High Molecular Weight Collagen-Like Protein Polymers

Collagen, a naturally occurring protein, finds wide application in industry. Chemically hydrolyzed natural collagen can be denatured and renatured by heating and cooling to produce gelatin, which is used in photographic and medical applications, among other applications. The chain property of collagen responsible for this phenomenon is its ability to spontaneously form interchain aggregates having a conformation designated as a triple helix. The helices are stabilized by weak interactions between chains, arising from the close proximity of the peptide backbone at locations every third residue occupied by glycine and kinks provided by proline and hydroxyproline at the two positions between glycine. The geometry of the three kinked chains allows for hydrogen bonding within the triple helix. The structure is loose and is readily accessible to interaction with water, small organic and inorganic molecules, other proteins, and cells. Although collagen consists of many different amino acid sequences, one of the more structurally stable segments exists at the amino and carboxyl terminal ends of the processed collagen Type I chains. These ends consist to a large degree of the repeating tripeptide sequence GPP (the second P is often hydroxylated).

With the advent of recombinant technology, the opportunity arose to produce collagen-like polymers, where the advantageous properties of collagen could be selectively retained, while new capabilities and characteristics could be introduced. By contrast with natural forms of collagen, recombinantly-produced collagen-like polymers may consist exclusively of a single repeating tripeptide sequence selected from a wide variety of GXY sequences, where X and Y can be any amino acid, whether derived from known natural sequences or not. Recombinant collagen-like polymers can also consist of different tripeptide sequences, which are repeated as blocks in the final polymer. Dissimilar blocks can also be used in a repeating fashion to create block copolymers in order to provide additional chemical or biological functionality.

The uniqueness of collagen, the repetitive tripeptide, is a challenge for recombinant technology in light of the high repetitiveness of the sequence and the frequent utility of the amino acids glycine and proline in the composition. Genes encoding proteins with high levels of glycine and proline are by necessity composed of high levels of the nucleotides guanidine and cytidine in self complementary sequences. Thus, as one synthesizes the gene, there is substantial opportunity for strands to loop out, single-stranded DNA to be excised, recombination events to occur which can result in loss of segments of the gene, and inefficient transcription and/or translation. Thus, there is substantial interest in developing techniques and compositions which provide the advantageous properties of collagen, while at the same time allow for stable expression of high molecular weight collagen-like proteins of at least about 30 kDal.

WO 88/05082 and Goldberg, et al. Gene (Amst.) 80:305-314 (1989) describe the preparation of relatively low molecular weight collagen analog proteins. See also PCT/US87/03360 and PCT›US 89/05016 which describe structural protein polymers.

High molecular weight, unnatural collagen-like polymers are provided wherein a major proportion of the amino acids of the polymers are present as triads having glycine as the first amino acid, where at least 40 number % of the triads comprise at least one proline and the total proline content of the triads, usually the entire polymer, is less than 45 number %. Also provided are genes encoding the subject polymers. The genes are prepared by synthesizing sequences having a plurality of tripeptide units, ligating the sequences together to provide multimers, cloning the multimers, and finally joining the multimers to provide for genes encoding the subject collagen-like polymers, which may be expressed, for the most part, in unicellular organisms.

Methods and compositions are provided for producing high molecular weight collagen-like polymers, where a major proportion of the amino acids of the polymers are present as triads having glycine as the first amino acid, where at least 40 number % of the triads comprise at least one proline and the total proline content of the triads, usually the entire polymer, is less than 45 number %. The subject polymers may be varied in a variety of ways, having a single repeating unit, having alternating repeating units, or having blocks of different repeating units. In addition to the repetitive sequences or units of triads, intervening functional sequences may also be present in the subject polymers, and sequences which will usually be present at the 5' and 3' termini that will contribute fewer than about 20 number %, more usually fewer then about 10 number % of the amino acids of the polymers. Also provided are genes encoding the subject collagen-like polymers and methods for their expression, isolation and purification. The subject collagen-like polymers find use in a variety of applications.

The collagen-like polymers of this invention will be characterized by having a molecular weight of at least about 30 kD (kiloDaltons), more usually at least about 40 kD and preferably at least about 50 kD, usually not exceeding about 150 kD, more usually not exceeding about 125 kD and frequently not exceeding about 100 kD. Being like collagen, the polymers will be further characterized in being capable of: providing helices; denaturation and renaturation; forming gels; etc. A major proportion of tripeptide triad or repetitive sequences of the subject polymers will preferably be triad sequences found in natural collagens, particularly mammalian collagen, where triad refers to a 3 amino acid peptide unit. Thus, usually at least 40%, more usually at least 50%, frequently at least 80% of the triads will be triads found in natural collagen, particularly mammalian collagen.

The subject polymers may be modified in a variety of ways, by introducing various functional units, where depending upon the functional units, they may be a part of the design, providing for the uniform alternating glycine at every third position or interrupting the uniformity, or may be present at the end of a block of repetitive units. While any of the 20 amino acids may be present, charged amino acids will usually be present in fewer than 30%, frequently in fewer than 15%, by number in the repetitive sequences.

The subject collagen-like polymers can be widely varied as to their repeating units or triads, the pattern of repeating units, the insertion of interrupting sequences, and the like. A major proportion of the amino acids present in the subject collagen-like polymers will be present as triads. As a major proportion of the amino acids are present as triads, generally at least 50 weight percent, usually at least 60 weight percent, more usually at least 80 weight percent, frequently at least 85 weight percent, of the amino acids will be present as triads (tripeptides with glycine as the first amino acid). The total number of triads in the subject polymers will usually be at least about 100, more usually at least about 150, and usually not more than about 500, more usually not more than about 400.

In the triads found in the subject polymers, glycine will be the first amino acid and the other two amino acids may vary, but will be selected so as to reduce the total proline content of the polymer between the glycines, i.e. the non-glycine two-thirds of the triads, to less than about 60 number %, usually to less than about 40 number %, but usually more than about 20 number %.

The compositions of this invention will now be described by formulae, where each capital letter indicates an amino acid, where the one letter description for an amino acid indicates that particular amino acid and where a letter which is not within the one letter description is used to symbolize any amino acid or a designated group of amino acids. The superscripts indicate that where there are a plurality of triads, the letter symbolic of amino acids may symbolize the same or different amino acid in each of the triads. Subscripts always intend the number of repeats of the symbol or formula to which the subscript relates.

For the most part, the polymers will be characterized by having, as a motif present at least twice in the collagen-like polymer, either contiguous or non-contiguous, a sequence having the following formula:

wherein X and O are any amino acids except that X and O are selected to have a proline content of the repetitive or triad sequences of the motif, usually the entire polymer, of less than about 45% by number, usually of less than about 40% by number, and may be less than 30% by number, but at least about 10% by number, usually at least about 15% by number.

.OMEGA. has from 0 to 50 amino acids, more usually from 0 to 30 amino acids, frequently from 0 to 15, and will usually be a sequence having functional capability and will be other than a repetitive glyXO motif;

n will be at least 4 and not more than about 100, more usually not more than about 75, frequently not more than about 50; and

m will be at least 1, may be 2, usually at least about 3 and not more than about 20, usually not more than about 12, where particularly m is smaller as n becomes larger.

Usually, the total number of different triads in the motif will be at least 2, more usually at least 3, and not more than about 24, more usually not more than about 16 and frequently not more than about 12. The total number of different amino acids in the motif will usually be not more than about 15, more usually not more than about 10.

The number of triads including proline will usually be at least 40 number percent, more usually at least 60 number percent, although all of the triads may include one proline.

One type of collagen-like polymer will for the most part have the following motif, as a repetitive motif

wherein X and 0 are as defined previously; x and o are the same number and will be in the range of 2 to 10, usually 3 to 8 and often 4 to 6, particularly 2, 3, 5 or 10, which intends that there will be up to and including that many different triads present in the sequence; .OMEGA. has been defined previously; .OMEGA. is 1 to m.sup.1 usually not greater than 3, frequently 1 to 2, preferably 1 where .OMEGA. intends different .OMEGA. groups, similar to the 1 5 definition of x, and m.sup.1 is at least 1, may be 2, usually at least about 3, and not more than about 20, usually not more than about 12, particularly as n.sup.1 becomes larger; and n.sup.1 is at least about 2 and not more than about 100, usually not more than about 75, more usually not more than about 50, generally not more than about 30.

For example, where x is 3, .OMEGA. is 0 amino acids, and ml is 1, one would have the formula:

where X.sup.1 is a particular amino acid, X.sup.2 could be the same or different amino acid, etc., and similarly for O; and

n.sup.1 will generally be at least about 2, more usually about 4, and not greater than about 33, usually not greater than about 25.

One technique for synthesis of the subject compounds lends itself to a particular motif of the formula:

wherein:

.alpha. has from 1 to 9 triads, usually 2 to 6 triads, preferably 2 to 4 triads, more preferably 3 triads, usually at least 1 triad having a proline, more usually at least 2 triads having a proline;

.beta. has from 1 to 24 triads, usually 2 to 18 triads, more usually 3 to 9 triads;

e will be at least 3, usually at least 6, and not more than about 50, usually not more than about 36;

g is at least 1 and not more than about 20, usually not more than about 10, more usually not more than about 8;

a and a.sup.1 may be the same or different; a will be at least 1 and not more than 6, usually not more than about 3, except that a or a.sup.1 may be 0.

It will be understood that the greater the number of triads present, the lower the number of repeats required to provide the desired molecular weight.

In a preferred embodiment, these extended motifs will have, for the most part, the following formula:

wherein:

X.sup.x, O.sup.o,.OMEGA..sup..OMEGA., m.sup.1 and n.sup.1 have all been defined previously:

U and II are any amino acids, frequently there being a proline present in at least one of the triads (see also the definitions for X and 0, which are included herein);

u and n have analogous meaning to x and o, indicating the same or different amino acids in the different triad (tripeptide) units; and

p and p.sup.1 will be 1 to 6, more usually 2 to 4, and the two p's may be the same or different, usually the same except that p may also be 0;

The amino acids of particular interest other than glycine will include alanine (A), isoleucine (I), leucine (L), valine (V), serine (S), threonine (T), asparagine (N), glutamine (Q), lysine (K), arginine (R), aspartic acid (D), glutamic acid (E), histidine (H), and proline (P), preferably there being at least one of a neutral polar amino acid, e.g., S or T, or a neutral aliphatic amino acid, e.g., A, I, L, or V. Usually, the aromatic hydrophobic amino acids will be avoided, e.g., F, Y and W, and the aliphatic hydrophobic amino acids (L, V, I), will usually be used only when a proline is present. For structural considerations, triad sequences containing proline, alanine, valine, serine, threonine, glutamine, or asparagine in the X or O positions form more stable triple helices. Increased stability is also conferred by triads containing hydroxyproline in the o position. For higher order assembly of triple helices, triads containing glutamic acid or aspartic acid at either the X or O positions, but especially at the X position, and triads containing lysine or arginine, at either the X or O position, but especially at the O position, are preferred.

Of particular interest is where at least one triad has proline at a second position, more preferably that two triads have proline at second positions or at least one triad has proline at a third position, sometimes having two triads having proline at a third position, there frequently being at least two triads having a proline at either the first or second position. For the most part, at least 30%, more usually at least 50% of the triads in the motifs will have proline at a second or third position and there may be some triads with proline at both positions, usually not more than 35 number percent.

The choice of triads utilized in a recombinant collagen like polymer are chosen in order to affect properties such as helix stability, hydration, solubility, gel point, adhesion, ability to cross-link, binding to metal ions, e.g. silver halides, biodegradation, and immunogenicity. For example, in order to minimize immunogenicity, triads are utilized consisting of amino acids with simple side chains such as glycine, alanine, serine, valine, and proline. When more complex amino acids are required, they can be incorporated by utilizing hexapeptide, nonapeptide, or longer triad sequences from natural collagen chains that contain these amino acids.

To a great extent, many of the polymers of the subject invention may be depicted by the following formula:

wherein all of the symbols have been described previously, except for:

J.sup.1 and J.sup.2 which are the same or different and are amino acid sequences of from about 1 to 40 amino acids, more usually from about 1 to 30 amino acids, and may be any sequence of convenience;

the two r subscripts are the same or different and are 0 or 1;

the two p.sup.2 subscripts are the same or different, and are 0 or p.sup.1.

A variety of repetitive sequences indicated by one letter amino acid designation defining the motifs may be illustrated by the following sequences: GAPGPAGPK (SEQ ID NO:01); GAPGPAGPPGAH (SEQ ID NO:02); GSPGAPGPA (SEQ ID NO:03); GAPGPAGSRGDPGPA (SEQ ID NO:04); GANGAPGPAGPAGAPGPP (SEQ ID NO:05); GAQGPAGPGGAPGPAGPG (SEQ ID NO:06); GAPGPAGAS (SEQ ID NO:07); GPAGAPGSRGDPGAPGPP (SEQ ID NO:08); GVSGPRGPAGAPGPP (SEQ ID NO:09); GAQGPAGPG (SEQ ID NO:10); GAPGPAGPP (SEQ ID NO: 133); GAPGPAGPPGSRGDPGPP (SEQ ID NO: 134) and GAQGPAGPGGSRGDPGPP (SEQ ID NO: 135).

