Lundstrom, K., Curr. Opin. Biotechnol.
5:578-582 (1997); Liljestrom, P., Curr. Opin. Biotechnol. 5:495-500 (1994)) and

as candidates for vaccine development. Recently, a number of patents have
issued directed to the use of alphaviruses for the expression of heterologous
proteins and the development of vaccines (see U.S. Patent Nos. 5,766,602;
5,792,462; 5,739,026; 5;789,245 and 5,814,482). The construction of the
alphaviral scaffold of the invention may be done by means generally known in the
art of recombinant DNA technology, as described by the aforementioned articles,
which are incorporated herein by reference.
A variety of different recombinant host cells can be utilized to produce a
viral-based core particle for antigen or antigenic determinant attachment. For
example, Alphaviruses are known to have a wide host range: Sindbis virus infects
cultured mammalian, reptilian, and amphibian cells, as well as some insect cells
(Clark, H., J. Natl. Cancer Inst. 57:645 (1973); Leake, C.,J. Gen. Virol. 35:335
(1977); Stollar, V. in THE TOGA VIRUSES, R. W. Schlesinger, Ed., Academic Press,
(1980), pp.583-621). Thus, numerous recombinant host cells can be used in the
practice of the invention. BHK, COS, Vero, HeLa and CHO cells are particularly
suitable for the production of heterologous proteins because they have the
potential to glycosylate heterologous proteins in a manner similar to human cells
(Watson, E. et al, Glycobiology 4:227, (1994)) and can be selected (Zang, M. et
al, Bio/Technology 73:389 (1995)) or genetically engineered (Renner W. et al,
Biotech. Bioeng. 4:476 (1995); Lee K. et al. Biotech. Bioeng. 50:336 (1996)) to
grow in serum-free medium, as well as in suspension.
Introduction of the polynucleotide vectors into host cells can be effected
by methods described in standard laboratory manuals (see, e.g., Sambrook, J. et
al. eds., MOLECULAR CLONING, A LABORATORY MANUAL. 2nd. edition, Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), Chapter 9;
Ausubel, F. et al, eds.. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John H.
Wiley & Sons, Inc. (1997), Chapter 16), including methods such as
electroporation, DEAE-dextran mediated transfection. transfection,
microinjection, cationic lipid-mediated transfection, transduction, scrape loading,
ballistic introduction, and infection. Methods for the introduction of exogenous

DNA sequences into host cells are discussed in Feigner, P. et al., U.S. Patent No.
5,580,859.
Packaged RNA sequences can also be used to infect host cells. These
packaged RNA sequences can be introduced to host cells by adding them to the
culture medium. For example, the preparation of non-infective alpahviral
particles is described in a number of sources, including "Sindbis Expression
System", Version C, (Invitrogen Catalog No. K750-1).
When mammalian cells are used as recombinant host cells for the
production of viral-based core particles, these cells will generally be grown in
tissue culture. Methods for growing cells in culture are well known in the art
(see, e.g., Cells, J., ed., CELL BIOLOGY, Academic Press, 2nd edition, (1998);
Sambrook, J. et al., eds., MOLECULAR CLONING, A LABORATORY MANUAL, 2nd.
edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989);
Ausubel, F. et al., eds., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John H.
Wiley & Sons, Inc. (1997); Freshney, R., CULTURE OF ANIMAL CELLS, Alan R.
Liss, Inc. (1983)).
As will be understood by those in the art, the first attachment site may be
or be a part of any suitable protein, polypeptide, sugar, polynucleotide, peptide
(amino acid), natural or synthetic polymer, a secondary metabolite or combination
thereof that may serve to specifically attach the antigen or antigenic determinant
of choice to the scaffold. In one embodiment, the attachment site is a protein or
peptide that may be selected from those known in the art. For example, the first
attachment site may selected from the following group: a ligand, a receptor, a
lectin, avidin, streptavidin, biotin, an epitope such as an HA or T7 tag, Myc, Max,
immunoglobulin domains and any other amino acid sequence known in the art
that would be useful as a first attachment site.
It should be further understood by those in the art that with another
embodiment of the invention, the first attachment site may be created secondarily
to the organizer (i.e., protein or polypeptide) utilized in constructing the in-frame
fusion to the capsid protein. For example, a protein may be utilized for fusion to

the envelope protein with an amino acid sequence known to be glycosylated in a
specific fashion, and the sugar moiety added as a result may then serve at the first
attachment site of the viral scaffold by way of binding to a lectin serving as the
secondary attachment site of an antigen. Alternatively, the organizer sequence
may be biotinylated in vivo and the biotin moiety may serve as the first
attachment site of the invention, or the organizer sequence may be subjected to
chemical modification of distinct amino acid residues in vitro, the modification
serving as the first attachment site.
One specific embodiment of the invention utilizes the Sinbis virus. The
Sinbis virus RNA genome is packaged into a capsid protein that is surrounded by
a lipid bilayer containing three proteins called El, E2, and E3. These so-called
envelope proteins are glycoproteins, and the glycosylated portions are located on
the outside of the lipid bilayer, where complexes of these proteins form the
"spikes" that can be seen in electron micrographs to project outward from the
surface of the virus. In a preferred embodiment of the invention, the first
attachment site is selected to be the JUN or FOS leucine zipper protein domain
that is fused in frame to the E2 envelope protein. However, it will be clear to all
individuals in the art that other envelope proteins may be utilized in the fusion
protein construct for locating the first attachment site in the scaffold of the
invention.
In a most preferred embodiment of the invention, the first attachment site
is selected to be the JUN-FOS leucine zipper protein domain that is fused in
frame to the Hepatitis B capsid (core) protein. However, it will be clear to all
individuals in the art that other viral capsid proteins may be utilized in the fusion
protein construct for locating the first attachment site in the scaffold of the
invention.
In another preferred embodiment of the invention, the first attachment site
is selected to be a lysine or cysteine residue that is fused in frame to the Hepatitis
core (capsid) protein. However, it will be clear to all individuals in the art that

other viral capsid or virus-like particles may be utilized in the fusion protein
construct for locating the first attachment in the scaffold of the invention.
Example 1 is provided to demonstrate the construction of an in-frame
fusion protein between the Sinbis virus E2 envelope protein and the JUN leucine
zipper protein domain using the pTE5'2J vector of Hahn et al. (JProc. Natl. Acad.
Sci. USA 89:2679-2683 (1992)). The JUN amino acid sequence utilized for the
first attachment site is the following:
CGGRIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVGC
(SEQ ID NO:59)
In this instance, the anticipated second attachment site on the antigen would be
the FOS leucine zipper protein domain and the amino acid sequence would be the
following:
CGGLTDTLQAETDQVEDEKSALQTEIANLLKEKEKLEFILAAHGGC(SEQ
ID NO:60)
These sequences are derived from the transcription factors JUN and FOS,
each flanked with a short sequence containing a cysteine residue on both sides.
These sequences are known to interact with each other. The original hypothetical
structure proposed for the JUN-FOS dimer assumed that the hydrophobic side
chains of one monomer interdigitate with the respective side chains of the other
monomer in a zipper-like manner (Landschulz et al, Science 240:1759-1764
(1988)). However, this hypothesis proved to be wrong, and these proteins are
known to form an -helical coiled coil (O'Shea et al., Science 243:538-542
(1989); O'Shea et al, Cell 65:699-708 (1992); Cohen & Parry, Trends Biochem.
Sci. 17:245-248 (1986)), Thus, the term "leucine zipper" is frequently used to
refer to these protein domains for more historical than structural reasons.
Throughout this patent, the term "leucine zipper" is used to refer to the sequences
depicted above or sequences essentially similar to the ones depicted above. The
terms JUN and. FOS are used for the respective leucine zipper domains rather than
the entire JUN and FOS proteins.

In one embodiment, the invention provides for the production of a Sinbis
virus E2-JUN scaffold using the pCYTts expression system (US Patent
Application Appl. No. 60/079,562; Filed March 27,1998). The pCYTts
expression system provides novel expression vectors which permit tight
regulation of gene expression in eucaryotic cells. The DNA vectors of this
system are transcribed to form RNA molecules which are then replicated by a
temperature-sensitive replicase to form additional RNA molecules. The RNA
molecules produced by replication contain a nucleotide sequence which may be
translated to produce a protein of interest or which encode one or more
untranslated RNA molecules. Thus the expression system enables the production
of recombinant Sinbis virus particles.
Example 2 provides details on the production of the E2- JUN Sinbis non-
natural, molecular scaffold of the invention. Additionally provided in Example
3 is another method for the production of recombinant E2-JUN Sinbis virus
scaffold using the pTE5'2JE2:JLW vector produced in Example 1. Thus the
invention provides two means, the pCYTts expression system (Example 2) and
the pTE5'2J vector system (Example 3) by which recombinant Sinbis virus E2-
JUN non-natural, molecular scaffold may be produced. An analysis of viral
particles produced in each system is proved in Figure 1 and Figure 2.
As previously stated, the invention includes viral-based core particles
which comprise a virus, virus-like particle, a phage, a viral capsid particle or a
recombinant form thereof. Skilled artisans have the knowledge to produce such
core particles and attach organizers thereto. By way of providing other examples,
the invention provides herein for the production of hepatitis B virus-like particles
and measles viral capsid particles as core particles (Examples 17 to 22). In such
an embodiment, the JUN leucine zipper protein domain or FOS leucine zipper
protein domain may be used as an organizer, and hence as a first attachment site,
for the non-natural molecular scaffold of the invention.
Examples 23-29 provide details of the production of Hepatitis B core
particles carrying an in-frame fused peptide with a reactive lysine residue and

antigens carrying a genetically fused cysteine residue, as first and second
attachment site, respectively.
B. Construction of an Antigen or Antigenic Determinant with a
Second Attachment Site
The second element in the composition of the invention is an antigen or
antigenic determinant possessing at least one second attachment site capable of
association through at least one non-peptide bond to the first attachment site of
the non-natural molecular scaffold. The invention provides for compositions that
vary according to the antigen or antigenic determinant selected in consideration
of the desired therapeutic effect. Other compositions are provided by varying the
molecule selected for the second attachment site.
Antigens of the invention may be selected from the group consisting of the
following: (a) proteins suited to induce an immune response against cancer cells;
(b) proteins suited to induce an immune response against infectious diseases; (c)
proteins suited to induce an immune response against allergens, and (d) proteins
suited to induce an immune response in farm animals.
In one specific embodiment of the invention, the antigen or antigenic
determinant is one that is useful for the prevention of infectious disease. Such
treatment will be useful to treat a wide variety of infectious diseases affecting a
wide range of hosts, e.g., human, cow, sheep, pig, dog, cat. other mammalian
species and non-mammalian species as well. Treatable infectious diseases are
well known to those skilled in the art, examples include infections of viral
etiology such as HIV, influenza, Herpes, viral hepatitis, Epstein Bar, polio, viral
encephalitis, measles, chicken pox, etc.; or infections of bacterial etiology such
as pneumonia, tuberculosis, syphilis, etc.; or infections of parasitic etiology such
as malaria, trypanosomiasis, leishmaniasis, trichomoniasis, amoebiasis, etc.
Thus, antigens or antigenic determinants selected for the compositions of the
invention will be well known to those in the medical art; examples of antigens or
antigenic determinants include the following: the HIV antigens gp 140 and gp 160;

the influenaza antigens hemagglutinin and neuraminidase. hepatitis B surface
antigen, circumsporozoite protein of malaria.
In another specific embodiment, the compositions of the invention are an
immunotherapeutic that may be used for the treatment of allergies or cancer.
The selection of antigens or antigenic determinants for the composition
and method of treatment for allergies would be known to those skilled in the
medical art treating such disorders; representative examples of this type of
antigen or antigenic determinant include the following: bee venom phospholipase
A2, Bet v I (birch pollen allergen), 5 Dol m V (white-faced hornet venom
allergen), Der p I (House dust mite allergen).
The selection of antigens or antigenic determinants for the composition
and method of treatment for cancer would be known to those skilled in the
medical art treating such disorders; representative examples of this type of
antigen or antigenic determinant include the following: Her2 (breast cancer),
GD2 (neuroblastoma), EGF-R (malignant glioblastoma), CE A (medullary thyroid
cancer), CD52 (leukemia).
In a particular embodiment of the invention, the antigen or antigenic
determinant is selected from the group consisting of: (a) a recombinant protein
of HIV, (b) a recombinant protein of Influenza virus, (c) a recombinant protein
of Hepatitis C virus, (d) a recombinant protein of Toxoplasma, (e) a recombinant
protein of Plasmodium falciparum, (f) a recombinant protein of Plasmodium
vivax, (g) a recombinant protein of Plasmodium ovale, (h) a recombinant protein
of Plasmodium malariae, (i) a recombinant protein of breast cancer cells, (j) a
recombinant protein of kidney cancer cells, (k) a recombinant protein of prostate
cancer cells, (1) a recombinant protein of skin cancer cells, (m) a recombinant
protein of brain cancer cells, (n) a recombinant protein of leukemia cells, (o) a
recombinant profiling, (p) a recombinant protein of bee sting allergy, (q) a
recombinant proteins of nut allergy, (r) a recombinant proteins of food allergies,
recombinant proteins of asthma, and a recombinant protein of Chlamydia.

Once the antigen or antigenic determinant of the composition is chosen,
at least one second attachment site may be added to the molecule in preparing to
construct the organized and repetitive array associated with the non-natural
molecular scaffold of the invention. Knowledge of what will constitute an
appropriate second attachment site will be known to those skilled in the art.
Representative examples of second attachment sites include, but are not limited
to, the following: an antigen, an antibody or antibody fragment, biotin, avidin,
strepavidin, a receptor, a receptor ligand, a ligand, a ligand-binding protein, an
interacting leucine zipper polypeptide, an amino group, a chemical group reactive
to an amino group; a carboxyl group, chemical group reactive to a carboxyl
group, a sulfhydryl group, a chemical group reactive to a sulfhydryl group, or a
combination thereof.
The association between the first and second attachment sites will be
determined by the characteristics of the respective molecules selected but will
comprise at least one non-peptide bond. Depending upon the combination of first
and second attachment sites, the nature of the association may be covalent, ionic,
hydrophobic, polar, or a combination thereof.
In one embodiment of the invention, the second attachment site may be
the FOS leucine zipper protein domain or the JLWleucine zipper protein domain.
In a most specific embodiment of the invention, the second attachment
site selected is the FOS leucine zipper protein domain, which associates
specifically with the JUN leucine zipper protein domain of the non-natural
molecular scaffold of the invention. The association of the JUN and FOS leucine
zipper protein domains provides a basis for the formation of an organized and
repetitive antigen or antigenic determinant array on the surface of the scaffold.
The FOS leucine zipper protein domain may be fused in frame to the antigen or
antigenic determinant of choice at either the amino terminus, carboxyl terminus
or internally located in the protein if desired.

