Thermostable DNA polymerase from Bacillus pallidus

Abstract: A novel Type I DNA polymerase derived from Bacillus pallidus is provided. The gene encoding the polymerase has been cloned and expressed. Characterization of the enzyme revealed, in addition to DNA polymerase activity, 5'-3' exonuclease activity, reverse transcriptase activity, strand displacing activity and the ability to initiate polymerization at a nick in double-stranded DNA. In certain constructs the domain encoding the 5'-3' exonuclease activity is deleted to provide an enzyme which is particularly useful for Strand Displacement Amplification. Anti- Bacillus pallidus Polymerase I antibodies and methods of using the antibodies are also provided.

Description: FIELD OF THE INVENTION The invention relates to DNA polymerases, genes coding for DNA polymerases, production of recombinant DNA polymerases. Also provided are antibodies to DNA polymerases and methods of using these antibodies BACKGROUND OF THE INVENTION Type I DNA polymerases (Pol I) are ubiquitous enzymes in Eubacteria. They are multifunctional/multidomain enzymes which appear to be involved in DNA repair and DNA replication. The E. coli Pol I, and most other Type I DNA polymerases characterized to date, have three enzymatic activities: DNA polymerization (5'-3'), 3'-5' exonuclease activity and 5'-3' exonuclease activity. Each of these activities has been localized to a particular region or domain of the protein. In E. coli Pol I, the N-terminal domain (amino acids 1-324) encodes the 5'-3' exonuclease activity, the central domain (amino acids 324-517) encodes the 3'-5' exonuclease activity and the C-terminal domain (amino acids 521-928) encodes the DNA polymerase activity. When E. coli Pol I is cleaved into two fragments by subtilisin digestion, the larger fragment (Klenow fragment) has 3'-5' exonuclease and DNA polymerase activities and the smaller fragment has 5'-3' exonuclease activity. DNA polymerase I has been isolated, cloned and sequenced from several eubacterial species, including Streptococcus pneumoniae (A. Diaz, et al. 1992. J. Bacteriol. 174:2014-2024), Bacillus stearothermophilus (S-M. Phang, et al. 1995. Gene 163:65-68 and WO 95/27067), Bacillus caldotenax (T. Uemori, et al. 1993. J. Biochem. 113:401-410), and Thermus aquaticus (Lawyer et al. 1993. PCR Methods and Applications. 2:275-287). The temperature optimum for activity of the E. coli and S. pneumoniae Pol I enzymes is about 37°C, i.e., they are mesophilic. In contrast, the polymerases of bacteria with higher temperature tolerance have higher temperature optima - about 60-70°C for the Bacillus species and about 80°C for T. aquaticus . These polymerases are thermophilic and may be useful at the temperatures of PCR and thermophilic SDA. Alignment of the amino acid sequences of DNA polymerase I from eubacterial and bacteriophage sources has shown conserved motifs in both the 5'-3' exonuclease domain and the DNA polymerase domain. These conserved sequences typically represent amino acids which are important for the structure and/or function of the enzyme. Based on knowledge of conserved sequences, "Klenow-like" forms of the polymerases of species other than E. coli (i.e., forms lacking the 5'-3' exonuclease activity) have also been reported. Absence of 5'-3' exonuclease activity is particularly important for use of the polymerases in Strand Displacement Amplification (SDA - G. T. Walker, et al. 1992. Proc. Natl. Acad. Sci. USA 89 , 392-396; G. T. Walker, et al. 1992. Nuc. Acids. Res. 20 , 1691-1696; U.S. Patent No. 5,455,166; U.S. Patent No. 5,270,184; EP 0 684 315), as the SDA polymerase must lack 5'-3' exonuclease activity, either naturally or by genetic manipulation, to prevent digestion of the strand downstream of the nick. For SDA, the polymerase must also incorporate the derivatized deoxynucleoside triphosphates (dNTPs) required for amplification (nucleotide analogs such as αthio-dNTPs) and displace a downsteam single strand from a double stranded molecule starting at a single stranded nick. It is also desirable, but not required, that the polymerase be capable of incorporating dUTP to allow amplicon decontamination. SUMMARY OF THE INVENTION A novel DNA polymerase I has been identified in Bacillus pallidus (Bpa Pol I) and the gene encoding this Pol I has been cloned, sequenced and expressed to produce the polymerase. The full-length wild-type enzyme has thermophilic DNA polymerase activity and thermophilic 5'-3' exonuclease activity. A Klenow-like deletion which inactivates