Although any triad may be incorporated into the subject collagen like polymers, the triads will generally be those triads found in naturally occurring collagens, particularly mammalian collagens, more particularly human collagens. A large number of human collagens have been sequenced, which sequences are known in the art, see e.g., Seyer and Kang, "Covalent Structure of Collagen: Amino Acid Sequence of .alpha.1(III)-CB9 from Type III Collagen of Human Liver," Biochemistry (1981) 20: 2621-2627; Bernard et al., "Nucleotide Sequences of Complementary Deoxyribonucleic Acids for the Pro Alpha 1 Chain of Human Type I Procollagen," Biochemistry (1983) 22:5213-5223; Muragaki et al., Eur. J. Biochem (1990) 192:703-708; Kimura et al., Eur. J. Biochem. (1989) 179:71-78; Christiano et al., J. Biol. Chem. (1994) 269:20256-20262; Christiano et al., Hum. Mol. Genet. (1992) 1:475-475; Parente et al., Proc. Natl. Acad. Sci. USA (1991) 88: 6931-6935; Gammon et al., J. Invest. Dermatol. (1992) 99:691-696; Tanaka et al., Biochem. Biphys. Res. Commun. (1992) 183:958-963; G reenspan, D.S., Hum. Mol. Genet. (1993) 2:273-278; Christiano et al., Nat. Genet. (1993) 4:62-66; Soininen et al., J. Biol. Chem. (1989) 264:13565-13571; Soininen et al., FEBS Lett. (1987) 225:188-194; Brazel et al., Eur. J. Biochem. (1987) 168:529-536; Glanville et al., Eur. J. Biochem. (1985) 152:213-219; Babel et al., Eur. J. Biochem. (1984) 143:545-556; Pihlajaniemi et al., J. Biol. Chem. (1985) 260:7681-7687; Brinker et al., Proc. Nati. Acad. Sci. USA (1985) 82:3649-3653; Soinenen et al., J. Biol. Chem. (1988) 263:17217-17220; Hostikka et al., J. Biol. Chem. (1988) 263:19488-19493; Takahara et al., J. Biol. Chem. (1991) 266: 13124-13129; and Woodberry et al., J. Biol. Chem. (1989) 264:2735-2738. Triads of particular interest include GAP, GPA, GPP, GAS, GPG, GPS, GAQ, GSP, GSQ, GLQ, GPR, GPK, GAK, GAR, GER, GDR, GEP, GDA, GAH and GEA, where combinations of these triads with other triads are of particular interest, there being at least about 30 number percent, usually at least about 50 number percent of the triads, more usually at least about 60 number percent, frequently at least 80 number percent, coming within the indicated triads. In addition, while the number of triads in any one repetitive sequence or unit may vary widely, desirably the number will be 3, 5 or a multiple thereof

Sequences defining the glyUII sequences indicated by one letter amino acid designation include:

GAHGPAGPK (SEQ ID NO: 11); GAHGPAGPR (SEQ ID NO: 12); GAVGAPGPK (SEQ ID NO:13); GPAGAPGEP(SEQ ID NO: 14); and GVSGPRGAP (SEQ ID NO:15)

In addition to the repeating sequences or units of triads, the subject polymers may further comprise intervening sequences or groups, where the intervening groups will be from about 1 to 50, usually from about 1 to 30, more usually from about 3 to 30 amino acids. Intervening sequences or groups of interest will be other than a repetitive unit, normally having a chemically reactive functionality, e.g. C, S, T, D, E, K or R, a physiologically active functionality, a chelating functionality, a crystal nucleating functionality, a grouping which modifies the conformational structure of the protein, or the like.

For the intervening oligomers or turns between strands of a polymer, (where by "strands" is intended an ordered sequence capable of alignment with a second strand or sequence having substantially the same or a complementary sequence, e.g. hydrophobic aligns with hydrophobic and hydrophilic aligns with hydrophilic) various sequences may be used, depending upon the desired purpose of the polymer. Thus, the intervening sequence may be unaligned, flexible, accessible, functional or combinations thereof Thus, the intervening sequence in association with the strand sequence can be designed to provide a wide variety of products which may be formed, fabricated, extruded, spun, woven, coated, or the like. The intervening sequence may provide for a ligand, which may serve to bind to antibodies, naturally occurring receptors, non-amino-acid molecules, or the like. In this way, the polymeric structures may be used to specifically bind a wide variety of molecules serving as affinity columns, photographic film, use in diagnosis, sensors, cell separation, device coatings having, for example, antithrombogenic properties, cell substrates, and the like.

The intervening sequence may provide chemically active amino acids for chemical crosslink sites, which may serve to covalently attach functional peptides, synthetic or natural polymers or proteins, non-amino acid molecules, and the like. The intervening sequence may be a naturally occurring sequence or a modified naturally occurring sequence. Specific intervening sequences of interest are listed in application Serial No. 07/609,716, now U.S. Pat. No. 5,514,581, the disclosure of which is herein incorporated by reference.

The genes may be synthesized with the method described in PCT/US87/02822 and PCT/US89/05616, the disclosures of which are herein incorporated by reference. Particularly, the genes are synthesized in accordance with the following protocol. Relatively short oligonucleotide strands are synthesized generally coding for at least 12 amino acids, and usually not more than about 60 amino acids. The complementary strands are annealed, cloned, and sequenced to establish that the correct sequences have been obtained. The ends may be blunt or staggered, usually staggered. A second approach depends on the synthesis of a single strand of the monomer. Synthetic techniques allow reasonably accurate oligonucleotide synthesis of 300 bases or more. For the most part the single strand will be in the range of about 100 to 300 bases, usually in the range of about 100 to 250 bases. The single strand is then used to produce a complementary strand, conveniently using the polymerase chain reaction ("PCR") and the resulting dsDNA cloned, purified and sequenced to ensure that it has the correct sequence. Appropriate primers may be employed, which may serve to extend the termini for multimerization by introducing a new restriction site consensus sequence, introduce intervening sequences, or the like. The monomer prepared this way will have the same limitations as to size and the number of amino acid repeating units which are encoded as the monomer prepared by the sequential or simultaneous cloning of dsDNA segments. The sequences are then multimerized and ligated and inserted into a cloning vector. After transforming into an appropriate host, the clones are analyzed for the oligomerization of the units and appropriate sized units are selected and used for expression. When flanking repetitive units of different sequences are desired, the sequence encoding the motif may be inserted at an appropriate restriction site between the flanking repetitive units, so that subsequently the gene may be excised with the appropriate flanking units. The resulting sequence encoding the motif with the flanking units may then be excised, oligomerized, and, as before, cloned and identified as to having the desired sequence and size.

The subject proteins are produced by transforming an appropriate unicellular host, such as E coli, B subtilis, yeast, S. pombe, S. cerevisiae, etc., fungi, Neurospora, Aspergillus, etc. A wide variety of expression vectors have been described in the literature and need not be exemplified here. The expression vector may provide for an inducible or constitutive promoter, whereby the subject proteins may be constitutively expressed or expressed only after induction. Numerous expression vectors have appropriate promoters, termination sequences, and polylinkers between the initiation and termination sequences, so that one may conveniently insert the desired gene into the polylinker to be under the transcriptional control of the promoter. In addition, the vectors may have one or more markers, which allow for selection in the transformed host. The vector may also allow for extrachromosomal maintenance or integration into the genome. The markers may provide for resistance to a toxin, e.g. an antibiotic, or complementation of an auxotrophic host to prototrophy. The choice of expression vector will depend upon on a number of factors, such as the host, economy, ease of manipulation, and the like.

Once the expression vector has been cloned, it will normally be analyzed to ensure that the gene is present and has not undergone any modification. The expression host can then be grown up in an expression media and after sufficient time, the cells lysed and the protein isolated. In some cases, the protein will be relatively insoluble and, therefore, may be separated from cellular debris by various convenient means, e.g. centrifugation. Depending on the degree of purity, the protein may be used as is, or may be further purified by extraction using a variety of solvents to extract out the impurities, while leaving the desired product in insoluble form. If desired, dilute acid solution may be used for solubilizing the protein and then precipitating the protein by dialysis. The conditions employed will vary with the particular protein produced, its solubility, the nature of the host, the nature of the contaminants, the ultimate use, and the like.

Small peptides may be prepared which include small segments of the collagen-like polymers, e.g., 15 to 36 amino acids. These segments may be used as haptens, by conjugating the segment to an appropriate immunogen, and the resulting immunogen used for production of antisera or monoclonal antibodies specific for the sequence. Thus, antibodies may be produced which specifically bind to the collagen-like polymers of the subject invention. Depending on the solubility of the subject polymers, the antibodies may be used for affinity purification, identification of the polymers on Western blots, or non-covalently crosslinking of the polymers to produce novel structures and the like.

The subject compositions may find use for a variety of applications, including medicine, research, industry, and the like. The subject collagen-like polymers are useful in the formulation of materials, such as fibers, membranes, films, hydrogels, colloid suspensions and molded articles, where the materials find use as coatings, structural materials, and the like, imparting unique characteristics to these materials and to a variety of surfaces from either naturally occurring or synthetic sources, the characteristics usually being associated with water absorption, biocompatibility, or interaction with non-protein compounds of either organic or inorganic nature, e.g. silver halide, dyes, etc. Coatings of 1 to 100 mm may find use, with adherency to a variety of surfaces from naturally occurring and synthetic sources. Distinctive properties of these polymers are their thermal reversible gelation at specific temperatures, their inherent biocompatibility and their bioresorption. Therefore, the subject polymers may find application in photographic films, as wound dressings allowing for neovascularization (see Peters, "Biological Dressings in Burns--A Review", Ann. Plas. Surg. (1980) 4:133-137), eye medications, bone cements, matrices and coatings for artificial organs (See Hilbert et al., "Tissue-Derived Biomaterials and their Use in Cardiovascular Prosthetic Devices," Med. Prog. Techol. (1988) 14: 115-163, Lane & Sandhu, "Current Approaches to Experimental Bone Grafting," Orthrop. Clin. North Am. (1987) 18:213-225, Alsbjorn, "In Search of the Ideal Skin Substitute," Scand. J. Plast. Reconstr. Surg. (1984) 18:127-133), plastice surgergy (See Flaguel & Halimi, "Injectable Collagen: An Evaluation After 10 Years Use as a Complement in Plastic Surgery", Ann. Chir. Plast. Esthet (1994) 39:765-771; Elson, "Soft Tissue Augmentation," Dermatol. Surg. (1995) 21:491-500), membranes, matrices and coatings for growing and/or studying cultures (See Visconti et al., Use of Reconstituted Basal Membranes for the Study of Invasion of Human Tumor Cells: Current Status and Future Prospects, "Boll. Soc. Ital. Biol. Sper." (1990) 66:365-372; Boswell & Swan, "Mononuclear Phagocytes and Collagen Matrices--A Review," Scan. Electron. Microsc. (1984) 4:2045-2058), implantable or injectable drug delivery systems (See Sadler & Horsey, "The New Gelatins . . . ," Anaesthesia (1987) 42:998-1004), and the like.

Furthermore, since natural collagen is cross-linked it cannot be redissolved for spinning, shaping, etc. without digestion and molecular weight reduction. Thus, the collagen-like polymers retain the desired collagen characteristics and are capable of being processed.

The following examples are offered by way of illustration and not by way of limitation.

1. Preparation of plasmid DNA from E. coli.

A. Small scale. Plasmid DNA was prepared from 1.5 ml cultures by either the boiling procedure or the alkaline lysis method (Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, (1982).

B. Large scale. A plasmid-carrying strain was grown overnight in 1 liter of Luria broth with the appropriate antibiotic. The cells were collected by centrifugation at 10,000.times.g for 5 minutes and resuspended in 10 ml of ice cold TE (10 mM Tris-HCl pH 8, 1 mM EDTA). The cells were centrifuged again, resuspended in 4 ml of TES (TE and 25 % w/v sucrose) and homogenized by vortexing. The samples were kept on ice for the following steps. Lysozyme (1 ml of 10 mg/ml) was added to the cell suspension and incubated for 5 minutes before the addition of 2 ml of 0.5 M EDTA pH 8. After 10 minutes incubation, 50 ml of proteinase K (40 mg/ml) were added followed 10 minutes later with 15 ml of lysing buffer (0.1% Triton X-100, 1 mM EDTA, 50 mM Tris-HCl pH 8). After 15-20 minutes, the cell lysate was centrifuged at 35,000xg for 90-120 minutes. The supernatant (19.8 ml) was transferred to a plastic tube with 20 mg of CsCl and 400 .mu.l of ethidium bromide (10 mg/ml). After dissolution, the mixture was divided into two polyallomer ultracentrifuge tubes, sealed with heat and centrifuged in a Beckman Ti 65 rotor at 60,000 rpm for 24 hours. The lower plasmid DNA band was removed from the tube with a hypodermic needle. The ethidium bromide was extracted three times with an equal volume of NaCl-saturated isopropanol. Two volumes of H.sub.2 O were added to the DNA solution, and then the DNA was precipitated with ethanol.

2. Deproteinization.

Phenol extraction was performed on a convenient volume of DNA sample, typically between 100 .mu.g.sup.1 to 10 ml. The DNA sample was diluted in 0.01 M Tris-HC1 pH 7.5, 1 mM EDTA and an equal volume of water-saturated phenol was added. The sample was vortexed briefly and placed on ice for 3 minutes. After centrifugation for 3 minutes in a microfuge, the aqueous layer was removed to a new tube and extracted once with an equal volume of chloroform:isoamylalcohol (24:1).

3. Ethanol precipitation.

DNA in an aqueous buffer was concentrated by ethanol precipitation. To the DNA sample was added 1/10 volume of 3 M sodium acetate pH 7.5 and 2-3 volumes of cold ethanol. The DNA was precipitated for 30 minutes at -70.degree. C. or overnight at -20.degree. C. and then pelleted by centrifugation in the microfuge for 15 minutes at 4.degree. C. The pellet was washed once with 200 .mu.l of cold 80 % ethanol and precipitated again for 10 minutes at 4.degree. C. After air drying or lyophilization, the pellets were resuspended in the appropriate buffer.

4. Phosphatase treatment of DNA.

A. Phosphatase treatment of DNA was performed by adding 1 .mu.l (25 units) of calf intestinal phosphatase (Boehringer Mannheim) directly to the restriction enzyme digestion reaction and continuing the incubation for 30 minutes at 37.degree. C. The phosphatase was inactivated for 60 minutes at 65.degree. C. prior to deproteinization by phenol extraction.