Several FOS fusion constructs are provided for exemplary purposes.
Human growth hormone (Example 4), bee venom phospholipase A2 (PLA)
(Example 9), ovalbumin (Example 10) and HIV gpl40 (Example 12).
In order to simplify the generation of FOS fusion constructs, several
vectors are disclosed that provide options for antigen or antigenic determinant
design and construction (see Example 6). The vectors pAV 1 -4 were designed for
the expression of FOS fusion in K coli; the vectors pAV5 and pAV6 were
designed for the expression of FOS fusion proteins in eukaryotic cells. Properties
of these vectors are briefly described:
1. pAVl: This vector was designed for the secretion of fusion proteins
with FOS at the C-terminus into the E. coli periplasmic space. The gene of
interest (g.o.i.) may be Iigated into the StuI/NotI sites of the vector.
2. p,AV2: This vector was designed for the secretion of fusion proteins
with FOS at the N-terminus into the E. coli periplasmic space. The gene of
interest (g.o.i.) Iigated into the Notl/EcoRV (or Notl/HindlH) sites of the vector.
3. pAV3: This vector was designed for the cytoplasmic production of
fusion proteins with FOS at the C-terminus in E. coli. The gene of interest (g.o.i.)
may be Iigated into the EcoRV/NotI sites of the vector.
4. pAV4: This vector is designed for the cytoplasmic production of
fusion proteins with FOS at the N-terminus in E. coli. The gene of interest (g.o.i.)
may be Iigated into the Notl/EcoRV (or Notl/HindlH) sites of the vector. The
N-terminal methionine residue is proteolytically removed upon protein synthesis
(Hirel et al., Proc. Nail. Acad. Sci. USA 5(5:8247-8251 (1989)).
5. pAV.S: This vector was designed for the eukaryotic production of
fusion proteins with FOS at the C-terminus. The gene of interest (g.o.i.) may be
inserted between the sequences coding for the hGH signal sequence and the FOS
domain by ligation into the Eco47III/NotI sites of the vector. Alternatively, a
gene containing its own signal sequence may be fused to the FOS coding region
by ligation into the StuI/NotI sites.

6. pAV6: This vector was designed for the eukaryotic production of
fusion proteins with FOS at the N-terminus. The gene of interest (g.o.i.) may be
ligated into the Notl/StuI (or Notl/Hindlll) sites of the vector.
As will be understood by those skilled in the art, the construction of a
FOS-antigen or -antigenic determinant fusion protein may include the addition of
certain genetic elements to facilitate production of the recombinant protein.
Example 4 provides guidance for the addition of certain E. coli regulatory
elements for translation, and Example 7 provides guidance for the addition of a
eukaryotic signal sequence. Other genetic elements may be selected, depending
on the specific needs of the practioner.
The invention is also seen to include the production of the FOS-antigen
or FOiS-antigenic determinant fusion protein either in bacterial (Example 5) or
eukaryotic cells (Example 8). The choice of which cell type in which to express
the fusion protein is within the knowledge of the skilled artisan, depending on
factors such as whether post-translational modifications are an important
consideration in the design of the composition.
As noted previously, the invention discloses various methods for the
construction of a FOS-anligzn or FOS-antigenic determinant fusion protein
through the use of the pAV vectors. In addition to enabling prokaryotic and
eukaryotic expression, these vectors allow the practitioner to choose between —
and C- terminal addition to the antigen of the FOS leucine zipper protein domain.
Specific examples are provided wherein — and C- terminal FOS fusions are made
to PLA (Example 9) and ovalbumin (Example 10). Example 11 demonstrates the
purification of the PLA and ovalbumin FOS fusion proteins.
In a most specific embodiment, the invention is drawn to an antigen or
antigenic determinant encoded by the HIV genome. More specifically, the HIV
antigen is gpl40. As provided for in Examples 11-15, HIV gp 140 may be created
with a FOS leucine zipper protein domain and the fusion protein synthesized and
purified for attachment to the non-natural molecular scaffold of the invention. As

one skilled in the art would know, other HIV antigens or antigenic determinants
may be used in the creation of a composition of the invention.
In a most specific embodiment of the invention, the second attachment
site selected is a cysteine residue, which associates specifically with a lysine
residue of the non-natural molecular scaffold of the invention. The chemical
linkage of the lysine residue (Lys) and cysteine residue (Cy s) provides a basis for
the formation of an organized and repetitive antigen or antigenic determinant
array on the surface of the scaffold. The cysteine residue may be engineered in
frame to the antigen or antigenic determinant of choice at either the amino
terminus, carboxyl terminus or internally located in the protein if desired. By way
of example, PL A and HIV gpl40 are provided with a cysteine residue for linkage
to a lysine residue first attachment site.
C. Preparation of the AlphaVaccine Particles
The invention provides novel compositions and methods for the
construction of ordered and repetitive antigen arrays. As one of skill in the art
would know, the conditions for the assembly of the ordered and repetitive antigen
array depend to a large extent on the specific choice of the first attachment site
of the non-natural scaffold and the specific choice of the second attachment site
of the antigen or antigenic determinant. Thus, practitioner choice in the design
of the composition (/. e., selection of the first and second attachment sites, antigen
and non-natural scaffold) will determine the specific conditions for the assembly
of the AlphaVaccine particle (the ordered and repetitive antigen array and non-
natural molecular scaffold combined). Information relating to assembly of the
AlphaVaccine particle is well within the working knowledge of the practitioner,
and numerous references exist to aid the practitioner (e.g.. Sambrook, J. et al,
eds.. MOLECULAR CLONING, A LABORATORY MANUAL, 2nd. edition, Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989); Ausubel, F. et al.,
eds.. CURRENT PROTOCOLS IN MOLECULARBIOLOGY, John H. Wiley & Sons, Inc.

(1997); Celis, J., ed., CELL BIOLGY, Academic Press. 2nd edition, (1998);
Harlow, E. and Lane, D., "Antibodies: A Laboratory Manual," Cold Spring
Harbor Laboratory, Cold Spring Harbor, N.Y. (1988). all of which are
incorporated herein by reference.
In a specific embodiment of the invention, the JUN and FOS leucine
zipper protein domains are utilized for the first and second attachment sites of the
invention, respectively. In the preparation of AlphaVaccine particles, antigen
must be produced and purified under conditions to promote assembly of the
ordered and repetitive antigen array onto the non-natural scaffold. In the
particular JUN/FOS leucine zipper protein domain embodiment, the FOS-antigen
or FOS-antigenic determinant should be treated with a reducing agent (e.g.,
Dithiothreitol (DTT)) to reduce or eliminate the incidence of disulfide bond
formation (Example 15).
For the preparation of the non-natural scaffold (i.e.. recombinant Sinbis
virus) of the JUN/FOS leucine zipper protein domain embodiment, recombinant
H2-JUN viral particles should be concentrated, neutralized and treated with
reducing agent (see Example 16).
Assembly of the ordered and repetitive antigen array in the JUN/FOS
embodiment is done in the presence of a redox shuffle. E2-JUN viral particles
are combined with a 240 fold molar excess of FOS-antigen or FOS-antigenic
determinant for 10 hours at 4°C. Subsequently, the AlphaVaccine particle is
concentrated and purified by chromatography (Example 16).
In another embodiment of the invention, the coupling of the non-natural
molecular scaffold to the antigen or antigenic determinant may be accomplished
by chemical crosslinking. In a most preferred embodiment, the chemical agent
is a hetero-bifunctional crosslinking agent such as e-maleimidocaproic acid N-
hydroxysuccinimide ester (Tanimori et al, J. Pharm. Dyn. 4:812 (1981);
Fujiwara et al., J. Immunol. Meth. 45:195 (1981), which contains (1) a
succinimide group reactive with amino groups and (2) a maleimide group reactive
with SH groups.. A heterologous protein or polypeptide of the first attachment

site may be engineered to contain one or more lysine residues that will serve as
a reactive moiety for the succinimide portion of the hetero-bifunctional
crosslinking agent. Once chemically coupled to the first attachment sites of the
non-natural molecular scaffold, the maleimide group of the hetero-bifunctional
crosslinking agent will be available to react with the SH group of a cysteine
residue on the antigen or antigenic determinant. Antigen or antigenic determinant
preparation in this instance may require the engineering of a cysteine residue into
the protein or polypeptide chosen as the second attachment site so that it may be
reacted to the free maleimide function on the crosslinking agent bound to the non-
natural molecular scaffold first attachment sites.
3. Compositions, Vaccines, and the Administration Thereof, and Methods
of Treatment
In one embodiment, the invention provides vaccines for the prevention of
infectious diseases in a wide range of species, particularly mammalian species
such as human, monkey, cow, dog, cat, horse, pig, etc. Vaccines may be designed
to treat infections of viral etiology such as HIV, influenza, Herpes, viral hepatitis,
Epstein Bar, polio, viral encephalitis, measles, chicken pox, etc.; or infections of
bacterial etiology such as pneumonia, tuberculosis, syphilis, etc.; or infections of
parasitic etiology such as malaria, trypanosomiasis, leishmaniasis, trichomoniasis,
amoebiasis, etc.
In another embodiment, the invention provides vaccines for the
prevention of cancer in a wide range of species, particularly mammalian species
such as human, monkey, cow, dog, cat, horse, pig, etc. Vaccines may be designed
to treat all types of cancer: lymphomas, carcinomas, sarcomas, melanomas, etc.
In another embodiment of the invention, the compositions of the invention
may be used in the design of vaccines for the treatment of allergies. Antibodies
of the IgE isotype are important components in allergic reactions. Mast cells bind
IgE antibodies on their surface and release histamines and other mediators of
allergic response upon binding of specific antigen to the IgE molecules bound on

the mast cell surface. Inhibiting production of IgE antibodies, therefore, is a
promising target to protect against allergies. This should be possible by attaining
a desired T helper cell response. T helper cell responses can be divided into type
1 (TH1) and type 2 (TH2) T helper cell responses (Romagnani, Immunol. Today
18:263-266 (1997)). TH1 cells secrete interferon-gamma and other cytokines
which trigger B cells to produce IgG 1 -3 antibodies. In contrast, a critical cytokine
produced by TH2 cells is IL-4, which drived B cells to produce IgG4 and IgE. In
many experimental systems, the development of TH1 and TH2 responses is
mutually exclusive sinceTHl cells suppress the induction of TH2 cells and vice
versa. Thus, antigens that trigger a strong TH1 response simultaneously suppress
the development of TH2 responses and hence the production of IgE antibodies.
Interestingly, virtually all viruses induce a TH1 response in the host and fail to
trigger the production of IgE antibodies (Coutelier et al.,J. Exp. Med. 165:64-69
(1987)). This isotype pattern is not restricted to live viruses but has also been
observed for inactivated or recombinant viral particles (Lo-Man et al., Eur. J.
Immunol. 25:1401-1407 (1998)). Thus, by using the processes of the invention
{e.g., AlphaVaccine Technology), viral particles can be decorated with various
allergens and used for immunization. Due to the resulting "viral structure" of the
allergen, a TH1 response will be elicited, "protective" IgG 1-3 antibodies will be
produced, and the production of IgE antibodies which cause allergic reactions will
be prevented. Since the allergen is presented by viral particles which are
recognized by a different set of helper T cells than the allergen itself, it is likely
that the allergen-specific IgGl -3 antibodies will be induced even in allergic
individuals harboring pre-existing TH2 cells specific for the allergen. The
presence of high concentrations of IgG antibodies may prevent binding of
allergens to mast cell bound IgE, thereby inhibiting the release of histamine.
Thus, presence of IgG antibodies may protect from IgE mediated allergic
reactions. Typical substances causing allergies include: grass, ragweed, birch or
mountain cedar pollens, house dust, mites, animal danders, mold, insect venom
or drugs {e.g. penicillin). Thus, immunization of individuals with allergen-

decorated viral particles should be beneficial not only before but also after the
onset of allergies.
As would be understood by one of ordinary skill in the art, when the
compositions of the invention are administered to an individual, they may be in
a composition which contains salts, buffers, adjuvants, or other substances which
are desirable for improving the efficacy of the composition. Examples of
materials suitable for use in preparing pharmaceutical compositions are provided
in numerous sources including REMINGTON'S PHARMACEUTICAL SCIENCES (Osol,
A, ed., Mack Publishing Co., (1980)).
The compositions of the invention are said to be "pharmacologically
acceptable" if their administration can be tolerated by a recipient individual.
Further, the compositions of the invention will be administered in a
"therapeutically effective amount" (i.e., an amount that produces a desired
physiological effect).
The compositions of the present invention may be administered by various
methods known in the art, but will normally be administered by injection,
infusion, inhalation, oral administration, or other suitable physical methods. The
compositions may alternatively be administered intramuscularly, intravenously,
or subcutaneously. Components of compositions for administration include
sterile aqueous (e.g., physiological saline) or non-aqueous solutions and
suspensions. Examples of non-aqueous solvents are propylene glycol,
polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters
such as ethyl oleate. Carriers or occlusive dressings can be used to increase skin
permeability and enhance antigen absorption.
In addition to vaccine technologies, other embodiments of the invention
are drawn to methods of medical treatment for cancer and allergies.
All patents and publications referred to herein are expressly incorporated
by reference.

Examples
Enzymes and reagents used in the experiments that follow included: T4
DNA ligase obtained from New England Biolabs; Taq DNA Polymerase,
QIAprep Spin Plasmid Kit, QIAGEN Plasmid Midi Kit, QiaExII Gel Extraction
Kit, QlAquick PCR Purification Kit obtained from QIAGEN; QuickPrep Micro
mRNA Purification Kit obtained from Pharmacia; Superscript One-step RT PCR
Kit, fetal calf serum (FCS), bacto-tryptone and yeast extract obtained from Gibco
BRL; Oligonucleotides obtained from Microsynth (Switzerland); restriction
endonucleases obtained from Boehringer Mannheim, New England Biolabs or
MBI Fermentas; Pwo polymerase and dNTPs obtained from Boehringer
Mannheim. HP-1 medium was obtained from Cell culture technologies
(Glattbrugg, Switzerland). All standard chemicals were obtained from
Fluka-Sigma-Aldrich, and all cell culture materials were obtained from TPP.
DNA manipulations were carried out using standard techniques. DNA
was prepared according to manufacturer instruction either from a 2 ml bacterial
culture using the QIAprep Spin Plasmid Kit or from a 50 ml culture using the
QIAGEN Plasmid Midi Kit. For restriction enzyme digestion, DNA was
incubated at least 2 hours with the appropriate restriction enzyme at a
concentration of 5-10 units (U) enzyme per mg DNA under manufacturer
recommended conditions (buffer and temperature). Digests with more than one
enzyme were performed simultaneously if reaction conditions were appropriate
for all enzymes, otherwise consecutively. DNA fragments isolated for further
manipulations were separated by electrophoresis in a 0.7 to 1.5% agarose gel,
excised from the gel and purified with the QiaExII Gel Extraction Kit according
to the instructions provided by the manufacturer. For ligation of DNA
fragments, 100 to 200 pg of purified vector DNA were incubated overnight with
a threefold molar excess of the insert fragment at 16 °C in the presence of 1 U T4
DNA ligase in the buffer provided by the manufacturer (total volume: 10-20 l).
An aliquot (0.1 to 0.5 l) of the ligation reaction was used for transformation of