the 5'-3' exonuclease activity has been constructed and expressed to produce a polymerase which is particularly useful in SDA. Bpa Pol I may also be used to immunize animals for production of antibodies which bind to Bpa Pol I. The specific subject-matter of the invention is indicated in the appended claims. DETAILED DESCRIPTION OF THE INVENTION Initially, the "Klenow-like" fragment of Bpa Pol was cloned using multiple sequence alignments of DNA Pol I genes of other species available in the GenBank sequence database to design degenerate PCR primers based on relatively conserved sequences within the 5'-3' exonuclease domain and at the C-terminal end of the polymerase gene. The primers were designed to include restriction enzyme recognition sites which allowed cloning and expression of amplification products in the pBLUESCRIPT plasmid (Stratagene). The forward primer was designed based on alignment of the B. caldotenax , B. stearothermophilus , E. coli and S. pneumoniae Pol I genes. The reverse primer was designed based on alignment of the B. caldotenax, B. stearothermophilus and S. pneumoniae Pol I genes. Two gene sequences for B. stearothermophilus were listed in GenBank, and both were used in the sequence alignments. The degenerate PCR primers were as follows: Bacillus pallidus (ATCC#51176) was grown in the ATCC recommended culture medium at 55°C and the genomic DNA was isolated using conventional techniques. Using the degenerate primers SEQ ID NO: 1 and SEQ ID NO:2, a 2 Kb segment of the genome was amplified. This segment was cloned in the pBLUESCRIPT vector and transformed into E. coli. The gene product was expressed in the transformants by induction with IPTG as recommended by the manufacturer of the cloning vector. Cell-free lysates were prepared and assayed for polymerase activity by incorporation of 32 P-labeled nucleotides into activated calf thymus DNA (Pharmacia), as follows. The polymerase was serially diluted at room temperature in freshly prepared enzyme diluent (25 mM K i PO 4 pH 7.5, 50 mM ammonium sulfate, 10 mM 2-mercaptoethanol, 1 mg/ml BSA) and mixed on a vortex mixer. Ninety µL of reaction buffer (25 mM K i PO 4 pH 7.5, 0.15 mM each dNTP, 4 mM MgCl 2 , 4.5 µg/reaction activated calf thymus DNA, 0.3 mg/reaction activated calf thymus DNA, 0.3 µL per reaction 3000 mCu/mmol α 32 -P-dCTP) was added to each reaction tube and prewarmed for 5 minutes at the selected reaction temperature. After prewarming, 10 µL of the polymerase dilution was added and mixed on a vortex mixer. Blank reactions had only 10 µL of the enzyme diluent added. The reactions were incubated for 15 minutes at the selected reaction temperature, removing 15 µL aliquots at 2, 5, 10 and 15 minutes and adding them to 45 µL of 25 mM EDTA to stop the reaction. Similar time points were taken from the blank control. After all time points were taken, 40 µL of the terminated reaction was spotted onto a DE-81 filter disk (representing 10 µL of the original reaction). The filters were washed at least four times in 0.3 M ammonium formate pH 8.0 (5 minutes each wash) using 10 mL per filter. Washing was performed by dropping the spotted filter into a beaker of ammonium formate and agitating gently every 2-3 minutes The waste was decanted and additional aliquots of the wash buffer were poured onto the filters. Following the last wash the filters were rinsed in methanol and placed on Whatman paper to dry for about 5 minutes. The filters were then placed in scintillation vials and counted. An increase in radioactivity retained by the filter indicated that the recombinant expression product of the transformant exhibited polymerase activity. Polymerase activity, wherein one unit (U) is defined as the amount required to incorporate 10 nmole of total nucleotide into acid insoluble form in 30 min., was calculated according to the following equation: U/mL = (net cpm) (nmole/cpm) (1 u/10 nmole) (100% dNTP/x%dXTP) (1/0.01 mL enz added) (dilution factor) wherein net cpm = total cpm incorporated at 30 min. point for total reaction, e.g., for the 100 µL reactions described above after 30 min., net cpm = (time point cpm) (10 µLcounted) (30 min./10 min. time point) nmole/cpm = specific activity of reaction 100% dNTP/x% dXTP = the ratio of total nucleotides to %G or C, or the ratio of total nucleotides to %A or T in the template DNA. Calf thymus DNA is about 22% G or C and 28% A or T. The value selected corresponds to the 32 -P labeled nucleotide employed. Specific activity of the reaction was typically determined by