B. Phosphatase treatment of DNA was also performed by resuspending ethanol precipitated DNA from the restriction enzyme digest in 20 mM Tris-HCI pH 8.0, 10 mM MgCl.sub.2 to a final DNA concentration of 20 .mu.g/ml. Shrimp Alkaline Phosphatase (SAP) was added at 2 U/.mu.g of DNA and the mixture was incubated at 37.degree. C. for one hour, heat inactivated for 20 minutes at 65.degree. C. and then passed through a Probind filter (Millipore) and subsequently a Bio-Spin column. The DNA was then ethanol precipitated and resuspended in suitable buffer.

5. Phosphorylation of DNA.

Phosphorylation before annealing was performed by using Polynucleotide Kinase 3'-phosphatase-free (Boehringer Mannheim). The reaction was carried out at 37.degree. C. for 30 minutes in a 50 .mu.l reaction volume containing: 12.5 .mu.g DNA, 5 .mu.l 10x kinase buffer (0.5M Tris pH 7.5, 10 mM Spermidine, 0.1 M MgCl.sub.2, 150 mM DTr, 1 mM EDTA), and 2 .mu.l Polynucleotide Kinase (10 U/.mu.l). After phosphorylation, salts and glycerol were removed from the DNA strands using a Bio-Spin 6 column (BioRad) equilibrated in TEAB.

6. Fill-in reaction with DNA polymerase I.

DNA was resuspended in buffer containing 50 mM Tris-HCI pH 7.4, 50 mM KCl, 5 mM MgCl.sub.2, and 400 .mu.M each of the four deoxynucleotide triphosphates. Ten units of Klenow DNA polymerase (BRL) were added, and the reaction was allowed to proceed for 15 minutes at room temperature. The DNA was then phenol extracted and ethanol precipitated.

7. Digestion with restriction endonucleases.

DNA was digested with restriction endonucleases (REN) in 1.times."AA" buffer ›10.times.AA buffer is 330 mM Tris-acetate, pH 7.9, 660 mM potassium acetate, 100 mM magnesium acetate, 50 mM dithiothreitol (DTT) and 1 mg/ml bovine serum albumin (nuclease free)!. Whenever possible, the concentration of DNA was kept below 1 .mu.g/25 .mu.l. Incubation was at 37.degree. C. for 1-4 hours for most restriction endonucleases except for Ball, Banl and Nael digestions which were incubated overnight.

8. Analytical agarose gel electrophoresis of DNA.

To DNA samples for gel analysis was added 0.2 volumes of loading buffer (5.times.electrophoresis buffer, 0.01% bromphenol blue dye, 50 mM EDTA, and 50% glycerol). Then the samples were loaded into lanes of a horizontal submerged electrophoresis unit containing a 1.0% (w/v) agarose gel. The electrophoresis buffer was either 1.times.TAC or 1/2.times.TBE. The 1.times.TAC is 40 mM Tris-base, 10 mM EDTA, adjusted to pH 7.8 with acetic acid. The 1/2.times.TBE is 0.045 M Tris-base, 0.045 M boric acid, 1 mM EDTA, pH 8. The gel was run at 40-50 V for 18 hours, then removed and stained with 0.5 ag/ml ethidium bromide for 30 minutes. The DNA bands were visualized on a long wavelength UV transilluminator.

9. Preparative agarose gel electrophoresis.

The procedures and materials are the same as for the analytical agarose gel electrophoresis. The only difference is the use of low melting point (LMP) agarose, ranging in concentration from 0.5 to 2.5 % (w/v) depending on the size of the DNA fragment to be purified. DNA restriction fragments were excised from the LMP agarose gels after visualization with ethidium bromide. For agarose ligation the buffer used was 1.times.TAE (50 mM Tris Acetate pH 7.8).

10. NACS purification.

Gel fragments containing DNA were melted at 70.degree. C. for 5 minutes and diluted approximately 5 fold with TE1 (10 mM Tris-HCl pH 7.5, 0.2 M NaCl). The gel solution was applied to a NACS column (BRL). The column was washed with 5 ml of the same buffer. The bound DNA was eluted with 300 ,ul of either TE2 (10 mM Tris-HCl pH 7.5, 1.0 M NaCi) for DNA fragments smaller than 1000 bp or TE3 (10 mM Tris-HCl pH 7.5, 2 M NaCl) for larger fragments. The eluted DNA was concentrated by ethanol precipitation.

11. DNA ligation.

Reactions for ligating cohesive ends contained: 1 .mu.g DNA, 1.times.AA buffer (see step 7, above) 1 mM ATP and 20 units of T4 DNA ligase (BRL) in a 20 .mu.l final reaction volume. The ligation was allowed to proceed for 16-18 hours at 15.degree. C. or 1-2 hours at room temperature. For blunt-ended ligations the reactions contained 1 .mu.g DNA, 25 mM Tris-HCl pH 7.5, 5 mM MgCl.sub.2, 5 mM DTT, 0.25 mM spermidine, 200 mg BSA, 1 mM hexamine cobalt chloride (HCC), 0.5 mM ATP and 400 units T4 DNA ligase (NEB) in a 20 .mu.l reaction volume. The ligation was allowed to proceed for 30 minutes to 1 hour at room temperature.

12. Agarose DNA ligation.

The agarose was melted at 65.degree. C., the temperature was then lowered to 37.degree. C. and ligation buffer (5X=100 mM Tris-HCl, pH 7.5, 50 mM MgCl.sub.2, 50 mM DTT, 1 mM ATP) was added; the tube was then placed at room temperature and ligase was added (1000 units T4 DNA ligase (NEB)), the reaction volume was usually 50 .mu.l. The reaction was incubated at 15.degree. C. for 16-18 hours.

13. Use of Filters and Columns for DNA Purification.

A. Ultrafree.RTM.-Probind filter unit ("Probind", Millipore): the DNA containing solution was applied to the filter unit and spun at 12,000 RPM for 30 seconds in a Sorvall Microspin 24S.

B. Microcon-30 filter (Amicon): the DNA containing solution was washed by applying to the filter and exchanging twice with H.sub.2 O by spinning at 12,000 RPM for 6 min in a microfuge.

C. Bio-Spin 6 column ("Bio-Spin", BioRad): Salts and glycerol were removed from the DNA solution by applying to the column, previously equilibrated in TEAB (triethyl ammonium bicarbonate pH 7.0), and spinning in a Sorvall RC5B centrifuge using an HB4 rotor at 2,500 RPM for 4 min.

14. Agarose DNA Purification Using Ultrafree.RTM.O-MC Filter Unit.

This procedure can be used for agarose slices up to 400 .mu.l in size. After agarose gel electrophoresis the DNA is visualized by ethidium bromide staining and the agarose block containing the DNA band of interest is excised. The agarose is then frozen at -20.degree. C. for 1 hour; then quickly thawed at 37.degree. C. for 5 minutes. The agarose is then thoroughly macerated. The pieces are then transferred into the sample cup of the filter unit and spun at 5,000.times.g in a standard microfuge for 20 minutes. The agarose is then resuspended in 200 .mu.l of Tris-EDTA, or other buffer, and incubated at room temperature for 30 min to allow for elution of additional DNA from the gel. The mixture is then centrifuged for an additional 20 min at 10,000 RPM. The DNA is, at this point, in the filtrate tube separated from the agarose fragments and ready for subsequent DNA manipulations.

1. Preparation of mRNA.

Summers, W. C. (Anal. Biochem. 33:459-463 (1970). Cells were grown at 30.degree. C. or 42.degree. C. in LB medium supplemented with kanamycin (50 .mu.g/ml). 10 ml of cells at OD.sub.600 1.0 were spun and the cell pellet was resuspended in 10 ml of protoplasting buffer (15 mM Tris-HCl pH 8.0, 0.45 M sucrose, 8 mM EDTA); 80 .mu.l of lysozyme at 50 mglml were added and the mixture was then incubated on ice for 15 minutes. The cell suspension was spun for 5 minutes at 7,000 RPM in an SS-34 rotor using an RC-SB centrifuge. The pellet was resuspended in 0.5 ml of lysing buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM Na-Citrate, 1.5% w/v SDS) and 15 .mu.l of DEPC. The suspension was mixed gently and then transferred to a 1.5 ml Eppendorf tube, incubated at 37.degree. C. for 5 minutes and then chilled on ice. 250 .mu.l of saturated NaCl (40% w/v) were added, mixed gently, and the incubation, on ice, was prolonged for an additional 10 minutes. The slurry was spun at 4.degree. C. for 15 minutes. The supernatant was placed in two 1.5 ml tubes and 1 ml of 100% ethanol was added to each. The RNA was precipitated in the cold and then spun at 4.degree. C. for 20 minutes. The pellets were rinsed in 70% ethanol and dried. The RNA was then resuspended in 0.1 ml H.sub.2 O and OD.sub.260 and OD.sub.280 were taken to measure the recovery and purity of the RNA. The average recovery of total RNA (5 % mRNA, 95% tRNA+rRNA), from 10 ml of growing cells, was between 0.5 and 1.0 mg.

2. Northern blot analysis.

The RNA, purified as described above, was run on agarose gel and transferred to nitrocellulose following the procedure described in Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor (1982), pp 202-203, using lOX SSC as transfer buffer. The ECL gene detection system kit (Amersham) was used for labelling of the probe, hybridization conditions and detection. The procedures were executed as described in: ECL gene detection system RPN2101, version 2, Amersham International plc.

1. Preparation of transformation-competent E. coli cells.

A culture of 200 ml of sterile L broth was inoculated with a small loopful of E. coli cells. This was incubated with shaking at 37.degree. C. until the OD.sub.600 was approximately 0.5. The culture was placed on ice for 10 minutes and centrifuged at 6,000.times.g for 10 minutes. The cell pellet was resuspended in 100 ml of ice-cold 0.1 M MgCl.sub.2, kept on ice for 30-40 minutes and centrifuged again. The pellet was resuspended in 2 ml of ice-cold 100 mM CaCl.sub.2, transferred to a sterile test tube and incubated on ice for 24 hours. The competent cells were then aliquoted and stored at -70.degree. C.

2. Transformation of E. coli.

An aliquot of frozen competent cells was thawed on ice. To 50 .mu.l of cells, 0.1 to 1 .mu.g of DNA was added and the mixture was incubated on ice for 30 minutes. The tube was removed from ice and placed in a 42.degree. C. bath for 2 minutes. L broth (1 ml) was added and the transformation mix incubated with shaking at the desired temperature (usually 30.degree. C. or 37.degree. C.) for 2 hours. Then one-tenth of the transformation was plated on L broth plates containing the appropriate antibiotic and, when necessary, XGAL and IPTG were added.

1. Preparation of antibody to artificially synthesized Peptides.

A synthetic peptide of sequence GAHGPAGPKGAHGPAGPKGAPGPAGPPGAPGPA-GPP (SEQ ID NO:16) (SequenceD-C.sub.2 A.sub.2) where C.sub.2 A.sub.2 defines an amino acid sequence motif indicated by one letter amino acid designation was coupled to keyhole limpet hemocyanin for use as an immunogen. The material was sent to Antibodies, Inc. for preparation of antibodies in rabbits. Peptide conjugates at a concentration of 1 mg/ml in complete Freund's adjuvant were used to immunize rabbits at day 0. Animals were re-injected with antigen in Freund's incomplete adjuvant at day 30 and titered at day 60. Positive sera was detected using a microfiter RIA using the synthetic peptide as antigen. Kagen and Glick (1979), in Methods of Radioimmunoassay, Jaffe and Berman (eds.), Academic Press, p 328. Antisera was obtained that reacted with synthetic peptides of the SequenceDl and SequenceD2 sequences.

Following the procedure described above an additional peptide was synthesized having the sequence (GAPGPAGPPGSRGDPGPP).sub.2 (SEQ ID NO: 17)(SequenceD-(AB).sub.2), which was also coupled to keyhole limpet hemocyanin for use as an immunogen. Polyclonal antisera were then prepared as described above, which bound to the synthetic peptide of the SequenceD3 sequence.

Following the procedure described above an additional peptide was synthesized having the sequence (GAPGAPGSQGAPGLQ).sub.2 YMK (SEQ ID NO: 18) which was also coupled to keyhole limpet hemocyanin for use as an immunogen. Polyclonal antisera were then prepared as described above, which bound to the synthetic peptide of the CLP 3. 1, CLP 3.7 and PPAS sequences described below.

2. Polyacrylamide gel electrophoresis of proteins.

Approximately 10.sup.9 E. coli cells from growing cultures were pelleted by centrifugation at 10,000.times.g for 5 minutes. The cell pellets were resuspended in 100 to 500 .mu.l of 2X sample buffer (100 mM Tris-HCl pH 6.8, 4% SDS, 10% .beta.-mercaptoethanol, 60% glycerol or sucrose) and sonicated for 30 seconds using a Tekmar sonic disrupter. Samples were boiled for approximately 5 minutes and 20 to 100 .mu.l of the cell lysates were loaded on an SDS-polyacrylamide gel (7.5 to 16% w/v). The gels were prepared following the procedure of Laemmli, U.K.(1970), Nature (London), 2:680-685. The proteins in the gels were stained with 2% Coomassie brilliant blue in 10% methanol, 7.5% acetic acid for 1 hour and destained in 10% methanol, 7.5% acetic acid overnight.

3. Protein expression analysis.

An overnight culture which had been grown at 30.degree. C. was used to inoculate 50 ml of LB media contained in a 250 ml flask. Kanamycin was added at a final concentration of 50 .mu.g per ml and the culture was incubated with agitation (200 rpm) at 300C. When the culture reached an OD.sub.600 of 0.8, 40 ml were transferred to a new flask prewarmed at 42.degree. C. and incubated at the same temperature for approximately 2 hours. The cultures (30.degree. C. and 42.degree. C.) were chilled on ice and OD.sub.600 was taken. Cells were collected by centrifugation and then divided in OD.sub.600 aliquots and used to perform western analysis using the appropriate antibodies.