E. coli XL 1 -Blue (Stratagene). Transformation was done by electroporation using
a Gene Pulser (BioRAD) and 0.1 cm Gene Pulser Cuvettes (BioRAD) at 200 Q,
25F, 1.7 kV. After electroporation, the cells were incubated with shaking for
1 h in 1 ml S.O.B. medium (Miller, 1972) before plating on selective S.O.B. agar.
Example 1:
Insertion of the JUN amphiphatic helix domain within E2
In the vector pTE5'2J (Hahn et al, Proc. Nad. Acad. Sci. USA
89:2679-2683, (1992)), Mlul and a BstEIl restriction enzyme sites were
introduced between codons 71 (Gin) and 74 (Thr) of the structural protein E2
coding sequence, resulting in vector pTE5"2JBM. Introduction of these
restriction enzymes sites was done by PCR using the following oligonucleotides:
Oligo 1:
E2insBstEII/BssHII:
5'-ggggACGCGTGCAGCAggtaaccaccgTTAAAGAAGGCACC-3' (SEQ ID
NO:1)
Oligo 2:
E2insMluIStuI:
5 '-cggtggttaccTGCTGCACGCGTTGCTTAAGCGACATGTAGCGG-3' (SEQ
ID NO:2)
Oligo 3:
E2insStuI: 5'-CCATGAGGCCTACGATACCC-3' (SEQ ID NO:3)
Oligo4:
E2insBssHII: 5'-GGCACTCACGGCGCGCTTTACAGGC-3' (SEQ ID NO:4)
For the PCR reaction, 100 pmol of each oligo was used with 5 ng of the
template DNA in a 100 1 reaction mixture containing 4 units of Taq or Pwo
polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4. All DNA concentrations were
determined photometrically using the GeneQuant apparatus (Pharmacia).
Polymerase was added directly before starting the PCR reaction (starting point
was 95 °C). Temperature cycling was done in the following manner and order:
95 °C for 2 minutes: 5 cycles of 95 °C (45 seconds), 53 °C (60 seconds), 72°C

(80 seconds); and 25 cycles of 95°C (45 seconds), 57°C (60 seconds), 72°C
(80 seconds).
The two PCR fragments were analyzed and purified by agarose
gelelectrophoresis. Assembly PCR of the two PCR fragments using oligo 3 and
4 for amplification was carried out to obtain the final construct.
For the assembly PCR reaction, 100 pmol of each oligo was used with
2 ng of the purified PCR fragments in a 100 l reaction mixture containing 4
units of Taq or Pwo polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4. All DNA
concentrations were determined photometrically using the GeneQuant apparatus
(Pharmacia). Polymerase was added directly before starting the PCR reaction
(starting point was 95 °C). Temperature cycling was done in the following
manner and order: 95°C for 2 minutes; 5 cycles of 95°C (45 seconds), 57°C
(60 seconds), 72°C (90 seconds); and 25 cycles of 95°C (45 seconds), 59°C
(60 seconds), 72°C (90 seconds).
The final PCR product was purified using Qia spin PCR columns
(Qiagen) and digested in an appropriate buffer using 10 units each of BssHII and
StuI restriction endonucleases for 12 hours at 37°C. The DNA fragments were
gel-purified and ligated into BssHII/StuI digested and gel-purified pTE5 '2J vector
(Hahn et al., Proc. Natl. Acad. Sci. USA SP:2679-2683). The correct insertion of
the PCR product was first analyzed by BstEII and MM restriction analysis and
then by DNA sequencing of the PCR fragment.
The DNA sequence coding for the JUN amphiphatic helix domain was
PCR-amplified from vector pJuFo (Crameri and Suter, Gem 137:69 (1993))
using the following oligonucleotides:
Oligo 5:
JLiVBstEII:
5 '-CCTTCTTTAAcggtggttaccTGCTGGCAACCAACGTGGTTCATGAC-3'
(SEQ ID NO:5)
Oligo 6:
MluUUN: 5 '-AAGCATGCTGCacgcgtgTGCGGTGGTCGGATCGCCCGGC-3'
(SEQ ID NO:6)

For the PCR reaction, 100 pmol of each oligo was used with 5 ng of the
template DNA in a 100 ul reaction mixture containing 4 units of Taq or Pwo
polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4. All DNA concentrations were
determined photometrically using the GeneQuant apparatus (Pharmacia).
Polymerase was added directly before starting the PCR reaction (starting point
was 95°C). Temperature cycling was done in the following order and manner:
95°C for 2 minutes; 5 cycles of 95°C (45 seconds), 60°C (30 seconds), 72°C
(25 seconds); and 25 cycles of 95°C (45 seconds), 68°C (30 seconds), 72°C
(20 seconds).
The final PCR product was gel-purified and ligated into EcoRV digested
and gel-purified pBIuescript II(KS"). From the resulting vector, the./LWsequence
was isolated by cleavage with MluVBstEll purified with QiaExII and ligated into
vector pTE5"2JBM (previously cut with the same restriction enzymes) to obtain
the vector pTE5"2J:E2JUN.
Example 2:
Production ofviral particles containing E2-JUN using the pCYTts system
The structural proteins were PCR amplified using pTE5'2J:E2JUN as
template and the oligonucleotides XbalStruct
(ctatcaTCTAGAATGAATAGAGGATTCTTTAAC) and StructBspl201
(tcgaatGGGCCCTCATCTTCGTGTGCTAGTCAG). For the PCR 100 pmol of
each loligo was used and 5 ng of the template DNA was used in the 100 ul
reaction mixture, containing 4 units of Tac or Pwo polymerase, 0.1 mM dNTPs
and 1.5 mM MgSO4. All DNA concentrations were determined photometrically
using the GeneQuant apparatus (Pharmacia). The polymerase was added directly
before starting the PCR reaction (starting point was 95 °C). The temperature
cycles were as follows: 95°C for 3 minutes, followed by 5 cycles of 92°C (30
seconds), 54°C (35 seconds), 72°C (270 seconds) and followed by 25 cycles of
92°C (30 seconds), 63°C (35 seconds), 72°C (270 seconds. The PCR product
was gel purified and digested with the restriction enzymes Xbal/Bspl201 and

ligated into vector pCYTts previously cleaved with the same enzymes (US Patent
Application Appl. No. 60/079,562; Filed March 27,1998)
Twenty g of pCYTtsE2-JUN were incubated with 30 U of Seal in an
appropriate buffer for at least 4 hours at 37°C. The reaction was stopped by
phenol/chloroform extraction, followed by an isopropanol precipitation of the
linerized DNA. The restriction reaction was checked by agarose gel
eletrophoresis. For the transfection, 5.4 g of linearized pCYTtsE2'JUN was
mixed with 0.6 ug of linearized pSV2Neo in 30 l H2O and 30 l of 1 M CaCl2
solution were added. After addition of 60 p.1 phosphate buffer (50 mM HEPES,
280 mM NaCl, 1.5 mM Na2 HPO4, pH 7.05), the solution was vortexed for 5
seconds, followed by an incubation at room temperature for 25 seconds. The
solution was immediately added to 2 ml HP-1 medium containing 2% FCS (2%
FCS medium). The medium of an 80% confluent BHK21 cell culture in a 6-well
plate was then replaced with the DNA containing medium. After an incubation
for 5 hours at 37°C in a CO2 incubator, the DNA containing medium was
removed and replaced by 2 ml of 15% glycerol in 2% FCS medium. The glycerol
containing medium was removed after a 3 0 second incubation phase, and the cells
were washed by rinsing with 5 ml of HP-1 medium containing 10% FCS. Finally
2 ml of fresh HP-1 medium containing 10% FCS was added.
Stably transfected cells were selected and grown in selection medium
(HP-1 medium, supplemented with G418) at 3 7 ° C in a CO2 incubator. When the
mixed population was grown to confiuency, the culture was split to two dishes,
followed by a 12 hours growth period at 37°C. One dish of the cells was shifted
to 30°C to induce the expression of the viral particles; the other dish was kept at
37°C.
The expression of viral particles was determined by Western blotting
(Figure 1). Culture medium (0.5 ml) was methanol/chloroform precipitated, and
the pellet was resuspended in SDS-PAGE sample buffer. Samples were heated
for 5 minutes at 95°C before being applied to 15% acrylamide gel. After
SDS-PAGE, proteins were transferred to Protan nitrocellulose membranes

(Schleicher & Schuell, Germany) as described by Bass and Yang, in Creighton,
T.E., ed., Protein Function: A Practical Approach, 2nd Edn., IRL Press, Oxford
(1997), pp. 29-55. The membrane was blocked with 1 % bovine albumin (Sigma)
in TBS (1 OxTBS per liter: 87.7 g NaCl, 66. lg Trizma hydro chloride (Sigma) and
9.7 g Trizma base (Sigma), pH 7.4) for 1 hour at room temperature, followed by
an incubation with an anti-El/E2antibody (polyclonal serum) for 1 hour. The blot
was washed 3 times for 10 minutes with TBS-T (TBS with 0.05% Tween20), and
incubated for 1 hour with an alkaline-phosphatase-anti-rabbit IgG conjugate (0.1
ug/ml, Amersham Life Science, England). After washing 2 times for 10 minutes
with TBS-T and 2 times for 10 minutes with TBS, the development reaction was
carried out using alkaline phosphatase detection reagents (10 ml AP buffer (100
mM Tris/HCl, 100 mM NaCl, pH 9.5) with 50 l NBT solution (7.7% Nitro Blue
Tetrazolium (Sigma) in 70% dimethylformamide) and 37 JJ.1 of X-Phosphate
solution (5% of 5-bromo-4-chloro-3-indolyl phosphate in dimethylformamide).
The production of viral particles is shown in Figure 1. The Western Blot
pattern showed that E2-JUN (lane 1) migrated to a higher molecular weight in
SDS-PAGE compared to wild type E2 (lane 2) and the BHK21 host cell line did
not show any background.
Example 3:
Production of viral particles containing E2-JUN
using thepTES '2JE2.-JUN vector
RNase-free vector (1.0 g) was linerarized by Pvul digestion.
Subsequently, in vitro transcription was carried out using an SP6 in vitro
transcription kit (InvitroscripCAP by InvitroGen, Invitrogen BV, NV Leek,
Netherlands). The resulting 5'-capped mRNA was analyzed on a reducing
agarose-gel.
In vitro transcribed mRNA (5 g) was electroporated into BHK 21 cells
(ATCC: CCL10) according to Invitrogen's manual (Sindbis Expression system,
Invitrogen BV, Netherlands). After 10 hours incubation at 37°C, the FCS
containing medium was exchanged by HP-1 medium without FCS, followed by

an additional incubation at 37°C for 10 hours. The supernatant was harvested
and analyzed by Western blot analysis for production of viral particles exactly as
described in Example 2.
The obtained result was identical to the one obtained with pCYTtsE2:JZ//V
as shown in Figure 2.
Example 4:
Fusion of human growth hormone (hGH) to the FOS leucine
zipper domain (OmpA signal sequence)
The hGH gene without the human leader sequence was amplified from the
original plasmid (ATCC 31389) by PCR. Oligo 7 with an internal Xbal site was
designed for annealing at the 5' end of the hGH gene, and oligo 9 with an internal
EcoRI site primed at the 3' end of the hGH gene. For the PCR reaction, 100 pmol
of each oligo and 5 ng of the template DNA was used in the 75 l reaction
mixture (4 units of Taq or Pwo polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4).
PCR cycling was performed in the following manner: 30 cycles with an
annealing temperature of 60°C and an elongation time of 1 minute at 72°C.
The gel purified and isolated PCR product was used as a template for a
second PCR reaction to introduce the ompA signal sequence and the
Shine-Dalgarno sequence. For the PCR reaction, 100 pmol of oligo 8 and 9 and
1 ng of the template PCR fragment was used in the 75 1 reaction mixture (4 units
of Taq or Pwo polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4). The annealing
temperature for the first five cycles was 55 °C with an elongation time of 60
seconds at 72°C; another 25 cycles were performed with an annealing
temperature of 65 °C and an elongation time of 60 seconds at 72°C.
Oligo7:
gggtctagattcccaaccattcccttatccaggctttttgacaacgctatgctccgcgcccatcgtctgcaccagct
ggcctttgacacc (SEQ ID NO:7)
Oligo 8:

gggtctagaaggaggtaaaaaacgatgaaaaagacagctatcgcgattgcagtggcactggctggtttcgctac
cgtagcgcaggccttcccaaccattcccttatcc (SEQ ID NO:8)
Oligo 9:
cccgaattcctagaagccacagctgccctcc (SEQ ID N0:9)
The resulting recombinant hGH gene was subcloned into pBluescript via
Xbal/EcoRI. The correct sequence of both strands was confirmed by DNA
sequencing.
The DNA sequence coding for the FOS amphiphatic helix domain was
PCR-amplified from vector pJuFo (Crameri & Sitter Gene 137:69 (1993)) using
the oligonucleotides:
omp-FOS:
5'- ccTGCGGTGGTCTGACCGACACCC-3' (SEQ ID NO: 10)
FOS-hgh:
5'- ccgcggaagagccaccGCAACCACCGTGTGCCGCCAGGATG-3' (SEQ ID
NO: 11)
For the PCR reaction, 100 pmol of each oligo and 5 ng of the template
DNA was used in the 75 l reaction mixture (4 units of Taq or Pwo polymerase,
0.1 mM dNTPs and 1.5 mM MgSO4). The temperature cycles were as follows:
95°C for 2 minutes, followed by 5 cycles of 95°C (45 seconds), 60°C
(30 seconds), 72°C (25 seconds) and followed by 25 cycles of 95 °C (45 seconds),
68 °C (30 seconds), 72°C (20 seconds).
The PCR product was purified, isolated and cloned into the StuI digested
pBluescript-ompA-hGH. The hybrid gene was then cloned into the pKK.223-3
Plasmid (Pharmacia).
Example 5:
Bacterial expression of FOS-hGH
The ompA-FOS-hGH in pkk223-3 was expressed under the control of the
inducible IPTG-dependend promoter using JM101 as E. coli host strain.
Expression was performed in shaker flask. Cells were induced with 1 mM IPTG

( final concentration) at an OD600of0.5. Expression was continued for 10 hours
a:37°C. Cells were harvested by centrifugation at 3600 at 10DC for 15 min. The
cell pellet was frozen (-20°C or liq. N2) and stored for 16 hours. The pellet was
then thawed at 4°C and resuspended in 10 ml 10 mM Tris-HCl, pH 7.4
containing 600 mM sucrose. After stirring for 15 min at 4°C, periplasmic
proteins were released by an osmotic shock procedure. Chilled (4°C) deionized
H,0 was added, and the suspension was stirred for 30 min at 4°C. The sludge
was diluted, resuspended, and Iysozyme was added to degrade the cell wall of the
bacteria. The cells and the periplasmic fraction spheroplasts were separated by
centrifugation for 20 min at 11000 g at 4°C. The FOS-hGH-containing
supernatant was analyzed by reducing and non-reducing SDS-Page and Dot Blot.
Dot Blot was carried out as described in Example 8, using an anti-hGH antibody
(Sigma) as the first antibody and an alkaline phosphatase (AP)-anti-mouse
antibody conjugate as the second antibody.
Full length, correctly processed FOS-hGH could be detected under
reducing and non-reducing conditions. Part of FOS-hGH was bound to other,
non-identified proteins due to the free cysteines present in the FOS amphiphatic
helix. However, more than 50% of expressed FOS-hGH occurred in its native
monomeric conformation ( Figure 3).
Purified FOS-hGH will be used to perform first doping experiments with
JL?v containing viral particles.
Example 6:
Construction of thepA V vector series for expression of FOS fusion proteins
A versatile vector system was constructed that allowed either cytplasmic
production or secretion of — or C-terminal FOS fusion proteins in E. coli or
production of - or C-terminal FOS fusion proteins in eukaryotic cells. The
vectors pAV 1 - pAV4 which was designed for production of FOS fusion proteins
in E. coli, encompasses the DNA cassettes listed below, which contain the
following genetic elements arranged in different orders: (a) a strong ribosome
binding site and 5'-untranslated region derived from the E. coli ompA gene