spotting 5 µL of the blank reaction (90 µL buffer mix + 10 µL enzyme diluent) onto each of three DE-81 filters, counting the filters and obtaining the average cpm. Specific activity was calculated as (5 µL)(0.15 nmoles)/average cpm = nmole/cpm. For example, the unit activity of a thermophilic polymerase was calculated as follows. The polymerase was assayed as described above using 10 µL of a 1:5000 dilution and 10 µL of a 1:10,000 dilution and α 32 P-dATP. Three time points were taken (5 minutes, 10 minutes and 15 minutes) and background counts on the filters as well as blank control reactions were included. The average background count on three filters was 1442 cpm. The average cpm of the blank control (2 µL spotted on each of two filters) was 240,536 cpm, resulting in a specific activity of 1.24x10 -6 nmole/cpm. Units/mL were calculated for each time point of each dilution. As an example, U/mL for the 5 minute time point of the 1:5000 dilution was calculated as follows: net cpm = (3714 cpm-1442 cpm)(10 µL)(30 min./5 min.) = 134,820 net cpm; U/mL = 134,820 net cpm (1.24x10 -6 nm/cpm)(0.1 U/nm)(3.57)(100)(5000) = 29,841. Units/mL for each time point were averaged for each dilution. The dilution averages were averaged to obtain a combined average U/mL. In this example, the combined average was 26,494 U/mL To simplify purification of the recombinant polymerase and to obtain higher expression levels, the amplified fragment was recloned into the pMAL-c plasmid (New England BioLabs) as recommended by the manufacturer. These constructs placed the large fragment of the Bpa polymerase under the control of the lac promoter of E. coli . Upon induction with IPTG, transformed host cells expressed a fusion product which contained the large fragment of Bpa Pol I fused to the maltose binding protein (MBP, the malE gene product). The coding sequence for this clone (clone MBP/Bpa-192) is shown in SEQ ID NO:5, wherein nucleotides 1-3237 code for the MBP/Bpa fusion protein and nucleotides 3238-3255 code for a polyhistidine affinity purification tag. The MBP portion of the fusion protein allows purification of the expression product on amylose resin. The MBP/Bpa Pol I fusion protein had a molecular weight of about 117 Kd and was expressed as about 5-10% of total cell protein. The deduced amino acid sequence of the fusion protein is shown in SEQ ID NO:6, amino acids 1-1078. The MBP/Bpa Pol I fusion protein was purified on amylose resin according to the protocol recommended by New England BioLabs. A temperature profile in the DNA polymerase activity assay showed activity between about 30°C and about 75°C with optimal activity at about 65°C. In a primer extension assay in which two adjacent primers were hybridized to a target sequence to stage a "nick", the polymerase was shown to be capable of initiating synthesis from a nick and displacing a downstream primer, indicating utility in SDA. Amplification was demonstrated in a thermophilic SDA reaction (EP 0 684 315), confirming strand displacing ability, the absence of 5'-3' exonuclease activity and an ability to incorporate dNTP analogs. The fewest number of initial targets tested for amplification (1,000) was detectable in the SDA reaction with 3 units of Bpa Pol I and 80 units of BsoBI. A unit of Bpa Pol I activity was defined in the 32 P-incorporation assay described above and corresponds to the amount of polymerase which incorporates 10 nM of nucleotide in 30 min. Reverse transcriptase activity in the presence of Mn 2+ was demonstrated in an assay in which the polymerase extended a DNA primer annealed to an RNA template. To isolate the full-length genomic copy of the Bpa Pol I gene, a genomic library of B. pallidus DNA was constructed by cloning genomic DNA digested with BclI into a λZAP vector (Stratagene). The library was screened by hybridization to the Bpa Pol I PCR product and a 5.8 Kb DNA fragment containing the Bpa Pol I gene was identified and isolated. The DNA sequence of this fragment was determined by conventional sequencing techniques and was found to contain the full-length coding sequence for Bpa Pol I as well as two open reading frames upstream from the Bpa Pol I gene and two open reading frames downstream from the Bpa Pol I gene. The coding sequence for the full-length Bpa Pol I is shown in SEQ ID NO:3 and the deduced amino acid sequence of the full-length polymerase encoded by SEQ ID NO:3 is shown in SEQ ID NO:4. The large fragment initially cloned, in which the 5'-3' exonuclease domain is deleted, corresponds to amino acids 