4. Immunoblotting of proteins in gels.

After protein electrophoresis, one of the flanking glass plates was removed from the polyacrylamide gel. The gel surface was wetted with transfer buffer (25 mM Tris-HCl, 192 mM glycine, 20% methanol). A piece of nitrocellulose paper (Sartorius, SM1 1307) was saturated with transfer buffer and laid on the gel. Air bubbles between the filter and the gel were removed. The gel and nitrocellulose filter were placed in the transfer unit as specified by the manufacturer (Bio-Rad). Transfer was allowed to proceed at 200 mA for 3-4 hours. Then the nitrocellulose filter was removed and stained with Amido-Schwartz for 3 minutes (0.05% Amido black, 45% deionized H.sub.2 O, 45% methanol, 10% acetic acid) and destained in H.sub.2 O. The filter was incubated for at least 10 minutes at room temperature in "BLOT0O" (5% w/v nonfat dry milk, 50 mM Tris-HCl pH 7.4, 0.9% w/v NaCl, 0.2% w/v sodium azide). The filter was placed in serum appropriately diluted (1:50 to 1:500) in 0.5X Blotto (2.5% nonfat dry milk, 50 mM Tris-HCl pH 7.4, 0.9% NaCl, 0.2% sodium azide) and was gently agitated for approximately 16 hours at room temperature. The filter was washed for 1 hour with 5 changes of TSA (50 mM Tris-HCl pH 7.4, 0.9% NaCl, 0.2% sodium azide). The blot was placed in 15 ml of 0.5X BLOTTO solution containing 1.times.10.sup.7 cpm of .sup.125 I-protein A and gently agitated for 2 hours at room temperature. The filter was washed for 2 hours with a minimum of 7 changes of TSA, rinsed once with deionized H20 and air dried. The blot was covered with Saran.RTM. wrap and autoradiographed.

An alternative to the .sup.125 1I-Protein A detection method was also used. This method relied on a chemiluminescent signal activated by horseradish peroxidase (HRP). The chemiluminescent reagents are readily available from several suppliers such as Amersham and DuPont NEN. The western blot was prepared and blocked with BLOTTO. A number of methods were used to introduce the HRP reporter enzyme including, for example, a hapten/anti-hapten-HRP, a biotinylated antibody/streptavidin-HRP, a secondary reporter such as a goat or mouse anti-rabbit IgG-biotinylated/streptavidin-HRP, or a goat or mouse-anti rabbit IgG-HRP. These reagents were bought from different sources such as BioRad or Amersham and occasionally biotinylated antibodies were prepared in our laboratory using Biotin NHS from Vector Laboratories, Burlingame, CA. (Cat. #SP-1200) following the procedure accompanying the product. The following is an example of a procedure used to detect the expression of protein polymers.

The blot was placed in 15 ml of BLOTTO solution containing biotinylated goat anti-rabbit IgG (BioRad) diluted in BLOTTO (1:7500) and gently agitated for 2 hrs at room temperature. The filter was then washed for 30 minutes with 3 changes of TSA (50 mM Tris-HCl pH 7.4, 0.9% NaCl, 0.2% sodium azide). The blot was then incubated for 20 minutes at room temperature with gentle rotation, in 20 ml of TBS (100 mM Tris Base, 150 mM NaCl, pH 7.5) HRP-Streptavidin (Amersham) diluted 1:1000 in TBS with 0.1 % Tween 20. The blot was then washed three times for 5 minutes each in TBS with 0.3% Tween 20 and then three times for 5 minutes each in TBS with 0.1 % Tween 20. The blot was then incubated for 1 minute with gentle agitation in 12 ml of development solutions #1 an #2 (Amersham) equally mixed. The blot was removed from the development solution and autoradiographed.

5. Amino Acid Analysis.

Amino acid compositions were determined by the PTC derivatization procedure of Henrickson and Meredith (1984). Protein samples were hydrolysed with 5.7 N constant boiling HCl at 108.degree. C. for 24 hours in vacuo. After reaction with PITC, amino acid derivatives were detected at 254 nm by HPLC reverse phase chromatography using a Hewlett Packard 1090 or Waters 600E system and a Supelco C18 column (4.6 mm.times.25 cm) with a linear gradient of 0-50% acetonitrile in 0.1 M NH.sub.4 OAc pH 6.78 as a mobile base. Henrickson, R. L. and Meredith, S. C. (1984) Amino Analysis by Reverse Phase High Performance Liquid Chromatography., Anal. Biochem. 137:65-74.

6. Peptide Synthesis.

Synthetic peptides were prepared by solid phase synthesis on an Applied Biosystems Model 430A Peptide Synthesizer using the standard symmetric anhydride chemistry as provided by the manufacturer. The coupling yield at each step was determined by the quantitative ninhydrin procedure of Sarin et al., (1981). The synthetic peptide was cleaved from the solid support and amino acid blocking groups were removed using anhydrous HF (Stewart and Young, (1984)). Crude peptides were desalted by chromatography over Sephadex G-50. Sarin, V.K., Kent, S. B. H., Tam, J. P. and Merrifield, R. B. (1981) Anal. Biochem. 237:927-936. Stewart, J. M. and Young, J. D. (1984) Solid Phase Peptide Synthesis, Pierce Chemical Company, Rockford, II pp 85-89.

1. In vitro DNA synthesis.

The N,N-diisopropyl phosphoramidites or .beta.-cyanoethyl phosphoramidites, controlled-pore glass columns and all synthesis reagents were obtained from Applied Biosystems, Foster City, Calif.

Synthetic oligonucleotides were prepared by the phosphite triester method with an Applied Biosystems Model 380A or 381A DNA synthesizer using a 10-fold excess of protected phosphoramidites and 1 .mu.mole or 0.2 .mu.mole of nucleotide bound to the synthesis support column. The chemistries used for synthesis are the standard protocols recommended for use with the synthesizer and have been described (Matteucci et al., J. Amer. Chem. Soc., 103:3185-3319 (1981)). Deprotection and cleavage of the oligomers from the solid support were performed according to standard procedures as described by McBride et al., Tetrahedron Letters, 24:245-248 (1983). The repetitive yield of the synthesis as measured by the optical density of the removed protecting group as recommended by Applied Biosystems (1984) was greater than 97.5 %.

The crude oligonucleotide mixture was purified by preparative gel electrophoresis as described by the Applied Biosystems protocols of Nov. 9, 1984 (User Bulletin No. 13) and as updated in 1992. The acrylamide gel concentration varied from 10 to 20% depending upon the length of the oligomer. If necessary, the purified oligomer was identified by UV shadowing, excised from the gel and extracted by the crush and soak procedure (Smith, Methods in Enzymology :371-379 (1980)).

For DNA synthesis of oligonucleotides longer than 100 bases, the synthesis cycle was changed from the protocol recommended by Applied Biosystems for the 381A DNA synthesizer. All the reagents used were fresh. All the reagents were supplied by Applied Biosystems except for the acetonitrile (Burdick and Jackson Cat#017-4 with water content less then 0.001 %) and the 2000 .ANG. pore size column (Glen Research). Due to the length of the oligo, interrupt pauses had to be inserted during the synthesis to allow changing the reagent bottles that emptied during synthesis. This interrupt pause was done at the cycle entry step and the pause was kept as short as possible. The washes after detritylation by TCA, through the beginning of each synthesis cycle, were increased from about 2x to 3x over the recommended time. The time allocated for the capping was also increased to limit truncated failure sequences. After the synthesis the deprotection was done at 550C for 6 hours. After desalting the synthesized DNA was amplified using PCR.

2. Sequencing of DNA.

DNA sequences were determined by the following methods. Fragments containing the region of interest were cloned into the multiple cloning site of M13mpl8 or M13mpl9 (Maniatis et al., 1982, and Norrander et al. 1983. Gene, 6:101-106). Single-stranded DNA was prepared and sequenced by the primer extension method (Sanger et al. 1977 Proc. Natl. Acad. Sci USA, 14:5463-5467 and Biggin et al., 1983. Proc. Natl. Acad. Sci.USA. 80:3963-3965) using 35S-deoxyadenosine 5'-(alpha-thio)-triphosphate (New England Nuclear) as label. In some cases, reverse transcriptase (Molecular Genetics) was used to extend the primer, using the dideoxy:deoxynucleoside triphosphate ratios utilized by Zagursky et al. Gene Anal. Techn. (1985) 2:89-94. Deoxyadenosine triphosphate labeled with either .sup.32 p or .sup.35 S was used in these reactions. Compression artifacts which appeared in some G-C rich sequences were overcome by eliminating deoxyguanosine triphosphate from the G reaction, and using deoxyinosine triphosphate (P-L Biochemicals) at a final concentration of 37.5 .mu.M instead. In the other mixes, the concentration of dideoxyGTP in the G reaction was 0.5 mM. All sequences were run on 6 or 8% polyacrylamide gels containing 8 M urea (Sanger et al. 1978, FEBS Letters, 87:107-110.). Primers used for sequencing were purchased from P-L Biochemicals. Storage and analysis of data utilized software from both DNAstar and International Biotechnologies, Inc for IBM personal computer and DNA Strider, DNA Inspection IIe or DNAid for Apple Macintosh personal computer.

3. Dideoxy DNA sequencing of double stranded plasmid DNA.

Plasmid DNA was prepared as described previously (Preparation of plasmid DNA from E. coli, Small scale, Maniatis et al.). Primers were synthesized using a DNA synthesizer as described previously, and were annealed to the plasmid DNA following the procedure described above for M13 sequencing. The sequencing reactions were done using Sequenase (United States Biochemicals) and the conditions were as recommended by the supplier. All sequences were run on polyacrylamide gels as described above.

4. PCR amplification:

The PCR reaction was performed in a 100 .mu.l volume in a Perkin Elmer thin-walled Gene Amp.TM. reaction tube. Approximately 1 .mu.l of each primer DNA (corresponding to a 0.1 .mu.M final concentration) was added to 1.times.PCR buffer (supplied by Perkin Elmer as 10.times.solution), 200 .mu.M of each dNT, 5U AmpliTaq, and several concentrations of the target DNA. Amplification was performed in a Perkin Elmer DNA Thermal cycler model 480 for 30 cycles with the following step cycles of 12 min each: 95.degree. C., 62.degree. C., and 72.degree. C. Aliquots from the different reactions were analyzed by Agarose Gel Electrophoresis using 1.5% Low Melting Point agarose in 0.5.times.TA buffer. The reaction mixtures that gave the desired band were pooled and spun through an Ultrafree-Probind filter unit (Millipore) at 12,000 rpm for 30 seconds in a Sorvall Microspin 24S to remove the AmpliTaq enzyme. The buffer was then exchanged with H.sub.2 O two times, using a Microcon-30 filter (Amicon) by spinning at 12,000 RPM for 6 min in a microfuge. Salts and glycerol were removed from the amplified dsDNA using a Bio-Spin 6 column (BioRad) equilibrated in TEAB, in a Sorvall RC5B centrifuge using an HB4 rotor at 2,500 RPM for 4 min. The DNA was then concentrated in vacuo.

The fermentor is a 15 L Chemap, 10 L working volume. The culture conditions are: temperature=30.degree. C., pH 6.8; NaOH 2.5 M is used for pH regulation. The headspace pressure is below 0.1 bar. The dissolved oxygen is regulated at 50%. The air flow varies from 0.5 L/min to 20 L/min. The agitation rate varies between 200 to 1500 rpm. The fermentor is inoculated with a 10% (v/v) inoculum grown in medium A for 15 hours at 30.degree. C. under agitation.

Medium B, C or D was the fermentor medium. The starting volume in the case of 10 liter fermentation is no less than 3 L, and in the case of a 1 liter fermentation, is no less than 0.5 liters.

If the fermentor starting volume is less than the final volume desired, then when the carbon source concentration reaches 1 %, a concentrated solution (5x) of medium B,C, or D, respectively, is added to the fermentor in order to keep the carbon source concentration approximately 1 %.

When the culture reached an OD.sub.600 of 60.0, the temperature was increased to 42.degree. C. for 10 min, then lowered to 39.degree. C. or 40.degree. C. for 2 to 3 hours. The cells were then harvested by centrifugation and frozen at -70.degree. C. until processed.

Other fermentors used for the expression of protein polymers were usually a 15 1 MBR, 10 1 working volume, or a 13 1 Braun Biostat E, 8.5 1 working volume. The choice of the fermentor and its size is not critical. Any media used for the growth of E. coli can be used. The nitrogen source ranged from NZAmine to inorganic salts and the carbon source generally used was glycerol or glucose. All fermentations were done with the appropriate selection conditions imposed by the plasmid requirements (e.g. kanamycin, ampicillin, etc.). The fermentation method used to express protein polymers in E. coli was the fed-batch method. This is the preferred method for the fermentation of recombinant organisms even if other methods can be used.

The fed-batch method exploits the stage of cell growth where the organisms make a transition from exponential to stationary phase. This transition is often the result of either depletion of an essential nutrient or accumulation of a metabolic byproduct. When the transition is the result of nutrient depletion, the addition of nutrients to the system causes cell division to continue. One or more essential nutrients can incrementally be added to the fermentation vessel during the run, with the net volume increasing during the fermentation process. The result is a controlled growth rate where biomass and expression levels can be optimized. When the cell number in the culture has reached or is approaching a maximum, protein polymer production is induced by providing an appropriate physical or chemical signal, depending upon the expression system used. Production will then continue until the accumulated product reaches maximum levels (Fiestchko, J., and Ritch, T., Chem. Eng. Commun. (1986), 45: 229-240. Seo, J. H.; Bailey, J. E., Biotechnol. Bioeng. (1986), 2: 1590-1594.