(aggaggtaaaaaacg) (SEQ ID NO: 13); (b) a sequence encoding the signal peptide
of E. coli outer membrane protein OmpA (MKKTAIAIAVALAGFATVAQA)
(SEQ ID NO: 14); (c) a sequence coding for the FOS dimerization domain flanked
on both sides by two glycine residues and a cystein residue
(CGGLTDTLQAETDQVEDEKSALQTEIANLLKEBCEKLEFILAAHGGC)
(SEQ ID NO: 15); and (d) a region encoding a short peptidic linker (AAASGG
(SEQ ID NO: 16) or GGSAAA (SEQ ID NO: 17)) connecting the protein of
interest to the FOS dimerization domain. Relevant coding regions are given in
upper case letters. The arrangement of restriction cleavage sites allows easy
construction of FOS fusion genes with or without a signal sequence. The
cassettes are cloned into the EcoRI/Hindin restriction sites of expression vector
pKK223-3 (Pharmacia) for expression of the fusion genes under control of the
strong tac promoter.
pAVl
This vector was designed for the secretion of fusion proteins with FOS at
the C-terminus into the E. coli periplasmic space. The gene of interest (g.o.i.)
may be ligated into the StuI/NotI sites of the vector.
EcoRI 31/11
craa, ttc agg agg taa aaa acg ATG AAA AAG ACA GCT ATC GCG ATT GCA GTG GCA CTG GCT
MKKTAIAIAVALA
61/21 StuI NotI
GGT TTC GCT ACC GTA GCG CAG_GCC_tgg gtg ggg GCG GCC GCT TCT GGT GGT TGC GGT GGT
G FATVAQA (goi) AAASGGCGG
121/41 151/51
CTG ACC GAC ACC CTG CAG GCG GAA ACC GAC CAG GTG GAA GAC GAA AAA TCC GCG CTG CAA
L TDTI.QAETDQVEDEKSAI..Q-
181/61 211/71
ACC GAA ATC GCG AAC CTG CTG AAA GAA AAA GAA AAG CTG GAG TTC ATC CTG GCG GCA CAC
T EIANLLKEKEKLEFILAAH
241/81 HiadIII
GGT GGT TGC taa get t (SEQ ID NO: 18)
c- G c * A (SEQ ID NOs:14 and l9)

PAV2
This vector was designed for the secretion of fusion proteins with FOS at
the N-terminus into the E. coli periplasmic space. The gene of interest (g.o.i.)
ligated into the Notl/EcoRV (or Notl/Hindlll) sites of the vector.
EcoRI 31/11
crae ttc agg agg taa aaa acg ATG AAA AAG ACA GCT ATC GCG ATT GCA GTG GCA CTG GCT
MKKTAIAIAVALA
61/21 StuI 91/31
GGT TTC GCT ACC GTA GCG CAG GCC TGC GGT GGT CTG ACC GAC ACC CTG CAG GCG GAA ACC
G FATVAQACGGLTDTLQAET
121/41 151/51
GAC CAG GTG GAA GAC GAA AAA TCC GCG CTG CAA ACC GAA ATC GCG AAC CTG CTG AAA GAA
D QVEDEKSALQTE IANLLKE
' 181/61 211/71 NotI
AAA GAA AAG CTG GAG TTC ATC CTG GCG GCA CAC GGT GGT TGC GGT GGT TCT GCG GCC GCT
K EKLEFILAAHGGCGGSAAA
241/81 EcoRV HindIII-
ggg tgt ggg gat ate aag ctt (SBQ ID NO:20)
(goi) (SEQ ID NO:21)
pAV3
This vector was designed for the cytoplasmic production of fusion
proteins with FOS at the C-terminus in E. coli. The gene of interest (g.o.i.) may
be ligated into the EcoRV/NotI sites of the vector.
EcoRI EcoRV NotI
qaa ttc agg agg taa aaa aat ate ggg tgt ggg GCG GCC GCT TCT GGT GGT TGC GGT GGT
(goi) AAASGGCGG
61/21 91/31
CTG ACC GAC ACC CTG CAG GCG GAA ACC GAC CAG GTG GAA GAC GAA AAA TCC GCG CTG CAA
L TDTLQAETDQVEDEKSALQ
121/41 151/51
ACC GAA ATC GCG AAC CTG CTG AAA GAA AAA GAA AAG CTG GAG TTC ATC CTG GCG GCA CAC
T ZIANLLKEKEKLEFILAAH
181/S1 HindIII
GGT GCT TGC taa get t (SEQ ID NO:22)
G G c * (SEQ ID NO:23)

pAV4
This vector is designed for the cytoplasmic production of fusion proteins
with FOS at the N-terminusin-E. coli. Thegeneofinterest(g.o.i.)may be ligated
into the Notl/EcoRV (or Notl/Hindm) sites of the vector. The N-terminal
methionine residue is proteolytically removed upon protein synthesis (Hirel et al.,
Proc. Natl. AcacL Sci. USA 56:8247-8251 (1989)).
EcoRI 31/11
gaa ttc agg agg taa aaa acg ATG GCT TGC GGT GGT CTG ACC GAC ACC CTG CAG GCG GAA
S FRE* KTMACGGLTDTLQAE
€1/21 91/31
ACC GAC CAG GTG GAA GAC GAA AAA TCC GCG CTG CAA'ACC GAA ATC GCG AAC CTG CTG AAA
TDQVEDEKSALQTEIANLLX
121/41 1S1/S1 NotI
GAA AAA GAA AAG CTG GAG TTC ATC CTG GCG GCA CAC GGT GST TGC GGT GGT TCT GCG GCC
E KEKLEFILAAHGGCGGSAA
181/61 EcoRV HindIII
GCT ggg tgt ggg erab ate aacr ctt (SEQ ED NOl24)
A (got) (SEQ ID NOs:88 and 25)
The vectors pAV5 and pAV6, which are designed for eukaryotic
production of FOS fusion proteins, encompasses the following genetic elements
arranged in different orders: (a) a region coding for the leader peptide of human
growth hormone (MATGSRTSLLLAFGLLCLPWLQEGSA) (SEQ ID NO:26);
(b) a sequence coding for the FOS dimerization domain flanked on both sides by
two glycine residues and a cysteine residue
(CGGLTDTLQAETDQVEDEKSALQTEIANLLKEKEKLEFILAAHGGC)
(SEQ ID NO. 15); and
(c) a region encoding a short peptidic linker (AAASGG (SEQ ID NO: 16) or
GOSAAA (SEQ ID NO: 17)) connecting the protein of interest to the FOS
dimerization domain. Relevant coding regions are given in upper case letters.
The arrangement of restriction cleavage sites allows easy construction of FOS
fusion genes. The cassettes are cloned into the EcoRI/Hindlll restriction sites of
the expression vector pMPSVEH (Artelt et al., Gene 55:213-219 (1988)).

pAV5
This vector is designed for the eukaxyotic production of fusion proteins
with FOS at the C-terminus. The gene of interest (go.i.) may be inserted between
the sequences coding for the hGH signal sequence and the FOS domain by ligation
into the Eco47III/NotI sites of the vector. Alternatively, a gene containing its
own signal sequence may be fused to the FOS coding region by ligation into the
StuI/NotI sites.
EcoRI StuI 31/11
craa. ttc agg cct ATG GCT ACA GGC TCC O3G ACG TCC CTO CTC CTG GCT TTT GGC CTG CTC
MATGSRTSLLLAFGI1I1
61/21 Eco47III HotI
TGC CTG CCC TGG CTT CAA GAG GGC AGC GCT ggg tgt sgg GCG GCC GCT TCT GGT GGT TGC
ci.PWLQ.EGSA (goi) A A A S G G C
121/41 151/51
GGT GGT CTG ACC GAC ACC CTG CAG GCG GAA ACC GAC CAG GTG GAA GAC GAA AAA TCC GCG
GGLTDTLQAETDQVEDEKSA
181/61 211/71
CTG CAA ACC GAA ATC GCS AAC CTG CTG AAA GAA AAA GAA AAG CTG GAG TTC ATC CTG GCG
I1QTEIAMLI1KEKEKLEFILA
241/81 HindIII
GCA CAC GGT GGT TGC taa get t (SEQ ID NO:27)
A H G G c * (SEQ ID NOs:26 and 28)
pAV6
This vector is designed for the eukaryotic production of fusion proteins
v/ithFOS at the N-terminus. The gene of interest (g.o.i.) may be ligated into the
Notl/StuI (or NotI/HindIII) sites of the vector.
EcoRI 31/11
Caa ttc ATG GCT ACA GGC TCC CGG ACG TCC CTG CTC CTG GCT TTT GGC CTG CTC TGC CTG
MATGSRTSLL.I,AFGIiI,CL
61/21 ECO47III 91/31
CCC TGG CTT CAA GAG GGC AGC GCT TGC GGT GGT CTG ACC GAC ACC CTG CAG GCG GAA ACC
P WLQEGSACGGLTDTLQAET
121/41 151/S1
GAC CAG GTG GAA GAC GAA AAA TCC GCG CTG CAA ACC GAA ATC GCG AAC CTG CTG AAA GAA
D QVEDEKSALQTE IAHLLKE

181/61 211/71 NotI
AAA GAA AAG CTG GAG TTC ATC CTG GCG GCA CAC GGT GGT TGC GGT GGT TCT GCG GCC GCT
KEKLEFILAAHGGCG GSAAA
24 1/81 StuI Hindlll
ggg tgt ggg aqq cct aag ctt (SEQ ID NO:29)
(goi) (SEQ ID NO:30)
Construction of expression vectors pA VI - pA V6
The following oligonucleotides have been synthesized for construction of
expression vectors pAVl - pAV6:
FOS-FORl:
CCTGGGTGGGGGCGGCCGCTTCTGGTGGTTGCGGTGGTCTGACC(SEQ
IDN0:31);
FOS-FOR2:
GGTGGGAATTCAGGAGGTAAAAAGATATCGGGTGTGGGGCGGCC
(SEQ ID NO:32);
FO5-FOR3:
GGTGGGAATTCAGGAGGTAAAAAACGATGGCTTGCGGTGGTCTGACC
(SEQ ID NO:33);
FOS-VOKA:
GCTTGCGGTGGTCTGACC (SEQ ID NO:34);
FOS-KEVl:
CCACCAAGCTTAGCAACCACCGTGTGC (SEQ ID NO:35);
FO5-REV2:
CCACCAAGCTTGATATCCCCACACCCAGCGGCCGCAGAACCACCGC
AACCACCG (SEQ ID NO:36);
FOS-REV3:
CCACCAAGCTTAGGCCTCCCACACCCAGCGGC (SEQ ID NO:37);
OmpA-FORl:
GGTGGGAATTCAGGAGGTAAAAAACGATG (SEQ ID NO:38);
hGH-FORl:

GGTGGGAATTCAGGCCTATGGCTACAGGCTCC (SEQ ID NO:39); and
hGH-F0R2:
GGTGGGAATTCATGGCTACAGGCTCCC (SEQ ID NO:40).
For the construction of vector pAV2, the regions coding for the OmpA
signal sequence and the FOS domain were amplified from the ompA-FOS-hGR
fusion gene in vector pKK223-3 (see Example 5) using the primer pair
OmpA-FORl/ FOS-REV2. The PCR product was digested with EcoRI/Hindlll
and ligated into the same sites of vector pKK223-3 (Pharmacia).
For the construction of vector pAVl, the FOS coding region was
amplified from the ompA-FCAS'-hGH fusion gene in vector pKK223-3 (see
Example 5) using the primer pair FOS-FORl IFOS-REV1. The PCR product was
digested with HindIII and ligated into Stul/HindIII digested vector pAV2.
For the construction of vector pAV3, the region coding for the FOS
domain was amplified from vector pAVl using the primer pair
FOS-FOR2/FOS-KEV1. The PCR product was digested with EcoRI/Hindlll and
ligated into the same sites of the vector pKK223-3 (Pharmacia).
For the construction of vector pAV4, the region coding for the FOS
domain was amplified from the ompA-FCW-hGH fusion gene in vector
pKK223-3 (see Example 5) using the primer pair FOS-VOR3/FOS-KEV2. The
PCR product was digested with EcoRI/Hindlll and ligated into the same sites of
the vector pKK223-3 (Pharmacia).
For the construction of vector pA V5, the region coding for the hGH signal
sequence is amplified from the hGH-FOS-hGH fusion gene in vector pSINrep5
(see Example 7) using the primer pair hGH-FORl/hGHRE VI. The PCRproduct
is digested with EcoRI/NotI and ligated into the same sites of the vector pAVl.
The resulting cassette encoding the hGH signal sequence and the FOS domain is
then isolated by EcoRI/HindIII digestion and cloned into vector pMPSVEH
(Anelt et al, Gene (55:213-219 (1988)) digested with the same enzymes.

For the construction of vector pAV6, the FOS coding region is amplified
from vector pAV2 using the primer pair FOS-FOR4/FOSREV3. The PCR
product is digested with Hindlll and cloned into Eco47III/HindIII cleaved vector
pAV5. The entire cassette encoding the hGH signal sequence and the FOS
domain is then reamplified from the resulting vector using the primer pair
hGH-FOR2/FOSREV3, cleaved with EcoRI/Hindlll and ligated into vector
pMPSVEH (Artelt et al., Gene (55:213-219 (1988)) cleaved with the same
enzymes.
Example 7:
Construction of FOS-hGH with human (hGH) signal sequence
For eukaryotic expression of the FOS-hGH fusion protein, the
OmpA-.FO.S'-hGH fusion gene was isolated from pBluescript::OmpA-FOS-hGH
{see Example 4) by digestion with Xbal/Bsp 1201 and cloned into vector pSINrep5
(Invitrogen) cleaved with the same enzymes. The hGH signal sequence was
synthesized by PCR (reaction mix: 50 pmol of each primer, dATP, dGTP, dTTP,
dCTP (200 M each), 2.5 U Taq DNA polymerase (Qiagen), 50 ul total volume
in the buffer supplied by the manufacturer; amplification: 92°C for 30 seconds,
55°C for 30 seconds, 72°C for 30 seconds, 30 cycles) using the overlapping
oligonucleotides Sig-hGH-FOR
(GGGTCTAGAATGGCTACAGGCTCCCGGACGTCCCTGCTCCTGGCTT
TTGGCCTGCTCTG) (SEQ ID NO:41) and Sig-hGH-REV
(CGCAGGCCTCGGCACTGCCCTCTTGAAGCCAGGGCAGGCAGAGCA
GGCCAAAAGCCAG) (SEQ ID NO:42). The PCR product was purified using
the QiaExII Kit, digested with Stul/Xbal and ligated into vector
pSINrep5::OmpA-F0S'-hGH cleaved with the same enzymes.

Example 8:
Eukaryotic expression of FOS-ItGH
RNase-free vector (1.0 ng) (pSINrep5::OmpA-FaS-hGH) and 1.0 ug of
DHEB (Bredenbeek et al.J Virol. 67:6439-6446 (1993)) were linerarized by
Seal restriction digest. Subsequently, in vitro transcription was carried out using
an SP6 in vitro transcription kit (InvitroscripCAP by InvitroGen, Invitrogen B V,
NV Leek, Netherlands). The resulting 5'-capped mRNA was analyzed on
reducing agarose-gel.
In vitro, transcribed mRNA 5 u.g was electroporated into BHK 21 cells
(ATCC: CCL10) according to Invitrogen's manual (Sindbis Expression system,
Invitrogen BV, Netherlands). After 10 hours incubation at 37°C the FCS
containing medium was exchanged by HP-1 medium without FCS, followed by
an additional incubation at 37°C for 10 hours. The supernatant was harvested
and analyzed by dot-blot analysis for production of FOS-hgh.
Culture media (2.5 ul) was spotted on a nitrocellulose membrane and
dried for 10 minutes at room temperature. The membrane was blocked with 1 %
bovine albumin (Sigma) in TBS (IOXTBS per liter: 87.7 g NaCI, 66. lg Trizma
hydrochloride (Sigma) and 9.7 g Trizma base (Sigma), pH 7.4) for 1 hour at room
temperature, followed by an incubation with 2 \xg rabbit anti-human hGH
antibody (Sigma) in 10 ml TBS-T (TBS with 0.05% Tween20) for 1 hour. The
blot was washed 3 times for 10 minutes with TBS-T and incubated for 1 hour
with alkaline phosphatase conjugated anti-rabbit IgG (Jackson ImmunoResearch
Laboratories, Inc.) diluted 1:5000 in TBS-T. After washing 2 times for 10
minutes with TBS-T and 2 times for 10 minutes with TBS, the blot was
developed by AP staining as described in Example 2. Results are shown in
Figure 3.