192-876 of SEQ ID NO:4 and is encoded by nucleotides 574-2628 of SEQ ID NO:3. Amino acid sequence comparison revealed 68% similarity to Bst polymerase (B. strearothermophilus , Riggs et al. 1995) and 67% similarity to Bca polymerase ( B. caldotenax, Uemori et al. 1993). The full-length Bpa Pol I gene was cloned into pMAL-c to produce a MBP fusion protein. This clone was designated MBP/Bpa-1 and was shown to express thermophilic DNA polymerase activity and thermophilic 5'-3' exonuclease activity in the assays previously described. MBP/Bpa-1 expresses the nucleic acid sequence shown in SEQ ID NO:7 to produce Bpa Pol I having the amino acid sequence shown in SEQ ID NO:8. Nucleotides 1-3810 of SEQ ID NO:7 code for the MBP/Bpa fusion protein and nucleotides 3811-3828 code for a polyhistidine affinity purification tag. In SEQ ID NO:8, amino acids 1-1270 represent the MBP/Bpa fusion protein and amino acids 1271-1276 are the added polyhistidine affinity purification tag. In addition, the large fragment with the 5'-3' exonuclease domain deleted was subcloned into plasmid pTRC99A (Pharmacia) without the MBP purification tag. This clone, designated pTRC/Bpa1 was deposited under the Budapest Treaty with the American Type Culture Collection, Rockville, Maryland, as ATCC Accession No. 98160 on August 30, 1996. The large fragment may be derived from the deposited full-length clone using conventional methods for genetic manipulation such as in vitro mutagenesis and cloning. Expression of the polymerase in pTRC/Bpa1 produced an unfused polymerase protein which was tested in SDA as previously described. The polymerase supported amplification, confirming that the 5'-3' exo- activity was inactive and that the unfused polymerase possessed the other activities required for SDA (strand displacing activity, initiation at a nick and incorporation of modified dNTPs). When no affinity purification tag is present the polymerase protein may be purified, for example, as follows. E. coli cells expressing recombinant Bpa Pol I (about 1.28 g of cell paste) were isolated from the culture medium and resuspended in 3 mL of lysis buffer (20 mM imidazole-HCl pH 6.94, 0.2 M KCl, 10% glycerol (w/v), 0.5 mM Na 2 EDTA, 1 mM DTT) and the cell clumps were broken up using a pipette. The cell suspension was sonicated for 10 minutes in 20 second bursts to lyse the cells and centrifuged to remove cell debris. Of course, when a secretory expression system for the recombinant polymerase is employed lysis of the cells is not necessary. In these systems the cells are separated from the culture medium and the culture medium rather than a cell lysate is processed according to the following protocol to isolate the polymerase. The supernatant of the centrifuged cell lysate was then heated at 55°C for 15 min. in a water bath and centrifuged 15 min. in a microcentrifuge to pellet the denatured proteins. Solid ammonium sulfate was added to the supernatant to 25% saturation. The sample was incubated with gentle agitation at 4°C for 15 min. and microcentrifuged in the cold for 15 min. The supernatant was removed to a new microcentrfuge tube and lysis buffer saturated with ammonium sulfate was added to give the desired % saturation, followed by gentle agitation for 15 min and centrifugation as before. The ammonium sulfate cuts taken were 35%, 45%, 55% and 65% saturation. The pellets of all ammonium sulfate cuts were quick-frozen in a dry ice-ethanol bath and stored at -76°C while polymerase activity assays as described above were performed on samples taken from the lysis and fractionation steps to evaluate the efficiency of the purification process. The 65% ammonium sulfate saturated supernatant was stored on ice during the polymerase assays. The polymerase activity present in the crude cell extract was stable through the heat treatment, with about 86% of total activity recovered and a 75% reduction in the total protein concentration as estimated by UV absorbance measurements. This corresponds to at least a 3-fold enrichment of the Bpa polymerase in a single simple step. Bpa Pol I appeared to be resistant to precipitation by ammonium sulfate. Most of the activity remained in the 65% saturated supernatant, although about 20% did precipitate and was recovered in the 55% and 65% pellets. Either method may therefore be employed at this step of the purification process, i.e., recovering the polymerase in the pellet at 55% ammonium sulfate or higher, or recovering the polymerase in the supernatant of about a 50-55% ammonium sulfate cut. The