The design of a collagen-like polymer with thermoreversible gelation character.

The collagen-like polymer CLP was designed predominantly of repeating GPP tripeptides (8 within each monomer segment). Other tripeptides were included in order to decrease the overall repetitiveness of the gene and to allow the use of additional codons which could be used to better manipulate the DNA. These were GAP (twice), GPA, GPV, and GSP. All of these triplets occur in natural collagen although never in the sequence and context used in CLP. The properties of CLP were designed to yield a protein polymer that would undergo thermoreversible gelatin at high temperatures, as well as being nonimmunogenic. The high stability of the helices should create high tensile strength in fibers or membranes formulated from CLP. These chain properties should allow the creation of hydrogel colloids in aqueous solutions which when applied to hard substrates should act as soft coatings. Because of the simple sequence of CLP, its optical absorbance should be minimal in all wavelengths down to 220 nm.

The design of a soft coating material with cell attachment function.

The versatile formulation properties of collagen-like polymers makes them ideal as biomaterials used in implantable devices. Either as a coating on the surface of prostheses or as a structural component of the device itself, CLP could promote tissue integration by providing improved blood and cellular interaction. The latter function is mediated in natural collagen by a specific amino acid sequence which acts as a ligand for a cellular receptor. In order to create a CLP polymer with cell attachment activity, the sequence GLPGPKGDRGDAGPKGADGSP (SEQ ID NO: 19) was included within the CLP monomer sequence (CLP-CB). In contrast to the hydrophobic GPP collagen-like flanking sequences, this block of 21 highly charged hydrophilic amino acids should form a destabilized flexible helical region accessible for interaction with cells. Promotion of epithelialization of the surface of an implanted device will improve the compatibility and rejection characteristics increasing its lifetime and safety. The subject compositions may find use as wound dressings, allowing for neovascularization, eye applications, matrices for artifical organs and the like.

Construction of CLP monomer.

The CLP (Collagen-Like Protein) synthetic gene was assembled from smaller parts. First, three double-stranded sections of DNA ranging from 40 to 60 bp in length were chemically synthesized as described above. ##STR1##

Sections A and C (the sequence of section C after the BanI REN site is not coding for CLP but is a modification of the multiple cloning site of the acceptor plasmid) were cloned separately into plasmid pUC19 (See United States Biochemical Life Science Research Products, 1994-1995 Catalogue, p 365) that had been digested with the appropriate REN. The DNA sequence was verified and two plasmids were selected pPTO 1 1 and pPTO1 12, carrying the correct sequence. Section B was ligated into PTO1 1 1 that had been digested with BanII and SmaI RENs. Plasmid pPTO1 13 was sequenced and found correct.

Plasmids pPTO1 12 and pPTO1 13 were digested with the appropriate RENs to release section C and Sections A+B, respectively. After purification, these DNA fragments were ligated into pSY937 (described in U.S. Pat. No. 5,243,038) previously digested with BanI and EcoRV RENs. The product of the ligation reaction was transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with BanI; clones containing inserts of the correct size were sequenced. Plasmid pPT0116 contained the desired sequence shown for section A+B+C (see Table 2). This plasmid was digested with BanI REN, and the digestion mixture was diluted and ligated with T4 DNA Ligase. E. coli HB 101 competent cells were transformed and screened for loss of the CLP insert; one plasmid, pPT0125, was selected to be used as the acceptor vector for subsequent constructions.

Construction of CLP-CB monomer.

Two oligonucleotide strands were synthesized as described in Example 1. ##STR6##

The two oligonucleotide strands were annealed and ligated with the DNA of plasmid pPT0116 (CLP monomer in pSY937) which had been digested with AvaI REN.

The products of this ligation reaction were transformed into F. DQii strain HB101. Plasmid DNA from transformants was purified and digested with BanI; clones containing inserts of the correct size were digested with PstI and BglI RENs for the determination of orientation. Plasmid DNA from correct clones was sequenced. Plasmid pPT0117 (shown in Table 3) contained the desired CLP-CB monomer sequence, olignonucleotides (i) and (ii) are shown below in bold and underlined.

CLP and CLP-CB Polymer Construction.

CLP

Plasmid DNA from pPT0116 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The CLP gene fragment, 117 bp, was excised and purified by NACS column (see Example 1). The purified fragment was ligated with plasmid pSY1262 which had been digested with REN BanI. The product of this ligation reaction was transformed into E. MU strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed for increased size due to CLP multiple DNA insertion. Several clones were obtained ranging in size from 0.5 kbp to 3.5 kbp. One clone pPT0190, with an insert of approximately 0.9 kbp was chosen for expression and protein analysis.

CLP-CB

Plasmid DNA from pPTO1 17 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The CLP-CB gene fragment, 180 bp, was excised and purified by NACS column (see Example 1). The purified fragment was ligated with plasmid pSY1261 which had been digeted with REN BanI. The product of this ligation reaction was transformed into E. c strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed for increased size due to CLP-CB multiple DNA insertion. Several clones were obtained ranging in size from 0.5 kbp to 3.5 kbp. One clone pPT0129, with an insert of approximately 1.1 kbp was chosen for expression and protein analysis.

Analysis

E. coli strain HB101 containing plasmid pPT0190 or pPT0129 were grown as described above. The proteins produced by these cells were analyzed by SDS-PAGE for detection of reactivity to CLP antibodies (see Example 1). In both analyses, a strong reactive band was observed of an apparent molecular weight of 45 kD and 60 kD, respectively. ##STR12##

where:

A=GAPGPAGPP (SEQ ID NO:34)

B=GSRGDPGPP (SEQ ID NO:35)

C=GAHGPAGPK (SEQ ID NO:ll)

Due to the complexity of the SequenceD polymer structures the design of the gene monomers was as follows:

1. design and synthesis of C.sub.2 units (5' and 3')

2. design and synthesis of A units

3. design and synthesis of AB units

The acceptor vector pPT0134 was designed and constructed specifically to accommodate the construction requirements of the SequenceD polymer genes. This vector contains two recognition sites for Fokl REN in its MCS (multiple cloning site).

Two oligonucleotide strands containing these sites were synthesized and purified as described in Example 1. ##STR13##

After annealing, the two oligonucleotide strands were ligated with pSY937 which had been digested with Banl and EcoRV RENs. The product of the ligation mixture was transformed into E. coli and selected on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from individual colonies was analyzed on agarose gel electrophoresis after digestion with Scal and Stul RENs. One plasmid pPT0124 contained the expected DNA fragment.

The new MCS was then moved to plasmid pSY1367. This plasmid is a derivative of pSY1299 (see U.S. Pat. No. 5,243,038). Plasmid pSY1299 was digested with Ncil REN and the large DNA fragment was purified by agarose gel electrophoresis and NACS purification. The purified DNA fragment was treated with DNA Polymerase (see Example 1), ligated, then digested with Fokl prior to transformation in E- coii strain HB101. Plasmid DNA from single colonies was purified and analyzed by restriction digests. One plasmid, pSY1366, was found to be correct and lacking the only Fokl site present in pSY1299.

Two oligonucleotide strands were synthesized and purified as described in Example 1: ##STR14##

Oligonucleotide strands 1.A and 1.B were annealed and ligated with the DNA of plasmid pSY1366 which had been digested with Banli and Fspl RENs. The products of this ligation reaction were transformed into a Qi strain HB101. Plasmid DNA from transformed colonies was purified and digested with Fokl. Clones which linearized with Fokl were sequenced. Plasmid pSY1367 contained the desired MCS sequence and was chosen for subsequent constructions.

Plasmids pPT0124 and pSY1367 were digested with Nrul and Ncol and the DNA fragments were purified by agarose gel electrophoresis and NACS purification. The small fragment (approximately 500 bp) from pPT0124 was ligated with the large fragment from pSY1367. The product of the ligation mixture was transformed into a coli. Plasmid DNA from single colonies was purified and analyzed by restriction digests and DNA sequencing. One plasmid, pPT0134, contained the desired sequence and was used as the acceptor vector for the SequenceD constructions.

Four oligonucleotide strands were synthesized and purified as described in Example 1. Each pair of oligonucleotide strands encodes a C.sub.2 unit, either the 5' or 3' C.sub.2 unit. ##STR15##

Oligonucleotide strands 2.A and 2.B were annealed and ligated with the DNA of plasmid pPT0134 which had been digested with Fold REN. The products of this ligation reaction were transformed into E. coli strain HB101. Plasmid DNA from transformed colonies was purified and digested with Sfil. Clones which linearized with Sfil were sequenced. Plasmid pPT0135 contained the desired C.sub.2 sequence and was chosen for subsequent constructions.

Strands 2.C and 2.D were annealed, ligated, and transformed as were strands 2.A and 2.B. Plasmid DNA from transformed colonies was purified and digested with Banll REN. Clones which linearized with Banll were sequenced. Plasmids pPT0137 and pPT0138 contained the correct C.sub.2 DNA sequence.

Plasmid pPT0135 and pPT0137 were digested with Banl and Stul RENs. The large fragment from pPT0135, containing the C.sub.2 (strands A+B), was ligated with the small fragment of pPT0137 containing the C.sub.2 fragment (strands C+D). The ligation products were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and two digestions were performed, Sfil-Stul and Banll-Stul RENs, respectively. Clones that released a DNA fragment of approximately 800 bp in both digestions were sequenced. Plasmid pPT0140 contained the correct C.sub.2 C.sub.2 sequence, as shown in Table 5, and was used for SequenceD gene monomer constructions.

Two oligonucleotide strands were synthesized and purified as described in Example 1. ##STR19##

The two oligonucleotide strands encoding A.sub.2 (3A & 3B) were annealed and ligated with plasmid DNA pPT0134 previously digested with Fokl REN. The products of the ligation mixture were transformed into E. coli strain HB101. Plasmid DNA from transformants was digested with Pstl REN and clones that were linearized were sequenced. Plasmid pPT0142 was found to be correct and used for the multimerization of A.sub.2 units.

Plasmid DNA from pPT0142 was digested with Fokl REN and the fragment containing the A.sub.2 unit was isolated by agarose gel electrophoresis and purified using a NACS column (see Example 1). The DNA fragment was self-ligated and the products of the ligation were ligated with pPT0134 previously digested with Fokl REN. The products of the ligation mixture were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with Fokl REN. Clones containing DNA inserts of 162 bp corresponding to A.sub.6 were selected for sequence analysis. Plasmid pPT0144 had the expected DNA sequence and was selected for subsequent constructions. Plasmid DNA from pPT0144 was digested with Fokl REN and the two DNA fragments generated by the digestion were separated using agarose gel electrophoresis. The smaller DNA fragment was purified using a NACS column (see Example 1). The DNA fragment carrying the A.sub.6 coding sequence was ligated with plasmid DNA pPT0140 previously digested with Fold. The products of the ligation were transformed into E. coli strain HB101. Plasmid DNA from individual colonies was analyzed for inserts containing multiple A.sub.6 DNA fragments by digestion with Fold. Several size inserts were found ranging from A.sub.6 to A.sub.24. One clone, pPT0147 (shown in Table 6) was identified to contain the desired SequenceD2 gene monomer sequence C.sub.2 A.sub.12 C.sub.2 and was used for further constructions.

The clone containing the SequenceDl gene monomer sequence C.sub.2 A.sub.24 C.sub.2 (shown in Table 7), necessary to construct the SequenceDl polymer gene, was found to be highly unstable during subsequent passages. This instability was attributed to the high copy number of the acceptor plasmid. For this reason, the gene monomer from this plasmid was recloned into pBR322 (F. Bolivar, et al. (1977) Gene 2:95-113). The plasmid DNA containing the C.sub.2 A.sub.24 C.sub.2 gene fragment was isolated from the plasmid by digestion with Nrul and EcoRV RENs, agarose gel electrophoresis, and purified on a NACS column. This DNA fragment was ligated with plasmid pBR322 DNA digested with EcoRV and Nrul RENs (see agarose ligation in Example 1). The products of this ligation were transformed into E. coli strain HB101 and selected on bacterial plates containing the antibiotic ampicillin at 100 .mu.g/ml. Plasmid DNA from individual colonies was analyzed by agarose gel electrophoresis. Clones containing the insert were further analyzed by digestion with several RENs and one, pPT0153, was chosen for the construction of the SequenceDl polymer gene. This plasmid was stable.

Plasmid from DNA pPT0153 was digested with Acyl REN and subsequently with Fokl REN. The DNA fragment containing the SequenceDl gene monomer, 756 bp, was isolated by agarose gel electrophoresis and purified using a NACS column (see Example 1). The monomer gene fragment was ligated with pSY1262 (see U.S. Pat. No. 5,243,038) which had been digested with Banl REN. The ligation product was transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic kanamycin. Plasmid DNA from individual colonies was analyzed for inserts containing multiple SequenceDl monomer fragments by digestion with BamHl and Pvull RENs and electrophoresis on agarose gel. One clone, pPT0164, contained the gene monomer (756 bp); another, pPT0165, a slightly larger fragment (approximately 1200 bp); and a third, pPT0166, a gene dimer (1512 bp).

E. coli strain HB101 containing plasmid pPT0164, pPT0165 or pPT0166 was grown as described above. The proteins produced by these cells were analyzed by western blot analysis for novel protein bands which reacted with SequenceD-C.sub.2 A.sub.2 peptide antisera. A band with an apparent molecular weight of approximately 45 kD was observed in the culture containing the plasmid pPT0164. A band of 68 kD was observed with pPT0165 and a light smear of bands with pPT0166.