Example 9:
Construction of FOS-PLA (TV- and C-terminal)
The following gene is constructed by chemical gene synthesis coding for
a catalytically inactive variant (Forster et al, J. Allergy Clin. Immunol. 95:
1229-1235 (1995)) of bee venom phospholipase A2 (PLA).
1/1 31/11
ATC ATC TAC CCA GGT ACT CTG TGG TGT GGT CAC GGC AAC AAA TCT TCT GGT CCG AAC GAA
I IYPGTLWCGHGNKSSGPNE
61/21 91/31
CTC GGC CGC TTT AAA CAC ACC GAC GCA TGC TGT CGC ACC CAG GAC ATG TGT CCG GAC GTC
LGRFKHTDACCRTQDMCPDV
121/41 151/51
ATG TCT GCT GGT GAA TCT AAA CAC GGG TTA ACT AAC ACC GCT TCT CAC ACG CGT CTC AGC
M SAGESKHGLTNTAS HTRLS
181/61 211/71
TGC GAC TGC GAC GAC AAA TTC TAC GAC TGC CTT AAG AAC TCC GCC GAT ACC ATC TCT TCT
CDCDDKFYDCLKNSADTISS
241/81 271/91
TAC TTC GTT GGT AAA ATG TAT TTC AAC CTG ATC GAT ACC AAA TGT TAC AAA CTG GAA CAC
Y FVGKMYFNLIDTKCYKLEH
301/101 331/111
CCG GTA ACC GGC TGC GGC GAA CGT ACC GAA GGT CGC TGC CTG CAC TAC ACC GTT GAC AAA
P VTGCGERTEGRC LHYTVDK
361/121 391/131
TCT AAA CCG AAA GTT TAC CAG TGG TTC GAC CTG CGC AAA TAC (SEQ ID NO ."43)
SKPKVYQWFDLRKY (SEQ ID NO:44)
For fusion of PLA to the N-terminus of the FOS dimerization domain, the
region is amplified using the oligonucleotides PLA-FOR1
(CCATCATCTACCCAGGTAC) (SEQ ID NO:45) and PLA-REV1
(CCCACACCCAGCGGCCGCGTATTTGCGCAGGTCG) (SEQ ID NO:46).
The PCR product is cleaved with NotI and ligated into vector pAVl previously
cleaved with the restriction enzymes Stul/Notl. For fusion of PLA to the
C-terminus of the FOS dimerization domain, the region is amplified using the
oligonucleotides PLA-FOR2
(CGGTGGTTCTGCGGCCGCTATCATCTACCCAGGTAC) (SEQ ID NO:47)
and PLA-REV2 (TTAGTATTTGCGCAGGTCG) (SEQ ID NO:47). The PCR

product is cleaved with NotI and ligated into vector pAV2 previously cleaved
with the restriction enzymes Notl/EcoRV.
Example 10:
Construction of FOS-Ovalbumin fusion gene (N- and C-terminal)
For cloning of the ovalbumin coding sequence, mRNA from chicken
oviduct tissue is prepared using the QuickPrep™ Micro mRNA Purification Kit
(Pharmacia) according to manufacturer instructions. Using the Superscript™
One-step RT PCR Kit (Gibco BRL), a cDNA encoding the mature part of
ovalbumin (corresponding to nucleotides 68-1222 of the mRNA (McReynolds et
al, Nature 275:723-728 (1978)) is synthesized using the primers Ova-FORl
(CCGGCTCCATCGGTGCAG) (SEQ ID NO:49) and Ova-REVl
(ACCACCAGAAGCGGCCGCAGGGGAAACACATCTGCC) (SEQ ID
NO:50). The PCR product is digested with NotI and cloned into StuI/NotI
digested vector pAVl for expression of the fusion protein with the FOS
dimerization domain at the C terminus. For production of a fusion protein with
the FOS dimerization domain at the N terminus, the Ovalbumin coding region is
amplified from the constructed vector (pAV 1: :Ova) using the primers Ova-FOR2
(CGGTGGTTCTGCGGCCGCTGGCTCCATCGGTGCAG) (SEQ ID NO:51)
and 0va-REV2 (TTAAGGGGAAACACATCTGCC) (SEQ ID NO:52). The
PCR product is digested with NotI and cloned into the Notl/EcoRV digested
vector pAV2. Cloned fragments are verified by DNA sequence analysis.
Example 11
Production and purification of FOS-PLA and
FOS ovalbumin fusion proteins
For cytoplasmic production of FOS fusion proteins, an appropriate E. coli
strain was transformed with the vectors pAV3::PLA,pAV4::PL A, pAV3::0va or
pAV4::Ova. The culture was incubated in rich medium in the presence of
ampicillin at 37°C with shaking. At an optical density (550nm) of 1, 1 mM IPTG
was added and incubation was continued for another 5 hours. The cells were

harvested by centrifugation, resuspended in an appropriate buffer (e.g. tris-HCl,
pH 7.2, 150 mM NaCl) containing DNase, RNase and lysozyme, and disrupted
by passage through a french pressure cell. After centrifugation (Sorvall RC-5C,
SS34 rotor, 15000 rpm, 10 min, 4°C), the pellet was resuspended in 25 ml
inclusion body wash buffer (20 mM tris-HCl, 23% sucrose, 0.5% Triton X-100,
1 mM EDTA, pH8) at 4°C and recentrifuged as described above. This procedure
was repeated until the supernatant after centrifugation was essentially clear.
Inclusion bodies were resuspended in 20 ml solubilization buffer (5.5 M
guanidinium hydrochloride, 25 mM tris-HCl, pH 7.5) at room temperature and
insoluble material was removed by centrifugation and subsequent passage of the
supernatant through a sterile filter (0.45 urn). The protein solution was kept at
4 ° C for at least 10 hours in the presence of 10 mM EDTA and 100 mM DTT and
then dialyzed three times against 10 volumes of 5.5 M guanidinium
hydrochloride, 25 mM tris-HCl, 10mMEDTA,pH6. The solution was dialyzed
twice against 5 liters of 2 M urea, 4 mM EDTA, 0.1 M NH4C1, 20 mM sodium
borate (pH 8.3) in the presence of an appropriate redox shuffle (oxidized
glutathione/reduced glutathione; cystine/cysteine). The refolded protein was then
applied to an ion exchange chromatography. The protein was stored in an
appropriate buffer with a pH above 7 in the presence of 2-10 mM DTT to keep
the cysteine residues flanking the FOS domain in a reduced form. Prior to
coupling of the protein with the alphavirus particles, DTT was removed by
passage of the protein solution through a Sephadex G-25 gel filtration column.
Example 12:
Constructions of gpl40-FOS
The gpl40 gene (Swiss-Prot:P03375) without the internal protease
cleavage site was amplified by PCR from the original plasmid pAbT4674 (ATCC
40829) containing the full length gp l60 gene using the following
oligonucleotides:

HIV-1:
5'-ACTAGTCTAGAatgagagtgaaggagaaatatc-3' (SEQ ID NO:53);
HIV-end:
5'-TAGCATGCTAGCACCGAAtttatctaattccaataattcttg-3' (SEQ ID NO:54);
HIV-Cleav:
5 '-gtagcacccaccaaggcaaagCTGAAAGCTACCCAGCTCG AGAAACTGgca-3'
(SEQ ID NO:55); and
HIV-Cleav2:
5 '-caaagctcctattcccactgcCAGTTTCTCGAGCTGGGTAGCTTTCAG-3' (SEQ ID
NO:56).
For PCR I, 100 pmol of oligo HIV-1 and HIV-Cleav2 and 5 ng of the
template DNA were used in the 75 l reaction mixture (4 units of Taq or Pwo
polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4). PCR cycling was done in the
following manner: 30 cycles with an annealing temperature of 60°C and an
elongation time of 2 minutes at 72°C.
For PCR II, 100 pmol of oligo HIV-end and HIV-Cleav and 5 ng of the
template DNA were used in the 75 l reaction mixture, (4 units of Taq or Pwo
polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4). PCR cycling was done in the
following manner: 30 cycles with an annealing temperature of 60°C and an
elongation time of 50 seconds at 72°C.
Both PCR fragments were purified, isolated and used in an assembly PCR
reaction. For the assembly PCR reaction, 100 pmol of oligo HIV-1 and HIV-end
and 2 ng of each PCR fragment (PCRI and PCR II) were used in the 75 (il (4 units
of Taq or Pwo polymerase, 0.1 mM dNTPs and 1.5 mM MgSO4). PCR cycling
was done in the following manner: 30 cycles with an annealing temperature of
60c C and an elongation time of 2.5 minutes at 72°C. The assembly PCR product
was digested Xbal and Nhel. The FOS amphiphatic helix was fused in frame to
the C-terminal end of gp-140.

The DNA sequence coding for the FOS amphiphatic helix domain was
PCR-amplified from vector pJuFo (Crameri & Suter Gene 137: 69 (1993)) using
the oligonucleotides:
FOS-UIV:
5'-ttcggtgctagcggtggcTGCGGTGGTCTGACCGAC-3' (SEQ ID NO:57); and
FOS-Apa:
5'-gatgctgggcccttaaccGCAACCACCGTGTGCCGCC-3' (SEQ ID NO:58).
For the PCR reaction, 100 pmol of each oligo and 5 ng of the template
DNA was used in the 75 ul reaction mixture (4 units of Taqor Pwo polymerase,
0.1 mM dNTPs and 1.5 mM MgSO4). Temperature cycling was done as follows:
95°C for 2 minutes, followed by 5 cycles of 95°C (45 seconds), 60°C (30
seconds), 72 °C (25 seconds) and followed by 25 cycles of 95°C (45 seconds),
68 ° C (3 0 seconds), 72 ° C (20 seconds). The obtained PCR fragment was digested
with Nhel and Bsp 120L.
The final expression vector for GP140-FOS was obtained in a 3 fragment
ligation of both PCR fragments into pSinRep5. The resultant vector
pSinRepS-GPMO-FOiS1 was evaluated by restriction analysis and DNA
sequencing.
GP 140-FOS was also cloned into pCYTts via Xbal and Bsp 120L to obtain
a stable, inducible GP14O-F0S expressing cell line.
Example 13:
Expression of GPUOFOS using pSinRep5-GP140FOS
RNase-free vector (1.0 ug) (pSinRep5-GP 140-FOS) and 1.0 ug of DHEB
(Bredenbeek et al, J. Virol. 67:6439-6446 (1993)) were linearized by restriction
digestion. Subsequently, in vitro transcription was carried out using an SP6 in
vitro transcription kit (InvitroscripCAP by InvitroGen, Invitrogen BV, NV Leek,
Netherlands). The resulting 5'-capped mRNA was analyzed on a reducing
agarose-gel.
In vitro transcribed mRNA (5 ug) was electroporated into BHK 21 cells
(ATCC: CCL10) according to Invitrogen's manual (Sindbis Expression System,

Invitrogen BV, Netherlands). After 10 hours incubation at 37°C, the FCS
containing medium was exchanged by HP-1 medium without FCS, followed by
an additional incubation at 37°C for 10 hours. The supernatant was harvested
and analyzed by Western blot analysis for production of soluble GP140-FOS
exactly as described in Example 2.
Example 14:
Expression ofGPUOFOS usingpCYTts-GPUOFOS
pCYT-GP 140-FOS 20 g was linearized by restriction digestion. The
reaction was stopped by phenol/chloroform extraction, followed by an
isopropanol precipitation of the linearized DNA. The restriction digestion was
evaluated by agarose gel eletrophoresis. For the transfection, 5.4 \xg of linearized
pCYTtsGPl 40-FOS was mixed with 0.6 ug of linearized pSV2Neo in 30 ul H2O
and 30 ul of 1 M CaCl2 solution was added. After addition of 60 ul phosphate
buffer (50 mM HEPES, 280 mMNaCl, 1.5 mM Na2 HPO4, pH 7.05), the solution
was vortexed for 5 seconds, followed by an incubation at room temperature for
25 seconds. The solution was immediately added to 2 ml HP-1 medium
containing 2% FCS (2% FCS medium). The medium of an 80% confluent
BHK21 cell culture (6-well plate) was then replaced by the DNA containing
medium. After an incubation for 5 hours at 37°C in a CO: incubator, the DNA
containing medium was removed and replaced by 2 ml of 15% glycerol in 2%
FCS medium. The glycerol containing medium was removed after a 30 second
incubation phase, and the cells were washed by rinsing with 5 ml of HP-1
medium containing 10% FCS. Finally 2 ml of fresh HP-1 medium containing
10% FCS was added.
Stably transfected cells were selected and grown in selection medium
(HP-1 medium supplemented with G418) at 37°C inaCO: incubator. When the
mixed population was grown to confluency, the culture was split to two dishes,
followed by a 12 h growth period at 37 °C. One dish of the cells was shifted to
30 °C to induce the expression of soluble GP140-FO5. The other dish was kept
at 37°C.

The expression of soluble GP14O-F0.S was determined by Western blot
analysis. Culture media (0.5 ml) was methanol/chloroform precipitated, and the
pellet was resuspended in SDS-PAGE sample buffer. Samples were heated for
5 minutes at 95 °C before being applied to a 15% acrylamide gel. After
SDS-PAGE, proteins were transferred to Protan nitrocellulose membranes
(Schleicher & Schuell, Germany) as described by Bass and Yang, in Creighton,
T.E., ed., Protein Function: A Practical Approach, 2nd Edn., IRL Press, Oxford
(1997), pp. 29-55. The membrane was blocked with 1 % bovine albumin (Sigma)
in TBS (IOXTBS per liter: 87.7 gNaCl, 66. lg Trizmahydrochloride (Sigma) and
9.7 g Trizma base (Sigma), pH 7.4) for 1 hour at room temperature, followed by
an incubation with an anti-GP140 or GP-160 antibody for 1 hour. The blot was
washed 3 times for 10 minutes with TBS-T (TBS with 0.05% Tween20), and
incubated for 1 hour with an alkaline-phosphatase-anti-
mouse/rabbit/monkey/human IgG conjugate. After washing 2 times for 10
minutes with TBS-T and 2 times for 10 minutes with TBS, the development
reaction was carried out using alkaline phosphatase detection reagents (10 ml AP
buffer (100 mMTris/HCl, 100 mMNaCl,pH9.5) with 50 ul NBT solution(7.7%
Nitro Blue Tetrazolium (Sigma) in 70% dimethylformamide) and 37 ul of
X-Phosphate solution (5% of 5-bromo-4-chloro-3-indolyl phosphate in
dimethylformamide).
Example 15:
Production and purification of GP140FOS
An anti-gpl 20 antibody was covalently coupled to a NHS/EDC activated
dextran and packed into a chromatography column. The supernatant, containing
GP14OF0S is loaded onto the column and after sufficient washing, GP14OF0S
was eluted using 0.1 M HC1. The eluate was directly neutralized during
collection using 1 M Tris pH 7.2 in the collection tubes.
Disulfide bond formation might occur during purification, therefore the
collected sample is treated with 10 mM DTT in 10 mM Tris pH 7.5 for 2 hours
at25°C.