pooled 65% ammonium sulfate supernatant and the resuspended 55% and 65% ammonium sulfate pellets were dialyzed for 4 hours against 750 volumes of Buffer A, diluted 5-fold in 20 mM imidazole-HCl pH 6.94, 20 mM KCl, 10% glycerol (w/v), 0.5 mM Na 2 EDTA, 1 mM DTT (Buffer A) and loaded at a flow rate of 0.25 mL/min. onto a DEAE cellulose column equilibrated in Buffer A. After sample loading, Buffer A flow was continued at 0.25 mL/min. until UV monitoring of the fluid exiting the column indicated protein was present. At this point, collection of 1 mL fractions was begun and the flow rate was increased to 1 mL/min. The column was washed with Buffer A for 20 min. at this flow rate. A linear gradient (60 mL total gradient volume) from Buffer A to Buffer B (Buffer A + 1 M KCl) was initiated . At the end of the gradient, Buffer B was continued for 20 min., then a linear gradient of Buffer B to Buffer A was initiated (20 mL total gradient volume). At the end of the second gradient, the column was washed with Buffer A for 20 min. The collected fractions were stored at 4°C until assayed for protein on 10% polyacrylamide, 0.1% SDS gels with 4% stacking gels and assayed for polymerase activity as described above. Polymerase activity eluted at about 0.3 M KCI, correlating with one of the absorbing peaks of the UV absorbance trace. There was about a two-fold concentration of activity when compared to the volume of sample loaded on the column. Photography of polyacrylamide gels stained with 30% methanol, 10% acetic acid, 0.05% Coomassie Brilliant Blue R-250 and destained in 30% methanol, 10% acetic acid showed that the protein was about 50% pure. The polymerase migrated slightly below the 68kd marker, consistent with its predicted size. The active fractions from the DEAE-cellulose column were pooled and dialyzed against KKEGD buffer (20 mM K 2 PO 4 pH 7.4, 20 mM KCl, 10% glycerol (w/v), 1 mM DTT, 0.5 mM Na 2 EDTA) for 4 hr. at 4°C. One mL of the dialyzed DEAE pool was diluted with 1 mL of KKEGD buffer and injected into a HITRAP Heparin column (Pharmacia) equilibrated with 20 mL of KKEGD buffer. Buffer flow was initiated at 0.25 mL/min. until UV absorbing material was detected in the eluate. The flow rate was then increased to 0.5 mL/min. and the column was washed for 10 min. with KKEGD buffer. A linear gradient from KKEGD to KKEGD, 1 M KCl was initiated (10 mL total gradient volume) and 0.5 mL fractions were collected. At the end of the gradient the KKEGD, 1 M KCl wash was continued for 10 min. and a linear gradient from KKEGD, 1 M KCl to KKEGD was initiated (5 mL total gradient volume). At the end of the gradient the column was washed with KKEGD for 10 min.. The collected fractions were stored at 4°C until assayed for protein and polymerase activity. The UV absorbance profile showed only a single peak. Analysis on polyacrylamide gels indicated the polymerase was greater than 90% pure after heparin column chromatography. The fractions containing the highest levels of polymerase activity were pooled, concentrated and exchanged into KKEGD buffer by CENTRICON-30 ultrafiltration. The unit concentration of the purified stock was about 38,000 units/mL and the total protein concentration was about 0.6 mg/mL based on a Bradford assay. Yield was about 30 µg from one third of the DEAE active pool. The yield per gram of cells was therefore calculated to be about 70 µg, i.e., about 1 mg of protein per 14 g of cells. The estimated specific activity of this prep was 63,000 units/mg of protein. It will be apparent from the foregoing description of the invention that several modifications are possible. First, the MBP affinity purification tag may be linked to either the N-terminus or the C-terminus of Bpa Pol I. Histidine residues (poly-histidine) added at the C-terminus or the N-terminus provide a heterologous amino acid sequence which is useful for purification of the polymerase by immobilized metal affinity chromatography (IMAC, e.g., nickel). The heterologous amino acids in the fusion protein do not adversely affect polymerase activity. Further, two heterologous sequences (e.g., two affinity purification tags) may be linked to the polymerase (one at each end), if desired, without significant adverse effects on polymerase activity. Additional alternative heterologous amino acid sequences are known in the art and may be linked to Bpa Pol I by conventional methods to produce various fusion proteins. Materials and methods for linking heterologous coding sequences such as affinity purification tags to the