Because of the low level of detectable expression in the strain containing pPT0166, the mRNA produced by the SequenceDl clones was analyzed. mRNA was prepared as described in Example 1. By northern blot analysis (see Example 1), the SequenceD specific mRNA from all clones, using as a probe the SequenceD2 monomer sequence, was shown to be full length and synthesized at approximately the same level regardless of the SequenceD gene size. ##STR26##

Plasmid DNA from pPT0147 was digested with Fokl REN and the digestion fragments were separated by agarose gel electrophoresis. The SequenceD2 gene fragment of 432 bp was excised and purified by NACS column (see Example 1). The purified fragment was ligated with pSY1262 which had been digested with Banl REN. The products of this ligation were transformed into E coli strain HB101 and the transformants were selected for growth on bacterial plates containing the antibiotic kanamycin. Plasmid DNA from individual colonies was purified and analyzed for multiple insertions of the SequenceD2 gene monomer fragment. Several clones were obtained ranging in size from 500 to 3,000 bp. See Table 8 for the results.

E. coli strain HB101 containing plasmids pPT0155 to pPT0163 were grown as described above. The proteins produced by these cells were analyzed by western blot analysis for a protein band reactive with SequenceD-C.sub.2 A.sub.2 peptide specific antisera. See Table 8 for the results.

Four oligonucleotide strands encoding (AB).sub.2 were synthesized and purified as previously described. ##STR28##

Oligonucleotide strands 4.A and 4.B were annealed and ligated with the DNA plasmid pPT0134 (see Example 1) which had been digested with Fokl REN. The products of this ligation were transformed into L DQii strain HB101. Plasmid DNA from transformed colonies was purified and digested with Pstl and Stul. Clones containing a fragment of approximately 800 bp were sequenced. Plasmid pPT0139, containing the desired sequence of strands 4.A and 4.B, was chosen for subsequent constructions.

Strands 4.C and 4.D were annealed and ligated with the DNA plasmid pPT0139 which had been previously digested with Xbal and Pstl RENs. The products of this ligation were transformed into , oQli strain HB101. Plasmid DNA from transformed colonies was purified and digested with Ncol and Dralll RENs. Clones containing a DNA fragment corresponding to the combined insertion of strands 4.A and B and 4.C and D were sequenced. Plasmid pPT0143, containing the correct (AB).sub.2 DNA sequence, as shown in Table 9 was chosen for further constructions.

Plasmid DNA from pPT0143 was digested with Fokl REN and the fragment containing the (AB).sub.2 gene fragment was isolated by agarose gel electrophoresis and purified on a NACS column. The DNA fragment was then ligated with pPT0134 that had been digested with Fokl REN. The products of the ligation were transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from individual colonies was analyzed for inserts containing multiple (AB)2 DNA fragments by digestion with Fokl REN. Several clones were obtained ranging from one copy to several copies of (AB).sub.2. One clone, pPT0169, containing (AB).sub.6 was used as an intermediate for the construction of the SequenceD3 gene monomer.

The (AB).sub.6 gene fragment was purified from pPT0169 by digestion with Fokl REN, agarose gel electrophoresis and NACS purification. This DNA fragment was then ligated with DNA plasmid pPT0140 that had been previously digested with Banl REN. The products of the ligation were transformed into E. coli strain HB101, and transformants were selected on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from individual colonies was analyzed by digestion with Fold REN for inserts containing multiple copies of the (AB).sub.6 gene fragment. One clone, pPT0171, containing C.sub.2 (AB).sub.12 C.sub.2 (shown in Table 10) was chosen as the SequenceD3 gene monomer for subsequent constructions.

Plasmid DNA from pPT0171 was digested with Fokl REN and the fragment containing the SequenceD3 gene monomer purified by agarose gel electrophoresis and NACS purification. The SequenceD3 monomer was then self-ligated and then ligated with DNA plasmid pSY1262 that had been digested with Banl REN. The products of the ligation were transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic kanamycin. Plasmid DNA from individual colonies was purified and analyzed after digestion with Xcml and Pvull RENs for insertions containing multiple copies of the SequenceD3 gene monomer fragment. Clones pPT0173, pPT0174, pPT0175 and pPT0176 containing monomer, dimer, trimer and tetramer forms of SequenceD3, respectively, were selected for expression analysis.

E. coli strain HB101 containing SequenceD3 plasmids pPT0173, pPT0174, pPT0175, or pPT0176 were grown as described above. The proteins produced by these cells were analyzed by western blot analysis for novel protein bands reactive with SequenceD-(AB).sub.2 peptide specific antisera. Reactive bands were observed with each clone (see Table 11 for results). However, the expression of the full length polymer decreased with the increased size of the genes. Northern analysis using the SequenceD3 monomer as a probe showed that the synthesis of full length mRNA in these clones was at equivalent levels.

where:

B=GSRGDPGPP (SEQ ID NO:35)

C=GAHGPAGPK (SEQ ID NO:ll)

D=GAQGPAGPG (SEQ ID NO:63)

Three double stranded DNA sections, coding for (DB).sub.3, were synthesized, purified and annealed as described in Example 1. ##STR37##

The three DNA sections were cloned separately. The first two strand section (5.A & 5.B) was ligated to pPT0138 previously digested with Banl REN. The ligation products were transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from individual colonies was digested with EcoOl09I and Stul RENs and analyzed by agarose gel electrophoresis. Plasmid DNA containing an appropriately sized DNA fragment was sequenced and one clone, pPT0221, was used in subsequent constructions.

The second pair of oligonucleotide strands (5.C & 5.D) were ligated with pPT0134 which had been digested with Fokl REN. After transformation of E. coli, plasmid DNA from individual colonies was analyzed by digestion with Banll and Stul RENs. DNAs that were digested by both enzymes were sequenced. One clone, pPT0222, had the expected sequence and was used for subsequent constructions.

Plasmid DNA from pPT0222 was digested with Fokl REN and the fragment (54 bp) containing the second pair of oligonucleotide strands (5C & SD) was isolated by agarose gel electrophoresis followed by NACS purification. This DNA fragment was ligated with pPT0221 previously digested with Banl REN. The products of the ligation were transformed into E. coli and plasmid DNA from single colonies was analyzed by agarose gel electrophoresis after digestion with Dralll and Stul RENs. One clone, pPT0223, was chosen, after DNA sequencing, to be the acceptor vector for the third synthesized SequenceD gene fragment.

Plasmid pPT0223 was digested with Banl REN and ligated with the third pair of oligonucleotides (5.E & 5.F). The product of the ligation reactions was transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from individual transformants was purified and digested with Fokl and Banl RENs. Clones containing the correct fragment size were sequenced. One clone, pPT0224, shown in Table 13 containing the desired sequence was used in the subsequent constructions of the SequenceD4 and SequenceD5 monomers.

Plasmid DNA from pPT0224 was digested with Fokl and Banl RENs and the digestion fragment carrying (DB).sub.3 was isolated by agarose gel electrophoresis and purified on a NACS column. The purified fragment was self-ligated and then cloned into pPT0140 which had been digested with Banl REN. The products of the ligation were transformed into E. coli strain HB 101. Plasmid DNA from individual colonies was analyzed for inserts containing multiple (DB).sub.3 DNA fragments by digestion with Fokl. Several size inserts were found ranging from (DB).sub.3 to (DB).sub.2. One clone, pPT0229, was identified to contain the desired SequenceD5 monomer sequence, C.sub.2 (DB).sub.6 C.sub.2, and was used for subsequent constructions. The clone containing the SequenceD4 gene monomer sequence C.sub.2 (DB).sub.12 C.sub.2 was found to be highly unstable during subsequent passages, as was observed during the construction of SequenceDl. Subsequently, a new plasmid was constructed to use as an acceptor for the SequenceD4 gene monomer fragment.

Plasmid pACYC 184 (Chang and Cohen, J. Bacteriol. 134, 1141-1156 ›1977!) was digested with BanI REN, purified by agarose gel electrophoresis, and the DNA fragment corresponding to approximately 2000 bp was further purified using a NACS column. This DNA fragment was filled in using DNA polymerase (see Example 1) and then self-ligated. The products of the ligation mixture were transformed into E. coli strain HB101 and selected on bacterial plates containing chloramphenicol at 30 ,g/ml. Plasmid DNA from individual colonies was lineazed by digestion with Eco47II. One clone, pPT0235, was used as the acceptor vector for the SequenceD4 monomer.

The plasmid DNA containing the SequenceD4 gene monomer fragment was isolated from the plasmid by digestion with DraI and PvuII RENs, followed by agarose gel electrophoresis. The agarose slice containing the SequenceD4 gene monomer fragment was ligated with plasmid pPT0235 previously digested with Eco47IH REN, and purified by agarose gel electrophoresis and NACS column. The products of this ligation were transformed into E. coli strain HB101 and selected on bacterial plates containing chloramphenicol at 30 .mu.g/ml. Plasmid DNA from individual colonies was analyzed by digestion with NruI and EcoRV RENs. One clone containing the SequenceD4 gene monomer fragment, pPTO237, was chosen for the construction of the SequenceD4 polymer gene. This plasmid was stably maintained in E. coli.

Plasmid DNA from pPT0237 was digested with Fokl REN. The DNA fragment containing the SequenceD4 gene monomer was isolated by agarose gel electrophoresis and purified using a NACS column (see Example 1). The monomer gene fragment was then ligated with pSY1262 which had been previously digested with Bani REN, treated with phosphatase, and purified by gel electrophoresis and NACS column. The ligation products were transformed into E. coli strain HB101 and the transformants were selected for growth on bacterial plates containing the antibiotic kanamycin at 50 ,g/ml. Plasmid DNA from individual colonies was purified and analyzed for multiple insertion of the SequenceD4 gene monomer fragment. Several clones were obtained containing one, two or four copies of the SequenceD4 gene monomer. Plasmids pPT0247, pPT0248, and pPT0249 containing respectively 1, 2, and 4 copies of the gene monomer, were selected for protein expression analysis.

E. coli strain HB101 containing plasmids pPT0247, pPT0248, and pPT0249 were grown as described above. The proteins produced by these cells were analyzed by western blot analysis for novel protein bands reactive with SequenceD-C.sub.2 A.sub.2 peptide specific antisera. A reactive band corresponding to full length product was observed with each clone. ##STR41##

Plasmid DNA from pPT0229 containing the SequenceD5 gene monomer was isolated after digestion with Fold REN by agarose gel electrophoresis followed by NACS purification. The gene fragment was ligated with pSY1262 which had been digested with Banl REN. The products of the ligation were transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic kanamycin at 50 .mu.g/ml. Plasmid DNA from individual colonies was purified and analyzed for inserts containing multiple copies of the SequenceD5 gene monomer sequence C.sub.2 (DB).sub.6 C.sub.2. Plasmids pPT0231 and pPT0232, respectively, contained three and four copies of the SequenceD5 gene monomer and were used for expression analysis.

E. coli strain HB101 containing plasmids pPT0231 and pPT0232 were grown as described above. The proteins produced by these cells were analyzed by western blot analysis for novel protein bands reactive with SequenceD-C.sub.2 A.sub.2 peptide specific antisera. A reactive band corresponding to full length product was observed with each clone. ##STR42##

Four oligonucleotide strands encoding D.sub.4, were synthesized, purified and annealed as described in Example 1. ##STR43##

The first oligonucleotide segment consisting of strands 6.A and 6.B was ligated to pPT0138 previously digested with Banl REN. The ligation products were transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from individual colonies was digested with EcoOl09I and Xmnl RENs and analyzed by agarose gel electrophoresis. Plasmid DNA containing the correct sized fragment was sequenced and one clone, pPT0219, containing the correct sequence was used for subsequent constructions.

Plasmid pPT0219 was digested with Banl and EcoO109I RENs and ligated with the second pair of oligonucleotides (6.C and 6.D). The products of the ligation were transformed into E. coli strain HB101 and selected for growth on bacterial plates containing the antibiotic chloramphenicol. Plasmid DNA from transformants was purified and digested with Fokl and Banl RENs. Clones containing the correct fragment size were sequenced. One clone, pPT0220, containing the sequence shown in Table 14 was used in subsequent constructions of the SequenceD6 gene monomer. ##STR44##

Plasmid DNA containing the D.sub.4 sequence was digested with Fokl and Banl RENs and the digestion fragment containing D.sub.4 was isolated by agarose gel electrophoresis followed by NACS purification. The purified fragment was self-ligated and subsequently ligated with DNA plasmid pPTO140 digested with Banl REN. The ligation products were transformed into E coli strain HB 101 and selected for growth on bacterial plates containing the antibiotic chloramphenicol. A transformant, pPT0242, containing the SequenceD6 gene monomer ((D4)6 flanked by C.sub.2 -C2) was used for subsequent constructions.

Plasmid DNA from pPT0242 was digested with Fokl REN. The DNA fragment containing the SequenceD6 gene monomer was isolated by agarose gel electrophoresis and purified using a NACS column. The monomer gene fragment was then ligated with pSY1262 which had been previously digested with Banl REN, treated with phosphatase, and purified by gel electrophoresis and NACS column. The ligation products were transformed into E coli strain HB 101 and the transformants were selected for growth on bacterial plates containing the antibiotic kanamycin at 50 .mu.g/ml. Plasmid DNA from individual colonies was purified and analyzed for multiple insertion of the SequenceD6 gene monomer sequence, C.sub.2 D.sub.24 C.sub.2. Several clones were obtained ranging from one to four repeats of the SequenceD6 gene monomer. Plasmids pPT0243, pPT0244, pPT0245, and pPT0246 containing respectively 1, 2, 3, and 4 repeats of the gene monomer were selected for protein expression analysis.

E. coli strain B1101 containing plasmids pPT0243 to pPT0246 were grown as described above. The proteins produced by these cells were analyzed by western blot analysis for novel protein bands reactive with SequenceD-C.sub.2 A.sub.2 peptide specific antisera. See Table 15 for the results.