DTT is remove by subsequent dialysis against 10 mM Mes; 80 mM NaC!
pH 6.0. Finally GP140FOS is mixed with alphavirus particles containing the
JUN leucine zipper in E2 as described in Example 16.
Example 16:
Preparation of the AlphaVaccine Particles
Viral particles (see Examples 2 and 3) were concentrated using Millipore
Ultrafree Centrifugal Filter Devices with a molecular weight cut-off of 100 kD
according to the protocol supplied by the manufacturer. Alternatively, viral
particles were concentrated by sucrose gradient centrifugation as described in the
instruction manual of the Sindbis Expression System (Invitrogen, San Diego,
California). The pH of the virus suspension was adjusted to 7.5 and viral
particles were incubated in the presence of 2-10 mM DTT for several hours.
Viral particles were purified from contaminating protein on a Sephacryl S-300
column (Pharmacia) (viral particles elute with the void volume) in an appropriate
buffer.
Purified virus particles were incubated with at least 240 fold molar excess
of FOS-antigen fusion protein in an appropriate buffer (pH 7.5-8.5) in the
presence of a redox shuffle (oxidized glutathione/reduced glutathione;
cystine/cysteine) for at least 10 hours at 4°C. After concentration of the particles
using a Millipore Ultrafree Centrifugal Filter Device with a molecular weight
cut-off of 100 kD, the mixture was passed through a Sephacryl S-300 gel
filtration column (Pharmacia). Viral particles were eluted with the void volume.
Example 17
Fusion of JUNamphipathic helix to the amino terminus of HBcAg(l-144)
The JUN helix was fused to the amino terminus of the HBcAg amino acid
sequence 1 to 144 (JUN-HBcAg construct). For construction of the JUN-HBcAg
DNA sequence, the sequences encoding the JUN helix and HBcAgO -144) were
amplified separately by PCR. The JUN sequence was amplified from the pJuFo

plasmid using primers EcoRI-JUN(s) and JUN-SacII(as). The EcoRI-JUN(s)
primer introduced an EcoRI site followed by a start ATG codon. The JUN-
SacII(as) primer introduced a linker encoding the amino acid sequence GAAGS.
The HBcAg (1-144) sequence was amplified from the pEco63 plasmid (obtained
from ATCC No. 31518) using primers JUN-HBcAg(s) and
HBcAg( 1 -144)Hind(as). JUN-HBcAg(s) contained a sequence corresponding to
the 3' end of the sequence encoding the JUN helix followed by a sequence
encoding the GAAGS linker and the 5' end of the HBcAg sequence. HBcAg(l-
144)Hind(as) introduces a stop codon and a HindIII site after codon 144 of the
HBcAg gene. For the PCR reactions, 100 pmol of each oligo and 50 ng of the
template DNAs were used in the 50 l reaction mixtures with 2 units of Pwo
polymerase, 0.1 mM dNTPs and 2 mM MgSO4. For both reactions, temperature
cycling was carried out as follows: 94°C for 2 minutes; and 30 cycles of 94°C (1
minute), 50°C (1 minute), 72°C (2 minutes).
Primer sequences:
EcoRI-JUN(s):
(5'-CCGGAATTCATGTGCGGTGGTCGGATCGCCCGG-3') (SEQ ID
NO:61);
JUN-SacII(as):
(5 '-GTCGCTACCCGCGGCTCCGCAACCAACGTGGTTCATGAC-3') (SEQ
ID NO:62);
JUN-HBcAg(s):
(5'-GTTGGTTGCGGAGCCGCGGGTAGCGACATTGACCCTTATAAAGAATTTGG-3')
(SEQ ID NO:63);

HBcAg(l-144)Hind(as):
(5 '-CGCGTCCCAAGCTTCTACGGAAGCGTTGATAGGATAGG-3') (SEQ
ID NO:64).
Fusion of the two PCR fragments was performed by PCR using primers
EcoRI-JUN(s) and HBcAg(l-144)Hind(as). 100 pmol of each oligo was used with
100ng of the purified PCR fragments in a 50 ul reaction mixture containing 2
units of Pwo polymerase, 0.1 mM dNTPs and 2 mM MgSO4. PCR cycling
conditions were: 94°C for 2 minutes; and 35 cycles of 94°C (1 minute), 50°C
(1 minute), 72 °C (2 minutes). The final PCR product was analyzed by agarose
gel electrophoresis, purified and digested for 16 hours in an appropriate buffer
with EcoRI and HindIII restriction enzymes. The digested DNA fragment was
ligated into EcoRI/HindIII-digested pKK vector to generate pKK-JUN-HBcAg
expression vector. Insertion of the PCR product was analyzed by EcoRI/HindIII
restriction analysis and by DNA sequencing of the insert.
Example 18
Fusion of JUN amphipathic helix to the carboxy terminus of HBcAg(l-144)
The JUN helix was fused to the carboxy terminus of the HBcAg amino
acid sequence 1 to 144 (HBcAg-JUN construct). For construction of the HBcAg-
JUN DNA sequence, the sequences encoding the JUN helix and HBcAg( 1 -144)
were amplified separately by PCR. The JUN sequence was amplified from the
pJuFo plasmid with primers SacII-JUN(s) and JUN-Hindlll(as). SacII-JUN(s)
introduced a linker encoding amino acids LAAG. This sequence also contains a
SacII site. JUN-HindIII(as) introduced a stop codon (TAA) followed by a Hindlll
site. The HBcAg(l -144) DNA sequence was amplified from the pEco63 plasmid
using primers EcoRI-HBcAg(s) and HBcAg(l -144)-JUN(as). EcoRI-HBcAg(s)
introduced an EcoRI site prior to the Start ATG of the HBcAg coding sequence.
HBcAg(l-144)-JUN(as) introduces a sequence encoding the peptide linker
(LAAG), which also contains a SacII site. For the PCR reactions, 100 pmol of

each oligo and 50 ng of the template DNAs were used in the 50 ul reaction
mixtures with 2 units of Pwo polymerase, 0.1 mM dNTPs and 2 mM MgSO4.
Temperature cycling was carried out as follows: 94°C for 2 minutes; and 30
cycles of 94°C (1 minute), 50°C (1 minute), 72°C (2 minutes).
Primer sequences
SacII-JUN(s):
(5'-CTAGCCGCGGGTTGCGGTGGTCGGATCGCCCGG-3') (SEQ ID
NO:65);
JUN-Hindlll(as):
(5'-CGCGTCCCAAGCTTTTAGCAACCAACGTGGTTCATGAC -3') (SEQ
ID NO:66);
EcoRI-HBcAg(s):
(5'-CCGGAATTCATGGACATTGACCCTTATAAAG-3') (SEQ ID NO:67);
and
HBcAg-JUN(as):
(5'-CCGACCACCGCAACCCGCGGCTAGCGGAAGCGTTGATAGGATAGG-3')
(SEQ ID NO:68).
Fusion of the two PCR fragments was performed by PCR using primers
EcoRI-HBcAg(s) and JUN-HindIII(as). For the PCR fusion, 100 pmol of each
oligo was used with lOOng of the purified PCR fragments in a 50 ul reaction
mixture containing 2 units of Pwo polymerase, 0.1 mM dNTPs and 2 mM
MgSO4. PCR cycling conditions were: 94°C for 2 minutes; and 35 cycles of
94°C(1 minute), 50°C(1 minute), 72°C (2 minutes). The final PCR product was
analyzed by agarose gel electrophoresis, and digested for 16 hours in an

appropriate buffer with EcoRI and Hindlll restriction enzymes. The DNA
fragment was gel purified and ligated into EcoRI/Hindlll-digested pKK vector to
generate pKK-HBcAg-JUN expression vector. Insertion of the PCR product was
analyzed by EcoRI/HindIII restriction analysis and by DNA sequencing of the
insert.
Example 19
Insertion of JUN amphipathic helix into the c/el epitope of HBcAg(l-144)
The c/el epitope (residues 72 to 88) of HBcAg is known to be located in
the tip region on the surface of the hepatitis B virus capsid. A part of this region
(residues 76 to 82) of the protein was genetically replaced by the JUN helix to
provide an attachment site for antigens (HBcAg-JUNIns construct). The HBcAg-
JUNIns DNA sequence was generated by PCRs: The JUN helix sequence and
t\Vo sequences encoding HBcAg fragments (amino acid residues 1 to 75 and 83
to 144) were amplified separately by PCR. The JUN sequence was amplified
from the pJuFo plasmid with primers BamHI-JUN(s) and JUN-SacII(as).
BamHI-JUN(s) introduced a linker sequence encoding the peptide sequence
GSGGG that also contains a BamHI site. JUN-SacII(as) introduced a sequence
encoding the peptide linker GAAGS followed by a sequence complementary to
the 3' end of the JUN coding sequence. The HBcAg(l-75) DNA sequence was
amplified from the pEco63 plasmid using primers EcoRIHBcAg(s) and
HBcAg75-JUN(as). EcoRIHBcAg(s) introduced an EcoRI site followed by a
sequence corresponding to the 5' end of the HBcAg sequence. HBcAg75-
JUN(as) introduced a linker encoding the peptide GSGGG after amino acid 75 of
HBcAg followed by a sequence complementary to the 5' end of the sequence
encoding the JUN helix. The HBcAg (83-144) fragment was amplified using
primers JUN-HBcAg83(s) and HBcAg(l-144)Hind(as). JUN-HBcAg83(s)
contained a sequence corresponding to the 3' end of the JUN-encoding sequence
followed by a linker encoding the peptide, GAAGS and a sequence corresponding
to the 5' end of the sequence encoding HBcAg (83-144). HBcAg(l-144)Hind(as)

introduced a stop codon and a HindIII site after codon 144 of the HBcAg gene.
For the PCR reactions, 100 pmol of each oligo and 50 ng of the template DNAs
were used in the 50 ul reaction mixtures (2 units of Pwo polymerase, 0.1 mM
dNTPs and 2 mM MgSO4). Temperature cycling was performed as follows:
94°C for 2 minutes; and 35 cycles of 94°C (1 minute), 50°C (1 minute), 72°C
(2 minutes).
Primer sequences:
BamHI-JUN(s):
(5'-CTAATGGATCCGGTGGGGGCTGCGGTGGTCGGATCGCCCGGCTCGAG-3')
(SEQ ID NO:69);
JUN-SacII(as):
(5 '-GTCGCTACCCGCGGCTCCGCAACCAACGTGGTTCATGAC-3') (SEQ
ID NO:70);
EcoRIHBcAg(s):
(5'- CCGGAATTCATGGACATTGACCCTTATAAAG-3') (SEQ ID NO:71);
HBcAg75-JUN (as):
(5 '-CCG ACCACCGCAGCCCCCACCGGATCCATTAGTACCCACCCAGGTAGC-3')
(SEQ ID NO:72);
JUN-HBcAg83(s):
(5'-GTTGGTTGCGGAGCCGCGGGTAGCGACCTAGTAGTCAGTTATGTC-3')
(SEQ ID NO:73); and

HBcAg(l-144)Hind(as):
(5 '-CGCGTCCCAAGCTTCTACGGAAGCGTTGATAGGATAGG-3') (SEQ
ID NO:74).
Fusion of the three PCR fragments was performed as follows. First, the
fragment encoding HBcAg 1-75 was fused with the sequence encoding JUN by
PCR using primers EcoRIHBcAg(s) and JUN-SacII(as). Second, the product
obtained was fused with the HBcAg(83-144) fragment by PCR using primers
EcoRI HBcAg(s) and HBcAg HindIII(as). For PCR fusions, 100 pmol of each
oligo was used with 100 ng of the purified PCR fragments in a 50 l reaction
mixture containing 2 units of Pwo polymerase, 0.1 mM dNTPs and 2 mM
MgSO4. The same PCR cycles were used as for generation of the individual
fragments. The final PCR product was digested for 16 hours in an appropriate
buffer with EcoRI and Hindlll restriction enzymes. The DNA fragment was
li gated into EcoRI/HindIII-digested. pKK vector, yielding the pKK-HBcAg-
JUNIns vector. Insertion of the PCR product was analyzed by EcoRI/HindIII
restriction analysis and by DNA sequencing of the insert.
Example 20
Fusion of the JUNamphipathic helix to the carboxy terminus of the
measles virus nucleocapsid (N) protein
The JUN helix was fused to the carboxy terminus of the truncated measles
virus N protein fragment comprising amino acid residues 1 to 473 (N473-JUN
construct). For construction of the DNA sequence encoding N473-JUN the
sequence encoding the JUN helix and the sequence encoding N473-JUN were
amplified separately by PCR. The JUN sequence was amplified from the pJuFo
plasmid with primers SacII-JUN(s) and JUN-HindIII(as). SacII-JUN(s)
introduced a sequence encoding peptide linker LAAG. This sequence also
contained a SacII site. The JUN-HindIII(as) anti-sense primer introduced a stop
codon (TAA) followed by a Hindlll site. The N (1-473) sequence was amplified
from the pSC-N plasmid containing the complete measles virus N protein coding

sequence (obtained from M. Billeter, Zurich) using primers EcoRJ-Nmea(s) and
Nmea-JUN(as). EcoRI-N(mea)(s) introduced an EcoRI site prior to the Start
ATG of the N coding sequence. N(mea)-JUN(as) was complementary to the 3'
end of the N(l -473) coding sequence followed by a sequence complementary to
the coding sequence for the peptide linker (LAAG). For the PCR reactions, 100
pmol of each oligo and 50 ng of the template DNAs were used in the 50 ul
reaction mixtures with 2 units of Pwo polymerase, 0.1 mM dNTPs and 2 mM
MgSO4. Temperature cycling was performed as follows: 94 °C for 2 minutes; and
35 cycles of 94°C (1 minute), 55°C (1 minute), 72°C (2 minutes).
Primer sequences:
SacII-JUN(s):
(5'-CTAGCCGCGGGTTGCGGTGGTCGGATCGCCCGG-3') (SEQ ID
NO:75);
JUN-HindIII(as):
(5'-CGCGTCCCAAGCTTTTAGCAACCAACGTGGTTCATGAC -3') (SEQ
ID NO.76);
EcoRI-Nmea(s):
(5'-CCGGAATTCATGGCCACACTTTTAAGGAGC-3')(SEQ ID NO:77);and
Nmea-JUN(as):
(5 '-CGCGTCCCAAGCTTTTAGCAACCAACGTGGTTC ATGAC-3') (SEQ ID
NO:78).
Fusion of the two PCR fragments was performed in a further PCR using
primers EcoRI-Nmea(s) and Nmea-JUN(as). For the PCR fusion, 100 pmol of
each oligo was used with 100 ng of the purified PCR fragments in a 50 l

reaction mixture containing 2 units of Pwo polymerase, 0.1 mM dNTPs and 2
m.M MgSO4. Temperature cycling was performed as follows: 94°C for 2
minutes; and 35 cycles of 94°C (1 minute), 50°C (1 minute), 72°C (2 minutes).
The PCR product was digested for 16 hours in an appropriate buffer with EcoRI
and HindIII restriction enzymes. The DNA fragment was gel purified and ligated
into EcoRI/HindIII-digested pKK vector, yielding the pKK-N473-JUN plasmid.
Insertion of the PCR product was analyzed by EcoRI/HindIII restriction analysis
and by DNA sequencing of the insert.
Example 21
Expression and partial purification of HBcAg-JUN
E. coli strain XL-1 blue was transformed with pKK-HBcAg-JUN. 1 ml
of an overnight culture of bacteria was used to innoculate 100 ml of LB medium
containing 100 g/ml ampicillin. This culture was grown for 4 hours at 37°C
until an OD at 600 nm of approximately 0.8 was reached. Induction of the
synthesis of HBcAg-JUN was performed by addition of IPTG to a final
concentration of 1 mM. After induction, bacteria were further shaken at 37 °C for
16 hours. Bacteria were harvested by centrifugation at 5000 x g for 15 minutes.
The pellet was frozen at -20°C. The pellet was thawed and resuspended in
bacteria lysis buffer (10 mM Na2HPO4 pH 7.0,30 mM NaCl, 0.25% Tween-20,
10 mM EDTA, 10 mM DTT) supplemented with 200 ug/ml lysosyme and 10 ul
of Benzonase (Merck). Cells were incubated for 30 minutes at room temperature
and disrupted using a French pressure cell. Triton X-l 00 was added to the lysate
to a final concentration of 0.2%, and the lysate was incubated for 30 minutes on
ice and shaken occasionally. Figure 4 shows HBcAg-JUN protein expression in
E. coli upon induction with IPTG. E. coli cells harboring pKK-HBcAg-JUN
expression plasmid or a control plasmid were used for induction of HBcAg-JUN
expression with IPTG. Prior to the addition of IPTG, a sample was removed from
the bacteria culture carrying the pKK-HBcAg-JUN plasmid (lane 3) and from a
culture carrying the control plasmid (lane 1). Sixteen hours after addition of