ends of the Bpa Pol I coding sequence and expression of the fusion proteins are well known in the art, as are methods for affinity purification of the fusion protein when the heterologous sequence is an affinity purification tag. Further, due to degeneracy of the genetic code, different but equivalent nucleotide sequences which code for the Bpa Pol I enzyme of the invention (e.g., as shown in SEQ ID NO:4, amino acids 192-876 of SEQ ID NO:4, SEQ ID NO:6 or SEQ ID NO:8) may be isolated or prepared without the exercise of inventive skill. Such degenerate coding sequences are included within the scope of the invention. It is also within the ordinary skill in the art to clone DNA fragments encoding the Bpa Pol I of the invention into a variety of cloning vectors and to express the recombinant Bpa Pol I protein under the control of a promoter in a variety of transformed prokaryotic and eukaryotic host cells. Extensive amino acid sequence analyses of prior art polymerase I enzymes have revealed highly conserved motifs. These motifs are known to correspond to regions of the protein required for the various activities. See, for example, L. Blanco, et al. 1991. Gene 100:27-38; M. Delarue, et al. 1990. Prot. Eng. 3:461-467; P. Gutman and K. Minton. 1993. Nucl. Acids Res. 21:4406-4407. By comparing the amino acid sequence of the Bpa Pol I of the invention to the teachings of these publications and others, it will be possible to identify the corresponding conserved motifs in the inventive polymerase. Amino acid substitutions in the regions of the protein outside the conserved motifs, particularly conservative amino acid substitutions, would be expected to have little if any effect on the biological activity of the polymerase. One skilled in the art would therefore expect that conservative (and certain non-conservative) amino acid substitutions in regions outside the conserved motifs would result in a Bpa Pol I variant which is substantially equivalent to the enzyme having the specific amino acid sequences herein disclosed. Such minor sequence variations are exemplified, but not limited to, the variant C-terminal sequences of SEQ ID NOs:6 and 8, where the amino acid sequence was altered in making the linkage to the histidine affinity purification tag. These variant Bpa Pol I polymerases and the nucleic acid sequences which encode them are considered to be substantial equivalents of the Bpa Pol I of the invention and are intended to be included within its scope. Monoclonal and polyclonal antibodies which recognize and bind to Bpa Pol I may be prepared using the Bpa Pol I of the invention. Polyclonal antibodies are generally produced by immunizing animals with an enriched or purified preparation of Bpa Pol I according to conventional protocols. The preferred antigen for immunization is a preparation of isolated or purified Bpa Pol I, but crude extracts may also be used. Isolated recombinant Bpa Pol I is the preferred antigen for immunization. The serum of animals thus immunized contains the polyclonal anti-Bpa Pol I antibodies, and the immune serum is often used directly in immunoassays. In this case, the anti-Bpa Pol I polyclonal antibodies are isolated in serum by separating the serum from red blood cells and other cellular components of blood. Monoclonal antibodies which recognize the Bpa Pol I of the invention may be prepared using the methods of Kohler and Milstein (1975 . Nature 256:495). Mice may be immunized with the Bpa Pol I antigen preparation, the spleen cells fused and the resulting hybridomas screened in enzyme-linked immunosorbent assays (ELISAs) or immunoblots for reactivity with the immunogen. Hybridomas secreting antibodies of interest are typically subcloned. The monoclonal antibody may be then be produced by culturing the hybridoma or in ascites in pristane-primed Balb/C mice. It is then typically isolated from the culture medium or ascites by chromatography on Protein A-Sepharose (Sigma Chemical Co., St. Louis, MO). Alternatively, Bpa Pol I may be coupled to a solid phase and used to purify polyclonal or monoclonal antibodies by affinity chromatography. Using these methods, a variety of hybridomas which produce anti-Bpa Pol I monoclonal antibodies may be identified. Monoclonal antibodies are preferred for immunoassays due to their improved specificity and affinity for the antigen to be detected. Anti-Bpa Pol I monoclonal antibodies which recognize different epitopes on the protein may also be useful in studies to evaluate protein structure and function. Anti-Bpa Pol