The protein polymer, SequenceD6, was purified in multigram quantities as produced from E. coli strain pPT0246 using standard protein purification, extraction, and separation methods. The lyophilized product was a white, spongy material. By amino acid compositional analysis, the product was shown to consist primarily of the amino acids glycine, alanine, proline and glutamine. The molar % glycine+alanine+proline out of the total amino acids were 82.8%. The molar ratio of glycine, alanine, proline, and glutamine was 1.95:0.89:1.00:0.89, respectively. The theoretical ratio of these amino acids for SequenceD6 polymer is 1.90:1.00:1.00:0.43.

The purified product was dried and analyzed for elemental composition. The chemical analysis showed the product to contain 50.5% carbon, 6.78% hydrogen, 19.5 % nitrogen, 11.3 % water and less than 0.1 % noncombustible ash. Theoretical elemental composition of SequenceD6 is 50.9% carbon, 6.49% hydrogen and 20.2% nitrogen. These analyses indicate that the dried product consists of approximately 85.7% protein, and that approximately 98.6% of that protein is SequenceD6.

The dried product is extremely soluble in water. 8% weight solutions or greater can be easily produced. At room temperature or above such solutions are viscous but fluid. Upon chilling to 0.degree. C. the solution forms a solid gel which does not flow and is semi-transparent. Upon heating to greater than 28.degree. C., the gel forms a thick solution. This thermoreversible transition between the liquid and gel phases of the polymer solution can occur repeatedly with no apparent physical change in the polymer structure.

Two oligonucleotide strands were synthesized and purified as described in Example 1: ##STR46##

The two oligonucleotide strands were annealed and ligated with the DNA of plasmid pPT0235 which had been digested with Eco47III and Snal RENs.

The product of this ligation reaction was transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with EcoRI in combination with Eco47III or SnaI or NruI RENs. Plasmid DNA from two clones that gave the correct digestion pattern was sequenced. One plasmid, designated pPT0285, was found to be correct and chosen for further contstructions.

The CLP 3.1 synthetic gene was assembled from smaller parts. First, four double-stranded sections of DNA were chemically synthesized. ##STR47##

The two strands of fragment 3 were phosphorylated before annealing using polynucleotide kinase 3'-phosphatase-free (see Example 1). All of the fragments were then individually annealed using the procedure described in Example 1.

Fragment 1, after annealing, was digested with PstI REN; the digestion mixture was treated with a BioSpin column as was the phosphorylated fragment 3 strands. All four fragments were then loaded on a 12% polyacrylamide gel in 0.5.times.TBE and the bands corresponding to double stranded DNA were identified by UV shadowing, excised from the gel and extracted by the crush and soak procedure (Smith, Methods in Enzymology, 65, 371-379 ›1980!).

The fragments were then ligated into pPT0285 previously digested with BanI and EcoRV RENs and further purified by NACS column (see Example 1). The product of the ligation reaction was transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with PvuII and SacII; clones containing inserts of the correct size were further analyzed with EcoRI in combination with several restriction endonucleases to determine the presence of unique restriction endonuclease sites prior to sequencing. One clone looked promising and was sequenced. Plasmid pPT0291 contained the sequence shown in Table 16, containing all four fragments, but had a deletion of 17 bases in fragment 3 including the DrallI restriction site.

This plasmid was used to construct the CLP 3.1 monomer. Fragment 3 was ligated with fragment 4 using the HCC ligation method, see Example 1. The product of the ligation mixture was electrophoresed in 2% low melting agarose gel and the band corresponding to the ligated product was excised from the gel and ligated with pPT0291 plasmid DNA that had been previously digested with BanII and SnaBI RENs and purified by agarose gel electrophoresis and NACS column.

The product of the ligation reaction was transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with BamHI and EcoRI RENs; clones that showed the correct restriction pattern were further analyzed with BanII or DraIlI RENs; three clones containing inserts of the correct size were sequenced. Plasmid pPT0292 contained the desired CLP 3.1 monomer sequence (see Table 17).

Plasmid DNA pSY1262 was digested with BanI REN. The digestion mixture was divided into two aliquots. One was treated with Calf Intestinal Phosphatase and the other was treated with Shrimp Alkaline Phosphatase (SAP), as described in Example 1.

Plasmid DNA from pPT0292 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The CLP 3.1 gene fragment, 180 bp, was excised and purified by NACS column (see Example 1) and then ligated with plasmid pSY1262 prepared as described above.

The product of this ligation reaction was transformed into E. coli strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed for increase size due to CLP 3.1 multiple DNA insertion. Several clones were obtained ranging in size from approximately 1.0 kbp to 3.0 kbp. Five clones, pPT0293 to pPT0297, containing respectively 6, 9, 11, 13, and 17 repeats of the gene monomer were selected for protein expression analysis.

Overnight cultures of E. coli strain HB101 containing plasmids pPT0293 to pPT0297 were grown as described above. The proteins produced by these cells were then used to perform dot blot and western blot analysis using CLP 3.1 peptide specific antisera (see Example 1). See Table 18 for the results. For purification and amino acids analysis larger cultures were used.

E. coli strain HBl01 containing plasmids pPT0293 to pPT0297 were grown as described above. The proteins produced by these cells were analyzed by SDS-PAGE for detection of reactivity to CLP 3.1 peptide specific antisera. In every analysis a strong reactive band was observed of an apparent molecular weight from 45 kD to 130 kD respectively. ##STR56##

One oligonucleotide strand coding for the CLP 3.7 gene monomer (see Table 19) was synthesized using an Applied Biosystems DNA synthesizer model 381A and a 2000A synthesis column supplied by Glen Research as described in Example 1. After the synthesis, the 226 base DNA fragment was deprotected and cleaved from the column support by treatment in NH.sub.4 OH at 55.degree. C. for 6 hrs.

Two additional DNA strands were synthesized to be used as primers for PCR amplification. The synthesis and purification of these DNA primers was performed as described in Example 1. The two strands are: ##STR58##

The PCR reaction was performed as described in Example 1.

The DNA was resuspended and digested with BanI REN as described in Example

1. The digested DNA was purified as described in Example 1, and then ligated with pPT0285 previously digested with BanI, treated with SAP, and purified as described in Example 1. The product of the ligation reaction was transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and analyzed as described below. Colonies were picked and transferred onto a plate and into a 0.5 ml microfuge tube containing 50 .mu.l of lysis buffer (1 % Tween 20, 10 mM Tris-HCl pH 8.0, 1 mM EDTA). The tube was closed, incubated at 95.degree. C. for 10 min and then cooled to room temperature. 5 .mu.l of lysate was added to 45 .mu.l MasterMix (1.times.PCR buffer as described previously, 5 U Amplitaq, 200 .mu.M dNTPs) in a 0.5 ml Perkin Elmer thin-walled Gene AmPm reaction tube. Amplification was performed in a Perkin Elmer DNA Thermal cycler model 480 for 30 cycles with the following step cycle of 1 min each: 95.degree. C., 52.degree. C., and 72.degree. C. Aliquots from different reactions were analyzed by agarose gel electrophoresis using 1.5% Low Melting Point agarose in 0.5'TAE buffer. Plasmid DNA from the clones showing the correct size insert was purified and anlyzed by DNA sequencing. Plasmid pPT0310 contained the desired CLP 3.7 monomer sequence (see Table 20).

Plasmid DNA from pPT0310 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The CLP 3.7 gene fragment, 180 bp, was excised and purified by NACS column. The purified fragment was ligated with plasmid pSY1262 which had been prepared as follows: pSY1262 plasmid DNA was digested with BanI REN and subsequently treated with Shrimp Alkaline Phosphatase (SAP) as described in Example 1.

The product of this ligation reaction was transformed into E. coli strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed for increased size due to CLP 3.7 multiple DNA insertion. Several clones were obtained and two of them containing inserts of approximately 1.25 kbp and 2.6 kbp (pPT0314 and pPT0312 respectively) were chosen to be used for expression of CLP 3.7.

E. coli strain HB101 containing plasmid pPT0312 or pPT0314 were grown as described in Example 1. The proteins produced by these cells were analyzed by SDS-PAGE for detection of reactivity to CLP antibodies. In every analysis a strong reactive band was observed with an apparent molecular weight of 130 kD and 50 kD respectively. ##STR63##

The sequence of fibrin and of the native cross-linking site is known. The bovine milk protein B-casein is a known substrate for factor XIIIa. Peptide blocks which include a factor XIIIa cross-linking site and retain activity towards factor XllIa were produced. These peptide blocks or similar amino acid sequences were then conjugated to high molecular weight carrier polymers or their design was used in the construction of protein polymers. When a formulation (aqueous and physiological) containing such polymers is mixed with factor XIIIa, it will undergo cross-linking leading to a setting reaction in which the polymer solution will be converted to a stiff gel or clot. The degree and spacing of cross-linking will influence the setting time and mechanical properties and cohesive strength of the gel. When applied on or in a tissue, an adhesive bond will be created both through physical adsorption to the tissue matrix and through covalent bonding to available tissue proteins.

A synthetic peptide was synthesized containing the amino acid sequence VLSLSQSKVLPVPE (SEQ ID NO: 103)(peptide 93.1) corresponding to residues 162-175 of bovine B-casein as published by Dumas, B.R., Brignon, G., Grosclaude, F., Mercier, J.C. (1972) Eur. J. Biochem. 25, 505-514. The peptide was shown to serve as a substrate for factor XIIIa cross-linking using HPLC analysis.

According to the sequence of human fibrin gamma chain (Rixon, M. W., Chung, D. W. and Davie, W. W., Biochemistry 22, 2077-2086, 1985), the carboxyl terminal 17 amino acids (residues 421 to 437, GEGQQHHLGGAKQAGDV (SEQ ID NO: 104) contain the residues glutamine (Q424) and lysine (K432) which participate in the isopeptide bond formed by the transglutaminase activity of factor XIIIa. Contained also within this sequence is a platelet binding activity. This peptide (Peptide 93.3) was synthesized and similarly shown to serve as a substrate for factor XIIIa.

Similar results were obtained with Peptide 93.2 (GEGQQHHLGGARQAGDV)(SEQ ID NO: 105). This sequence corresponds to amino acids 421-437 of human fibrin gamma-A protein except that K432 of the natural sequence has been substituted with arginine (R). This substitution conserves the overall charge of the peptide block while eliminating the primary amino group of lysine which may participate in transglutaminase activity. It retains the reactive glutamine Q424 and the flanking recognition sequences for cross-linking. The K to R substitution prevents factor XIIIa cross-linking the peptide with itself.

An additional amino acid sequence (Peptide 93.4) was designed that lacks the reactive glutamine Q424. Since this sequence block only includes fibrin gamma chain residues 429-437 (GGAKQAGDV)(SEQ ID NO: 106), it can only serve as a lysine donor to factor XIIIa mediated cross-linking.

PPAS polymers were designed to include oligopeptide blocks of human fibrin gamma chain which contain either all or part of the site of factor XIIIa cross-linking. The amino acid sequences of Peptides 93.3, 93.2, and 93.4 were incorporated within a structural backbone consisting of 3 complete repeats of a 15 amino acid peptide block of human collagen type I (GAPGTPGPQGLPGSP,(SEQ ID NO:107) the CLP3.7 monomer repeating amino acid sequence) and designated PPAS1-A, PPAS1-B, and PPAS 1-C, respectively.

A variety of structural backbones can be used in the design of adhesive polymers with the option of changing the physical properties of the polymer chain. The composition of the backbone will effect the solubility of the polymer as well as its rheological properties. CLP (collagen-like protein) polymers are useful in this respect in that they are extremely soluble in water, allowing protein solutions of greater than 10 weight percent to be formed while still maintaining good flow properties. CLP polymers have good adhesion to hydrophilic surfaces such as glass and therefore may adhere well to tissue.

The 17 amino acid fibrin block of Peptide 93.3 was integrated with the CLP3.7 monomer sequence so as to recreate its hydrophobicity and secondary structure environment matching, as closely as possible, that of human fibrin. Although, this 17 amino acid block is the C-terminal sequence of fibrin gamma chain (chain-A), a variant gamma chain (chain-B) exists in the blood which contains an additional 16 amino acids beyond the cross-linking site. Because the gamma-B chain also participates in factor XIIIa cross-linking, it follows that the 17 amino acid sequence block does not have to be C terminal for activity. Thus, it can be expected that protein polymers consisting of tandem repeats of monomer blocks containing the fibrin gamma factor XIIIa cross-linking sequence, will contain multiple, active sites of potential cross-linking. Cross-linking may occur between polymer chains and with neighboring tissue. During normal healing of the wound, the protein based adhesive will be degraded and resorbed using essentially the same mechanisms of proteolysis by which normal blood clots are dissolved. The products of degradation are peptides of essentially human sequence or amino acids which may be reutilized by the body.

The PPAS1-A amino acid monomer sequence with the fibrin gamma sequence shown in bold is as follows: ##STR64##

One oligonucleotide strand (see Table 21) was synthesized as described in Example 1. After the synthesis, the 123 base DNA fragment was deprotected and cleaved from the column support by treatment in ammonium hydroxide at 55.degree. C. for 6 hrs.

The PCR reaction was then performed as previously described using the same primers as were used in the construction of the CLP3.7 monomer. The amplified DNA was then resuspended and digested with ApaLI and DraI RENs. The digested DNA was then purified using a Probind filter followed by a Bio-Spin column and then ligated with pPT0310 previously digested with ApaLI and EcoRV RENs and purified by NACS column. The products of the ligation reaction were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and analyzed by digestion using EcoO109, HincII and HindIII RENs. Plasmid DNA from the clones showing the correct size insert was purified and analyzed by DNA sequencing. Plasmid pPT0318 contained the desired PPAS 1-A gene monomer sequence (see Table 22).