IPTG, samples were again removed from the culture containing pKK-HBcAg-
JUN (lane 4) and from the control culture (lane 2). Protein expression was
monitored by SDS-PAGE followed by Coomassie staining.
The lysate was then centrifuged for 30 minutes at 12,000 x g in order to
remove insoluble cell debris. The supernatant and the pellet were analyzed by
Western blotting using a monoclonal antibody against HBcAg (YVS1841,
purchased from Accurate Chemical and Scientific Corp., Westbury, NY, USA),
indicating that a significant amount of HBcAg-JUN protein was soluble (Fig. 5).
Briefly, lysates from E. coli cells expressing HBcAg-JUN and from control cells
were centrifuged at 14,000 x g for 30 minutes. Supernatant (= soluble fraction)
and pellet (= insoluble fraction) were separated and diluted with SDS sample
buffer to equal volumes. Samples were analyzed by SDS-PAGE followed by
Western blotting with anti-HBcAg monoclonal antibody YVS 1841. Lane 1:
soluble fraction, control cells; lane 2: insoluble fraction, control cells; lane 3:
soluble fraction, cells expressing HBcAg-JUN; lane 4: insoluble fraction, cells
expressing HbcAg-JUN.
The cleared cell lysate was used for step-gradient centrifugation using a
sucrose step gradient consisting of a 4 ml 65% sucrose solution overlaid with 3
ml 15% sucrose solution followed by 4 ml of bacterial lysate. The sample was
centrifuged for 3 hrs with 100,000 x g at 4°C. After centrifugation, 1 ml fractions
from the top of the gradient were collected and analyzed by SDS-PAGE followed
by Coomassie staining. (Fig. 6). Lane 1: total E. coli lysate prior to
centrifugation. Lane 1 and 2: fractions 1 and 2 from the top of the gradient.
Lane 4 to 7: fractions 5 to 8 (15% sucrose). The HBcAg-JUN protein was
detected by Coomassie staining.
The HBcAg-JUN protein was enriched at the interface between 15 and
65% sucrose indicating that it had formed a capsid particle. Most of the bacterial
proteins remained in the sucrose-free upper layer of the gradient, therefore step-
gradient centrifugation of the HBcAg-JUN particles led both to enrichment and
xo a partial purification of the particles.

Example 22
Covatent Coupling ofltGH-FOS to HBcAg-JUN
In order to demonstrate binding of a protein to HBcAg-JUN particles, we
chose human growth hormone (hGH) fused with its carboxy terminus to the FOS
helix as a model protein (hGH-FOS). HBcAg-JUN particles were mixed with
partially purified hGH-FOS and incubated for 4 hours at 4°C to allow binding of
the proteins. The mixture was then dialyzed overnight against a 3000-fold
volume of dialysis buffer (150 mM NaCl, 10 mM Tris-HCl solution, pH 8.0) in
order to remove DTT present in both the HBcAg-JUN solution and the hGH-FOS
solution and thereby allow covalent coupling of the proteins through the
establishment of disulphide bonds. As controls, the HBcAg-JUN and the hGH-
FOS solutions were also dialyzed against dialysis buffer. Samples from all three
dialyzed protein solutions were analyzed by SDS-PAGE under non-reducing
conditions. Coupling of hGH-FOS to HBcAg-JUN was detected in an anti-hGH
immunoblot (Fig. 7). hGH-FOS bound to HBcAg-JUN should migrate with an
apparent molecular mass of approximately 53 kDa, while unbound hGH-FOS
migrates with an apparent molecular mass of 31 kDa. The dialysate was analyzed
by SDS-PAGE in the absence of reducing agent (lane 3) and in the presence of
reducing agent (lane 2) and detected by Coomassie staining. As a control, hGH-
FOS that had not been mixed with capsid particles was also loaded on the gel in
the presence of reducing agent (lane 1).
A shift of hGH-FOS to a molecular mass of approximately 53 kDa was
observed in the presence of HBcAg-JUN capsid protein, suggesting that efficient
binding of hGH-FOS to HBcAg-JUN had taken place.
Example 23
Insertion of a peptide containing a Lysine residue into the
c/el epitope ofHBcAg(l-149)
The c/el epitope (residues 72 to 88) of HBcAg is located in the tip region
on the surface of the hepatitis B virus capsid (HBcAg). A part of this region

(Proline 79 and Alanine 80) was genetically replaced by the peptide Gly-Gly-Lys-
Gly-Gly (HBcAg-Lys construct). The introduced Lysine residue contains a
reactive amino group in its side chain that can be used for intermolecular
chemical crosslinking of HBcAg particles with any antigen containing a free
Cysteine group.
The HBcAg-Lys DNA sequence was generated by PCRs: The two
fragments encoding HBcAg fragments (amino acid residues 1 to 78 and 81 to
149) were amplified separately by PCR. The primers used for these PCRs also
introduced a DNA sequence encoding the Gly-Gly-Lys-Gly-Gly peptide. The
HBcAg (1 to 78) fragment was amplified from pEco63 using primers
EcoRIHBcAg(s) and Lys-HBcAg(as). The HBcAg (81 to 149) fragment was
amplified from pEco63 using primers Lys-HBcAg(s) and HBcAg(l-
149)Hind(as). Primers Lys-HBcAg(as) and Lys-HBcAg(s) introduced
complementary DNA sequences at the ends of the two PCR products allowing
fusion of the two PCR products in a subsequent assembly PCR. The assembled
fragments were amplified by PCR using primers EcoRIHBcAg(s) and HbcAg(l -
149)Hind(as).
For the PCRs, 100 pmol of each oligo and 50 ng of the template DNAs
were used in the 50 ul reaction mixtures with 2 units of Pwo polymerase, 0.1 mM
dNTPs and 2 mM MgSO4. For both reactions , temperature cycling was carried
out as follows: 94°C for 2 minutes; 30 cycles of 94°C (1 minute), 50°C (1
minute), 72°C (2 minutes).
Primer sequences:
EcoRIHBcAg(s):
(5"-CCGGAATTCATGGACATTGACCCTTATAAAG-3:) (SEQ ID NO:79);
Lys-HBcAg(as):
.;5"-CCTAGAGCCACCTTTGCCACCATCTTCTAAATTAGTACCCACCCAG

GTAGC-3') (SEQ ID NO:80);
Lys-HBcAg(s):
(5'-GAAGATGGTGGCAAAGGTGGCTCTAGGGACCTAGTAGTCAGTTAT
GTC-3')(SEQ ID NO:81);
HBcAg(l-149)Hind(as):
(5'-CGCGTCCCAAGCTTCTAAACAACAGTAGTCTCCGGAAG-3') (SEQ
ID NO:82).
For fusion of the two PCR fragments by PCR 100 pmol of primers
EcoRIHBcAg(s) and HBcAg(l-149)Hind(as) were used with 100 ng of the two
purified PCR fragments in a 50 l reaction mixture containing 2 units of Pwo
polymerase, 0.1 mM dNTPs and 2 mM MgSCX,. PCR cycling conditions were:
94°C for 2 minutes; 30 cycles of 94-°C (1 minute), 50°C (1 minute), 72°C (2
minutes). The assembled PCR product was analyzed by agarose gel
electrophoresis, purified and digested for 19 hours in an appropriate buffer with
EcoRI and HindIII restriction enzymes. The digested DNA fragment was ligated
into EcoRI/HindIII-digested pKK vector to generate pKK-HBcAg-Lys expression
vector. Insertion of the PCR product into the vector was analyzed by
EcoRI/HindIII restriction analysis and DNA sequencing of the insert.
Example 24
Expression and partial purification of HBcAg-Lys
E. coli strain XL-1 blue was transformed with pKK-HBcAg-Lys. 1 ml of
an overnight culture of bacteria was used to innoculate 100 ml of LB medium
containing 100 ug/ml ampicillin. This culture was grown for 4 hours at 37°C
until an OD at 600 nm of approximately 0.8 was reached. Induction of the
synthesis of HBcAg-Lys was performed by addition of IPTG to a final
concentration of 1 mM. After induction, bacteria were further shaken at 37 °C for

16 hours. Bacteria were harvested by centrifugation at 5000 x g for 15 minutes.
The pellet was frozen at -20°C. The pellet was thawed and resuspended in
bacteria lysis buffer (10 mM Na2HPO4, pH 7.0, 30 mM NaCl, 0.25% Tween-20,
10 mM EDTA, 10 mM DTT) supplemented with 200 g/ml lysosyme and 10 l
of Benzonase (Merck). Cells were incubated for 30 minutes at room temperature
and disrupted using a French pressure cell. Triton X-100 was added to the lysate
to a final concentration of 0.2%, and the lysate was incubated for 30 minutes on
ice and shaken occasionally. E. coli cells harboring pKK-HBcAg-Lys expression
plasmid or a control plasmid were used for induction of HBcAg-Lys expression
with IPTG. Prior to the addition of IPTG, a sample was removed from the
bacteria culture carrying the pKK-HBcAg-Lys plasmid and from a culture
carrying the control plasmid. Sixteen hours after addition of IPTG, samples were
again removed from the culture containing pKK-HBcAg-Ly s and from the control
culture. Protein expression was monitored by SDS-PAGE followed by
Coomassie staining.
The lysate was then centrifuged for 30 minutes at 12,000 x g in order to
remove insoluble cell debris. The supernatant and the pellet were analyzed by
Western blotting using a monoclonal antibody against HBcAg (YVS1841,
purchased from Accurate Chemical and Scientific Corp., Westbury, NY, USA),
indicating that a significant amount of HBcAg-Lys protein was soluble. Briefly,
lysates from E. coli cells expressing HBcAg-Lys and from control cells were
centrifuged at 14,000 x g for 30 minutes. Supernatant (= soluble fraction) and
pellet (= insoluble fraction) were separated and diluted with SDS sample buffer
to equal volumes. Samples were analyzed by SDS-PAGE followed by Western
blotting with anti-HBcAg monoclonal antibody YVS 1841.
The cleared cell lysate was used for step-gradient centrifugation using a
sucrose step gradient consisting of a 4 ml 65% sucrose solution overlaid with 3
ml 15% sucrose solution followed by 4 ml of bacterial lysate. The sample was
centrifuged for 3 hrs with 100,000 x gat 4°C. After centrifugation, 1 ml fractions
from the top of the gradient were collected and analyzed by SDS-PAGE followed

by Coomassie staining. The HBcAg-Lys protein was detected by Coomassie
staining.
The HBcAg-Lys protein was enriched at the interface between 15 and
65% sucrose indicating that it had formed a capsid particle. Most of the bacterial
proteins remained in the sucrose-free upper layer of the gradient, therefore step-
gradient centrifugation of the HBcAg-Lys particles led both to enrichment and to
a partial purification of the particles.
Example 25
Chemical coupling of FLAGpeptide to HBcAg-Lys
using the heterobifunctional crosslinker SPDP
Synthetic FLAG peptide with a Cysteine residue at its amino terminus
(amino acid sequence CGGDYKDDDDK) was coupled chemically to purified
HBcAg-Lys particles in order to elicit an immune response against the FLAG
peptide. 600 l of a 95% pure solution of HBcAg-Lys particles (2 mg/ml) were
incubated for 30 minutes at room temperature with the heterobifunctional
crosslinker N-Succinimidyl 3-(2-pyridyldithio) propionate (SPDP) (0.5 mM).
After completion of the reaction, the mixture was dialysed overnight against 1
liter of 50 mM Phosphate buffer (pH 7.2) with 150 mM NaCl to remove free
SPDP. Then 500 l of derivatized HBcAg-Lys capsid (2 mg/ml) were mixed with
0.1 mM FLAG peptide (containing an ammo-terminal cysteine) in the presence
of 10 mM EDTA to prevent metal-catalyzed sufhydryl oxidation. The reaction
was monitored through the increase of the optical density of the solution at 343
nm due to the release of pyridine-2-thione from SPDP upon reaction with the free
cysteine of the peptide. The reaction of derivatised Lys residues with the peptide
was complete after approximately 30 minutes.
The FLAG decorated particles were injected into mice.