I antibodies as described above, preferably monoclonal antibodies, may also be coupled to Protein A-Sepharose as is known in the art for use in affinity purification of naturally-occurring or recombinant Bpa Pol I. SEQUENCE LISTING: (1) GENERAL INFORMATION: (i) APPLICANT: BECTON, DICKINSON AND COMPANY (A) NAME: BECTON, DICKINSON AND COMPANY (B) STREET: 1 Becton Drive (C) CITY: Franklin Lakes (D) STATE: New Jersey (E) COUNTRY: USA (F) ZIP: 07417 (ii) TITLE OF INVENTION: THERMOSTABLE DNA POLYMERASE FROM BACILLUS PALLIDUS (iii) NUMBER OF SEQUENCES: 8 (iv) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: PatentIn Release #1.0, Version #1.30 (v) CURRENT APPLICATION DATA: (A) APPLICATION NUMBER: (B) FILING DATE: (C) CLASSIFICATION: (2) INFORMATION FOR SEQ ID NO:1: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 39 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: (2) INFORMATION FOR SEQ ID NO:3: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2631 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 1..2628 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: (2) INFORMATION FOR SEQ ID NO:4: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 876 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: (2) INFORMATION FOR SEQ ID NO:5 (i) SEQUENCE CHARACTERISTICS; (A) LENGTH: 3255 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 1..3252 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: (2) INFORMATION FOR SEQ ID NO:6: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1084 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: (2) INFORMATION FOR SEQ ID NO:7: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 3831 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 1..3828 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: (2) INFORMATION FOR SEQ ID NO:8: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1276 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:

Claims: An isolated nucleic acid sequence selected from the group consisting of nucleic acid sequences encoding SEQ ID NO:4, nucleic acid sequences encoding amino acids 192-876 of SEQ ID NO:4, SEQ ID NO:3, nucleotides 574-2628 of SEQ ID NO:3, SEQ ID NO:5, nucleotides 1-3237 of SEQ ID NO:5, nucleic acid sequences encoding amino acids 1-1078 of SEQ ID NO:6, SEQ ID NO:7, nucleotides 1-3810 of SEQ ID NO:7, and nucleic acid sequences encoding amino acids 1-1270 of SEQ ID NO:8. A recombinant vector comprising a nucleic acid sequence according to Claim 1. The recombinant vector of Claim 2 wherein the nucleic acid sequence is linked to a nucleic acid sequence encoding a heterologous amino acid sequence. A host cell transformed with the recombinant vector of Claim 2. A method for producing a recombinant DNA polymerase comprising culturing the transformed host cell of Claim 4 in a culture medium under conditions whereby the recombinant DNA polymerase is expressed by the transformed host cell. The method of Claim 5 further comprising purifying the expressed recombinant DNA polymerase from a cell lysate or the culture medium. An isolated DNA polymerase selected from the group consisting of SEQ ID NO:4, amino acids 192-876 of SEQ ID NO:4, fusion proteins comprising SEQ ID NO:4, and fusion proteins comprising amino acids 192-876 of SEQ ID NO:4. The DNA polymerase of Claim 7 wherein the fusion protein is SEQ ID NO:6 or SEQ ID NO:8. A method of making a recombinant vector for expression of a DNA polymerase in a transformed host cell comprising cloning a nucleic acid sequence selected from the group consisting of SEQ ID NO:3, nucleotides 574-2628 of SEQ ID NO:3, nucleic acid sequences encoding SEQ ID NO:4 and nucleic acid sequences encoding amino acids 192-876 of SEQ ID NO:4 into an expression vector under control of a promoter such that the polymerase is expressible in the transformed host cell. The method of Claim 9 further comprising linking the nucleic acid sequence in the vector to a nucleic acid sequence encoding a heterologous amino acid sequence such that expression of the polymerase produces a fusion protein. An isolated anti-Bpa Pol I antibody, said Bpa Pol I having the amino acid sequence of any of the polymerases of claims 7. A hybridoma which produces an anti-Bpa Pol I antibody, said Bpa Pol I having the amino acid sequence of any of the polymerases of claims 7.

Inventors: HAMILTON PAUL T, HAMILTON, PAUL T.
Applicants: BECTON DICKINSON CO, BECTON, DICKINSON AND COMPANY
Application year: 1997
Main classification: C12N15
IPC codes: C12R1, C12N5, C12N15, C07K16, C12P21, C12N1, C12N9