Plasmid DNA pSY1262 was linearized with PvuII REN, then passed through a Probind filter followed by a Bio-Spin column. The DNA was then treated with SAP and ligated with a DNA fragment from pQE-17 (QIAGEN Catalog #33173 ) prepared as follows. Plasmid DNA pQE-17 was digested with BgIIII and HindIII RENs and the 36 bp fragment (see Table 23) was purified using a Probind filter and then a Bio-Spin column. The DNA was purified further using a Microcon-30 filter and the filtrate containing the 36 bp was kept. The DNA was then treated with DNA Polymerase I and purified through a Probind filter and then a Bio-Spin column.

The products of the ligation reaction were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and analyzed by digestion using BstYI and Bstl1O71 RENs. Plasmid DNA from the clones showing the correct restriction pattern was purified and analyzed by DNA sequencing. Plasmid pPT0317 contained the desired DNA insert and was used for further DNA manipulations.

Plasmid DNA from pPT0318 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The PPAS1-A gene fragment, 213 bp, was excised and purified using the Ultrafree-MC filter. The purified fragment was ligated with plasmid pPT0317 which had been prepared as follows. Plasmid DNA pPT0317 was digested with BanI REN, then passed through a Probind filter and then a Bio-Spin column. The DNA was then treated with SAP.

The products of the ligation reaction were transformed into E. coli strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed using EcoRI and EcoRV RENs for the presence of PPAS 1-A multimer gene inserts. Several clones were obtained with insert sizes ranging from 200 bp to approximately 4 kb. Several clones containining from 10 to 20 repeats were chosen for use in expression of the PPAS1-A polymer.

E. coli strain HB101 containing plasmid pPT0321, pPT0325, pPT0326, or pPT0327 was cultured as previously described. The proteins produced by these cells showed strong reactive bands of apparent molecular weights ranging from 80 kD to 180 kD when analyzed by western blot for reactivity to CLP antibody. One clone, pPT0321, containing 10 repeats of the PPAS1-A monomer was selected for further study. ##STR75##

The PPAS1-B amino acid monomer sequence with the fibrin gamma sequence shown in bold is as follows: ##STR76##

Two oligonucleotide strands (see Table 24) were synthesized and purified as previously described.

These oligonucleotide strands were annealed and ligated with plasmid pPT0318 which had been digested with BstXI and AatII RENs. The products of this ligation reaction were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with NcoI and SacI RENs to determine whether they had the correct restriction pattern. Plasmid DNA from correct clones was sequenced. Plasmid pPT0320 (shown in Table 25) (SEQ ID NOS: 118 & 119) contained the desired PPAS1-B monomer sequence.

Plasmid DNA from pPT0320 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The PPAS 1-B gene fragment, 213 bp, was excised and purified using an Ultrafree-MC filter. The purified fragment was ligated with plasmid pPT0317 prepared as described above.

The products of this ligation reaction were transformed into E. coli strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed using EcoRI and EcoRV RENs for DNA inserts containing multimers of the PPAS1-B gene monomer. Several clones were obtained containing inserts up to 5 kb in size.

E. coli strain HB101 containing plasmid pPT0324, containing 10 repeats of the PPAS1-B monomer sequence, was cultured as previously described. The proteins produced by these cells were analysed by western blot for reactivity to CLP antibody. A strong reactive band was observed with an apparent molecular weight of approximately 90 kD. ##STR83##

The PPAS1-C amino acid monomer sequence with the fibrin gamma sequence shown in bold is as follows: ##STR84##

Two oligonucleotide strands (see Table 26) were synthesized and purified as previously described.

These oligonucleotide strands were annealed and ligated with plasmid pPT0310 which had been digested with ApaLI and EcoRV RENs. The products of this ligation reaction were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with BsaHI and HindIII RENs to determine their restriction pattern. Plasmid DNA from correct clones was sequenced. Plasmid pPT0319 (shown in Table 27) (SEQ ID NOS: 124 & 125) contained the desired PPASl-C gene monomer sequence.

Plasmid DNA from pPT0319 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis. The PPAS 1-C gene fragment, 192 bp, was excised and purified using an Ultrafree-MC filter. The purified fragment was ligated with plasmid pPT0317 which had been prepared as described above. The products of this ligation reaction were transformed into E. coli strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed using EcoRI and EcoRV RENs for DNA inserts containing multimers of PPAS1-C gene monomer. Several clones were obtained and one of them, pPT0322, containining an insert of approximately 2 kb, containing 10 repeats of the PPAS1-C gene monomer, was chosen for expression analysis.

E. coli strain HBO1 containing plasmid pPT0322 was cultured as previously described. The proteins produced by these cells were analysed by western blot reactivity with CLP antibody. A strong reactive band was observed with an apparent molecular weight of approximately 80 kD. ##STR91##

The PPAS1-D amino acid monomer sequence with the fibrin gamma POLSITE sequence shown in bold is as follows: ##STR92##

One oligonucleotide strand coding for the POLSITE portion of the gene monomer (see Table 28) was synthesized as previously described. After the synthesis, the 126 base DNA strand was deprotected and cleaved from the column support by treatment in ammonium hydroxide at 55.degree. C. for 6 hrs.

The PCR reaction was then performed as previously described using the same primers as were used in the construction of the CLP3.7 monomer. The DNA was resuspended and digested with DralII and HincII RENs and the digested DNA was purified using a Probind filter followed by a Bio-Spin column and then ligated with pPT0320 previously digested with DraIII and HincII RENs and purified with a Probind filter followed by a Bio-Spin column. The products of the ligation reaction were transformed into E. coli strain HB101. Plasmid DNA from transformants was purified and digested with NlaIII and plasmids giving the correct restriction pattern were sequenced. A plasmid containing the desired PPASl-D monomer sequence, pPT0328, (see Table 29) (SEQ ID NOS: 129 & 130) was used for further DNA constructions.

ppPT0328 plasmid DNA containing the gene monomer coding for PPAS1-D is digested with BanI REN and the digestion fragments are separated by agarose gel electrophoresis. The PPAS1-D gene fragment, 219 bp, is excised and purified using an Ultrafree-MC filter. The purified fragment is ligated with plasmid pPT0317 prepared as described above. The products of this ligation reaction are transformed into E. coli strain HB101. Transformants are selected for resistance to kanamycin. Plasmid DNA from individual transformants is purified and analyzed using EcoRI and EcoRV RENs for DNA inserts containing multimers of the PPAS 1-D gene monomer. An approriate clone containing a DNA insert from 1 to 4 kb is analyzed for PPAS1-D polymer expression. ##STR99## Where n=2-20

E. coli strain PPT0321 containing the PPAS1-A polymer gene was produced by fermentation. The product was purified from the cellular biomass by means of cellular lysis, clearance of insoluble debris by centrifugation, and affinity chromatography. The purified product was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, immunoreactivity with CLP antibody, and amino acid analysis. A protein band of apparent molecular weight 85,000 was observed by amido black staining of SDS-PAGE separated and transferred samples and the same band reacted with the CLP antibody on western blots. As expected, amino acid analysis indicated that the product was enriched for the amino acids glycine (34.3%), alanine (7.3%), proline (28.5%), and glutamine (7.0%). The amino acid composition (see Table 30) shows the correlation between the composition of the purified product and the expected theoretical composition as deduced from the synthetic gene sequence.

Purified PPAS 1-A was analyzed for its ability to serve as a substrate for the blood Clotting enzyme, factor XIIIa. The data indicated that PPAS1-A serves as a substrate for the blood clotting factor XIIIa. By incorporating the fibrin oligopeptide block containing the active glutamine residue within the PPAS -A chain, synthetic protein substrate for factor XIIIa was created. In the presence of BAPA or other compounds such as proteins which contain a reactive primary amino group equivalent to lysine, factor XIIIa will cause the lige of such compounds with PPAS 1-A. The activity of such polymers and factor XIIIa has utility as an adhesive, sealant, or bonding agent. They may be used in the creation of cross-linked hydrogel materials which can encapsulate live cells, tissues or organs. They may be used to incorporate small molecules or active agents to proteins through nonhydrolyzing but proteolytically susceptible linkages. This chemistry can be used to attach pharmaceuticals to resorbable protein matrices for use in drug delivery.

Plasmid DNA pPT0312 was linearized with PvuII REN, then passed through a Millipore Probind f ilter . The DNA was then t reat ed w ith SA P. The linearized pPT0312 DNA was then ligated with a DNA f ragment from pQE-17 as described above.

The products of the ligation reaction were transformed into E. coli strain HB1t1. Plasmid DNA from transformants was purified and analyzed by digestion using Bst1107I and EcoRV RENs. Clones containing the de sired DNA fragment were further digested with Bstl 1071 and BstYI RENs to determine the orientation of the insert. Plasmid DNA from the clones showing the correct restriction pattern was purified and an alyzed by DNA sequencing. Plasmid pPT337 contained the desired DNA insert a nd w as used for further DNA manipulation.

Plasmid DNA pbPT0337 wa s digested with XcmI REN, followed by Mung Bean Nuclease treatment for 30 min. at 37.degree. C. The DNA was then purified using Probind and Biospin and then treated with SAP followed by Probind and Biospin column purification.

The PCR amplified DNA, coding for the PPAS1-A (Table 22), was digested with ApaLI and BglII RENs, the fragments were purified by agarose gel electrophoresis followed by Ultrafree MC gel purification. The DNA was then treated with DNA Polymerase I Klenow fragment and then purified using a Probind column followed by a Biospin column as described previously. The DNA was then ligated with pPT0337.

The products of the ligation reaction were transformed into E coli strain HB101. Plasmid DNA from transformants was purified and analyzed by digestion using EcoRI and Dral RENs. Plasmid pPT0334 contained the desired insert and was used for subsequent constructions.

pThe PCR amplified DNA coding for PPAS 1-A was again digested with EcoRV REN, then the enzyme was removed with a Probind column followed by treatment with BsaJI REN, then purified by Probind and Biospin columns and concentrated in vacuo. The DNA was treated with DNA Polymerase Klenow fragment followed by Probind column purification, then the DNA fragments were purified by agarose gel electrophoresis followed by Ultrafree MC gel purification, and then concentrated in vacuo followed by Biospin column purification. The DNA was then ligated with plasmid DNA pPT0334 previously digested with EcoRV REN followed by Probind and Biospin columns and then treated with SAP followed by Probind and Biospin columns.

The products of the ligation reaction were transformed into E.coli strain HB101. Plasmid DNA from transformants was purified and analyzed by digestion using BstXI REN. The clones containing the desired DNA fragment were further digested with AccI and EcoRV RENs to determine the orientation of the insert. Plasmid pPT0338 contained the DNA fragment in the correct orientation and was used for subsequent constructions.

Plasmid DNA pPT0338 was digested with BanI REN and the digestion fragments were separated by agarose gel electrophoresis, the DNA was excised and self-ligated. The products of the ligation mixture were transformed into E coli strain HB101. Plasmid DNA from transformants was purified and analyzed by digestion using BamRI and Bst1107I RENs. Plasmid pPT339 contained the desired deletion and was used for subsequent constructions.

Plasmid DNA pPT0339 was digested with BanI REN, followed by Probind and Biospin columns and then treated with SAP followed by Probind and Biospin columns. The plasmid DNA so treated was ligated with the CLP gene fragments from pPT0312. Plasmid DNA pPT0312 was digested with BanI REN and the CLP gene fragments purified by agarose gel electrophoresis followed by NACS and Biospin columns.

The products of this ligation reaction were transformed into E. coli strain HB101. Transformants were selected for resistance to kanamycin. Plasmid DNA from individual transformants was purified and analyzed for DNA inserts containing multimers of PPAS1-F gene monomers. Several clones were obtained and one of them (pPT0348) containing an insert of approximately 2.2 kb (12 repeats of the CLP 3.7 gene monomer) was chosen for expression analysis.

An overnight culture of E. coli strain HB101 containing plasmid pPT0348 was grown as previously described. The proteins produced by these cells were analysed by western blot reactivity with anti-CLP antibody. A strong reactive band was observed with an apparent molecular weight of approximately 94 kD. The expected amino acid sequence of the PPAS1-F polymer encoded by plasmid pPT0348 is shown below. ##STR100##

The fibrin gamma chain sequence is shown in bold.PPAS I-F was determined to be a substrate for Factor XIIIa and can be used in crosslinking reactions with suitable amine donors.

As is evident from the above results, highly repetitive sequences can be prepared, cloned, and used for expression of high molecular weight collagen-like polymers to produce a wide variety of products which may mimic the properties of naturally occurring products, as well as comprise novel properties. In the high molecular weight collagen-like polymers according to the subject invention, specific amino-acid sequences may be made readily available to the environment, while providing for structural or non-structural capabilities such as fiber, film, and membrane formation, emulsions, coatings, etc. The subject high molecular weight collagen like polymer may be comprised of strands which interact to provide for structural characteristics, such as article formation with good mechanical, e.g., tensile properties, while at the same time providing for amino acid sequences which may be used in a wide variety of biological and chemical applications. By designing recombinant synthetic collagen-like polymers to comprise less than 45 number percent prolines, a variety of useful collagen-like polymers may be formed having properties similar to collagen, but enjoying unique characteristics. The products find use as films, fibers, molded objects, admixed with other natural or synthetic polymers or coatings on fibers, films, labware or other surfaces, e.g., prosthetic devices, and the like. The subject compositions may be used for binding a wide variety of specific binding materials, as catalytic substances, where the amino acid sequence may specifically chelate a wide variety of elements, as purification media, as composites, laminates, adhesives, combined with inorganic or organic materials, such as carbon fibers, nylon fibers, nitrocellulose, etc., as flask coatings or in synthetic matrices for the growth and study of cells, as affinity columns, as supports for biological materials, and the like.

All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

The invention now being fully described, it will be apparent to one of ordinary in the art that many changes and modifications can be made thereto without ting from the spirit or scope of the appended claims.