Example 26
Construction of pMPSV-gpl40cys
The gpl40 gene was amplified by PCR from pCytTSgpl40FOS using
oligos gpl40CysEcoRI and SalIgpl40. For the PCRs, 100 pmol of each oligo
and 50 ng of the template DNAs were used in the 50 u.1 reaction mixtures with 2
units of Pwo polymerase, 0.1 mM dNTPs and 2 mM MgSO4. For both reactions
, temperature cycling was carried out as follows: 94°C for 2 minutes; 30 cycles
of 94°C (0.5 minutes), 55°C (0.5 minutes), 72°C (2 minutes).
The PCR product was purified using QiaEXII kit, digested with
Sall/EcoRI and ligated into vector pMPSVHE cleaved with the same enzymes.
Oligo sequences:
Gpl40CysEcoRI:
5'-GCCGAATTCCTAGCAGCTAGCACCGAATTTATCTAA-3' (SEQ ID
NO:83);
SalIgpl40
5'- GGTTAAGTCGACATGAGAGTGAAGGAGAAATAT-3' (SEQ ID NO:84).
Example 27
Expression ofpMPSVgpl40Cys
pMPSVgpHOCys (20 g) was linearized by restriction digestion. The
reaction was stopped by phenol/chloroform extraction, followed by an
isopropanol precipitation of the linearized DNA. The restriction digestion was
evaluated by agarose gel eletrophoresis. For the transfection. 5.4 ug of linearized
pMPSVgpl40-Cys was mixed with 0.6 ug of linearized pSV2Neo in 30 ul H2O
and 30 ul of 1 M CaCU solution was added. After addition of 60 ul phosphate
buffer (50 mM HEPES, 280 mM NaCl, 1.5 mM Na2 HPO4, pH 7.05), the solution
was vortexed for 5 seconds, followed by an incubation at room temperature for

25 seconds. The solution was immediately added to 2 ml HP-1 medium
containing 2% FCS (2% FCS medium). The medium of an 80% confluent
BHK21 cell culture (6-well plate) was then replaced by the DNA containing
medium. After an incubation for 5 hours at 37°C in a CO2 incubator, the DNA
containing medium was removed and replaced by 2 ml of 15% glycerol in 2%
FCS medium. The glycerol containing medium was removed after a 30 second
incubation phase, and the cells were washed by rinsing with 5 ml of HP-1
medium containing 10% FCS. Finally 2 ml of fresh HP-1 medium containing
10% FCS was added.
Stably transfected cells were selected and grown in selection medium
(HP-1 medium supplemented with G418) at 37°C in a CO2 incubator. When the
mixed population was grown to confluency, the culture was split to two dishes,
followed by a 12 h growth period at 37°C. One dish of the cells was shifted to
30° C to induce the expression of soluble GP140-FO5. The other dish was kept
at 37°C.
The expression of soluble GP140-Cys was determined by Western blot
analysis. Culture media (0.5 ml) was methanol/chloroform precipitated, and the
pellet was resuspended in SDS-PAGE sample buffer. Samples were heated for
5 minutes at 95°C before being applied to a 15% acrylamide gel. After
SDS-PAGE, proteins were transferred to Protan nitrocellulose membranes
(Schleicher & Schuell, Germany) as described by Bass and Yang, in Creighton,
T.E., ed., Protein Function: A Practical Approach, 2nd Edn., IRL Press, Oxford
(1997), pp. 29-55. The membrane was blocked with 1 % bovine albumin (Sigma)
in TBS (IOXTBS per liter: 87.7 gNaCl, 66.1gTrizma hydrochloride (Sigma) and
9.7 g Trizma base (Sigma), pH 7.4) for 1 hour at room temperature, followed by
an incubation with an anti-GP140 or GP-160 antibody for 1 hour. The blot was
washed 3 times for 10 minutes with TBS-T (TBS with 0.05% Tween20), and
incubated for 1 hour with an alkaline-phosphatase-anti-
mouse/rabbit/monkey/human IgG conjugate. After washing 2 times for 10
minutes with TBS-T and 2 times for 10 minutes with TBS, the development

reaction was carried out using alkaline phosphatase detection reagents (10ml AP
buffer (100 mM Tris/HCl, 100 mM NaCl, pH 9.5) with 50 ul NBT solution (7.7%
Nitro Blue Tetrazolium (Sigma) in 70% dimethylformamide) and 37 ul of
X-Phosphate solution (5% of 5-bromo-4-chloro-3-indolyl phosphate in
dimethylformamide).
Example 28
Purification ofgpl40Cys
An anti-gpl20 antibody was covalently coupled to a NHS/EDC activated
dextran and packed into a chromatography column. The supernatant, containing
GP140Cys is loaded onto the column and after sufficient washing, GP140Cys was
eluted using 0.1 M HC1. The eluate was directly neutralized during collection
using 1 M Tris pH 7.2 in the collection tubes.
Disulfide bond formation might occur during purification, therefore the
collected sample is treated with 10 mM DTT in 10 mM Tris pH 7.5 for 2 hours
at25°C.
DTT is remove by subsequent dialysis against 10 mM Mes; 80 mM NaCl
pH 6.0. Finally GP 1 AQCys is mixed with alphavirus particles containing the JUN
residue in E2 as described in Example 16.
Example 29
Construction of PLA2-Cys
The PLA2 gene was amplified by PCR from pAV3PLAfos using oligos
EcoRIPLA and PLA-Cys-hind. For the PCRs, 100 pmol of each oligo and 50 ng
of the template DNAs were used in the 50 ul reaction mixtures with 2 units of
Pwo polymerase, 0.1 mM dNTPs and 2 mM MgSO4. For both reactions ,
temperature cycling was carried out as follows: 94°C for 2 minutes; 30 cycles of
94°C (0.5 minutes), 55°C (0.5 minutes), 72°C (2 minutes).
The PCR product was purified using QiaEXII kit, digested with
EcoRI/HinDIII and ligated into vector pAV3 cleaved with the same enzymes.

Oligos
EcoRIPLA:
5'-TAACCGAATTCAGGAGGTAAAAAGATATGG-3' ,'SEQ ID NO:85)
PLACys-hind:
5'-GAAGTAAAGCTTTTAACCACCGCAACCACCAGAAG-3' (SEQ ID
NO:86).
Example 30
Expression and purification of PLA-cys
For cytoplasmic production of Cys tagged proteins. E. coli XL-1-Blue
strain was transformed with the vectors pAV3: :PL A and pPL A-Cys. The culture
was incubated in rich medium in the presence of ampicillin at 3 7 °C with shaking.
At an optical density (550rim) of, 1 mM IPTG was added and incubation was
continued for another 5 hours. The cells were harvested by centrifugation,
resuspended in an appropriate buffer (e.g. Tris-HCl, pH 7.2, 150 mM NaCl)
containing DNase, RNase and lysozyme, and disrupted by passage through a
french pressure cell. After centrifugation (Sorvall RC-5C, SS34 rotor,
15000 rpm, 10 min, 4°C), the pellet was resuspended in 25 ml inclusion body
wash buffer (20 mM tris-HCl, 23% sucrose, 0.5% Triton X-100, 1 mM EDTA,
pH8) at 4°C and recentrifuged as described above. This procedure was repeated
until the supernatant after centrifugation was essentially clear. Inclusion bodies
were resuspended in 20 ml solubilization buffer (5.5 M guanidinium
hydrochloride, 25 mM tris-HCl, pH 7.5) at room temperarure and insoluble
material was removed by centrifugation and subsequent passage of the
supernatant through a sterile filter (0.45 um). The protein solution was kept at
4 " C for at least 10 hours in the presence of 10 mM EDTA and 100 mM DTT and
then dialyzed three times against 10 volumes of 5.5 M guanidinium
hydrochloride, 25 mM tris-HCl, 10 mM EDTA, pH 6. The solution was dialyzed
twice against 51 2 M urea, 4 mM EDTA, 0.1 M NH4C1, 20 mM sodium borate

• pH 8.3) in the presence of an appropriate redox shuffle (oxidized
glutathione/reduced glutathione; cystine/cysteine). The refolded protein was then
applied to an ion exchange chromatography. The protein was stored in an
appropriate buffer with a pH above 7 in the presence of 2-10 mM DTT to keep
the cysteine residues in a reduced form. Prior to coupling of the protein with the
alphavirus particles, DTT was removed by passage of the protein solution through
a Sephadex G-25 gel filtration column.

We claim:
1. A composition comprising:
a) a non-naturally occurring molecular scaffold comprising:
(i) a core particle selected from the group consisting of:
(1) a core particle of non-natural origin; and
(2) a core particle of natural origin; and wherein said
core particle comprises a virus-like particle or a recombinant
form thereof;
(ii) an organizer comprising at least one first attachment
site,
wherein said organizer is connected to said core particle
by at least one covalent bond; and
b) an antigen or antigenic determinant with at least one second
attachment site, said second attachment site being selected from the group
consisting of:
(i) an attachment site not naturally occurring with said
antigen or antigenic determinant; and
(ii) an attachment site naturally occurring with said antigen
or antigenic determinant,
wherein said second attachment site is capable of association through
at least one non-peptide bond to said first attachment site; and
wherein said antigen or antigenic determinant and said scaffold interact
through said association to form an ordered and repetitive antigen array,
wherein said antigen is selected from the group consisting of (a) proteins
suited to induce an immune response against allergens and (b) proteins suited
to induce an immune response against cancer cells.
2. The composition as claimed in Claim 1, wherein:
a) said core particle is a virus-like particle or a recombinant form
thereof; and
b) said organizer is a polypeptide or residue thereof; and
c) said second attachment site is a polypeptide or residue thereof.

3. The composition as claimed in Claim 2, wherein said first and/or said
second attachment site comprises:
a) an antigen;
b) an antibody or antibody fragment;
c) biotin;
d) avidin;
e) strepavidin;
f) a receptor;
g) a receptor ligand;
h) a ligand-binding protein;
i) a ligand;
j) an interacting leucine zipper polypeptide;
k) an amino group;
1) a chemical group reactive with an amino group;
m) a carboxyl group;
n) a chemical group reactive with a carboxyl group;
o) a sulfhydryl group;
p) a chemical group reactive with a sulfhydryl group; or
q) a combination thereof.
4. The composition as claimed in Claim 3, wherein said second attachment
site does not naturally occur with said antigen or antigenic
determinant.
5. The composition as claimed in Claim 2, where in said core particle is a
recombinant alphavirus; and wherein said recombinant alphavirus is
Sindbis virus and said first attachment site and said second attachment
site each comprise an interacting leucine zipper polypeptide, wherein
said first attachment site and said second attachment site are the JUN
and/or FOS leucine zipper polypeptides.
6. The composition as claimed in Claim 2, wherein said first attachment site
is an amino group and said second attachment site is a sulfhydryl
group.

7. The composition as claimed in Claim 2, wherein said virus-like particle is
a hepatitis B virus capsid protein.
8. The composition as claimed in Claim 2, wherein said virus-like particle is
a Measles virus capsid protein.
9. The composition as claimed in Claim 2, wherein said core particle is
selected from the group consisting of:
a) recombinant proteins of Rotavirus,
b) recombinant proteins of Norwalk virus,
c) recombinant proteins of Alphavirus,
d) recombinant proteins of Foot and Mouth Disease virus,
e) recombinant proteins of Retrovirus,
f) recombinant proteins of Hepatitis B virus,
g) recombinant proteins of Tobacco mosaic virus,
h) recombinant proteins of Flock House Virus, and
i) recombinant proteins of human Papilomavirus.
10. The composition as claimed in Claim 1, wherein said core particle is of
non-natural origin.
11. The composition as claimed in Claim 1, wherein said antigen is:
a) a recombinant protein of breast cancer cells,
b) a recombinant protein of kidney cancer cells,
c) a recombinant protein of prostate cancer cells,
d) a recombinant protein of skin cancer cells,
e) a recombinant protein of brain cancer cells,
f) a recombinant protein of leukemia cells,
g) a recombinant protein of bee sting allergy,
h) a recombinant protein of nut allergy,
i) a recombinant protein of food allergies, or
j) a recombinant protein of asthma..

12. The composition as claimed in Claim 1, wherein said antigen or antigenic
determinant is selected from proteins suited to induce an immune
response against cancer cells.
13. The composition as claimed in Claim 1, wherein said antigen or antigenic
determinant is Her2.
14. The composition as claimed in Claim 1, wherein said antigen or antigenic
determinant is selected from proteins suited to induce an immune
response against allergens.
15. The composition as claimed in Claim 1, wherein said antigen or antigenic
determinant is a recombinant protein of nut allergy.
16. The composition as claimed in Claim 1, wherein said antigen or antigenic
determinant is a recombinant protein of asthma.
17. The composition as claimed in any one of Claim 1 to 16, wherein said first
attachment site is a lysine residue and said second attachment site is a
cysteine residue.
18. A process for producing a non-naturally occurring, ordered and repetitive
antigen array comprising:
a) providing a non-naturally occurring molecular scaffold
comprising:
(i) a core particle selected from the group consisting of:
(1) a core particle of non-natural origin; and
(2) a core particle of natural origin; and wherein said
core particle comprises a virus-like particle or a recombinant
form thereof; and
(ii) an organizer comprising at least one first attachment
site,
wherein said organizer is connected to said core particle by at least one
covalent bond; and

b) providing an antigen or antigenic determinant with at least one
second attachment site, wherein said antigen is selected from the group
consisting of (a) proteins suited to induce an immune response against
allergens and (b) proteins suited to induce an immune response against cancer
cells, and wherein said second attachment site being selected from the group
consisting of:
(i) an attachment site not naturally occurring with said
antigen or antigenic determinant; and
(ii) an attachment site naturally occurring with said antigen
or antigenic determinant,
wherein said second attachment site is capable of association through at least
one non-peptide bond to said first attachment site; and
c) combining said non-naturally occurring molecular scaffold and
said antigen or antigenic determinant,
wherein said antigen or antigenic determinant and said scaffold interact
through said association to form an ordered and repetitive antigen array.
19. A pharmaceutical composition comprising:
a) the composition as claimed in any one of Claim 1 to 17; and
b) an acceptable pharmaceutical carrier or an adjuvant.
20. A pharmaceutical composition as claimed in claim 19 is a vaccine
composition.
21. The vaccine composition as claimed in Claim 20, wherein said first
attachment site is an amino group and said second attachment site is a
sulfhydryl group.
22. The vaccine composition as claimed in Claim 20, wherein said core
particle comprises a Hepatitis B virus-like particle.

23. The vaccine composition as claimed in Claim 20, wherein said core
particle comprises a measles virus-like particle.

The invention provides compositions and processes for the production of ordered and repetitive antigen or antigenic determinant
arrays. The compositions of the invention are useful for the production of vaccines for the prevention of infectious diseases, the treatment
of allergies and the treatment of cancers. Various embodiments of the invention provide for a virus, virus-like particle, viral capsid particle,
phage or recombinant form thereof coated with any desired antigen in a highly ordered and repetitive fashion as the result of specific
interactions. In one specific embodiment, a versatile new technology based on a cassette-type system (Alpha Vaccine Technology) allows
production of antigen coated viral particles. Other specific embodiments allow the production of antigen coated hepatitis B virus-like
particles or antigen coated Measles virus-like particles.

Documents:

IN-PCT-2001-686-KOL-CORRESPONDENCE.pdf

IN-PCT-2001-686-KOL-FORM 27.pdf

in-pct-2001-686-kol-granted-abstract.pdf

in-pct-2001-686-kol-granted-assignment.pdf

in-pct-2001-686-kol-granted-claims.pdf

in-pct-2001-686-kol-granted-correspondence.pdf

in-pct-2001-686-kol-granted-description (complete).pdf

in-pct-2001-686-kol-granted-drawings.pdf

in-pct-2001-686-kol-granted-examination report.pdf

in-pct-2001-686-kol-granted-form 1.pdf

in-pct-2001-686-kol-granted-form 13.pdf

in-pct-2001-686-kol-granted-form 18.pdf

in-pct-2001-686-kol-granted-form 2.pdf

in-pct-2001-686-kol-granted-form 3.pdf

in-pct-2001-686-kol-granted-form 5.pdf

in-pct-2001-686-kol-granted-gpa.pdf

in-pct-2001-686-kol-granted-reply to examination report.pdf

in-pct-2001-686-kol-granted-specification.pdf


Patent Number 228095
Indian Patent Application Number IN/PCT/2001/686/KOL
PG Journal Number 05/2009
Publication Date 30-Jan-2009
Grant Date 28-Jan-2009
Date of Filing 28-Jun-2001
Name of Patentee CYTOS BIOTECHNOLOGY AG
Applicant Address WAGISTRASSE 25, CH-8802 SCHLIEREN
Inventors:
# Inventor's Name Inventor's Address
1 RENNER, WOLFGANG, A GRANZSTEIG 9, CH-8952 KILCHBERG
2 BACHMANN, MARTIN F GOLDCKERWEG 8, CH-8472 SEUZACH
3 HENNEKE, FRANK AUFWIESENSTRASSE 14, CH-8305 DIETILIKON
4 NIEBA, LARS HUBACKERWEG 12A, CH-1153 REINACH
PCT International Classification Number A61K 39/00
PCT International Application Number PCT/IB99/01925
PCT International Filing date 1999-11-30
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/110,414 1998-11-30 U.S.A.
2 60/142,788 1999-07-08 U.S.A.