Patent Publication Number: US-8114653-B2

Title: Thermostable Y-family polymerases and chimeras

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This is a divisional of U.S. patent application Ser. No. 11/596,783, filed Nov. 17, 2006, now issued as U.S. Pat. No. 7,745,188 on Jun. 29, 2010; which is the U.S. National Stage of International Application No. PCT/US2005/017941, filed May 20, 2005, which was published in English under PCT Article 21(2), and which claims the benefit of U.S. provisional application No. 60/623,490 filed Oct. 29, 2004, and U.S. provisional application No. 60/573,684 filed May 20, 2004. These applications are incorporated by reference herein in their entirety. 
    
    
     FIELD 
     The present disclosure is related to thermostable Y-family polymerases and their use, in particular several novel Y-family polymerases and chimeras made therefrom, as well as methods of identifying other Y-family polymerases and methods of generating other chimeric Y-family polymerases. 
     BACKGROUND 
     Remarkable progress has been made in the past few years in understanding the molecular mechanisms of damage-induced mutagenesis. It has been suggested that a significant proportion of mutations arise when damaged genomic DNA is replicated in an error-prone manner by one or more low-fidelity polymerases (Goodman et al.,  Annu. Rev. Biochem.  71:17-50, 2002). These polymerases appear to have evolved to specifically facilitate replication of a wide variety of DNA lesions that might otherwise block the high fidelity replication machinery. Most of these specialized polymerases are phylogenetically related to each other and have been collectively termed “Y-family” polymerases (Ohmori et al.,  Mol. Cell.  8:7-8, 2001). 
     The Y-family polymerases are ubiquitous and are found in all three kingdoms of life, with many organisms often possessing more than one family member. This suggests that Y-family polymerases play important roles in cellular survival or evolutionary “fitness” (Friedberg et al.,  Science  296:1627-30, 2002; Yeiser et al.,  Proc. Natl. Acad. Sci. USA  99:8737-41, 2002). Indeed, defects in human Polη result in the sunlight-sensitive and cancer prone xeroderma pigmentosum variant (XP-V) syndrome (Masutani et al.,  Nature  399:700-04, 1999; Johnson et al.,  Science  285:263-65, 1999), whilst mutations in  Escherichia coli  dinB reduces the cell&#39;s ability to undergo adaptive mutagenesis in stationary phase (McKenzie et al.,  Mol. Cell.  7:571-79, 2001; Tompkins et al.,  J. Bacteriol.  185:3469-72, 2003). 
     In vivo, DNA polymerases participate in a spectrum of DNA synthetic processes including DNA replication, DNA repair, recombination, and gene amplification (Kornberg and Baker,  DNA Replication , pp. 929, W.H. Freeman and Co., New York, 1992). In vitro, DNA polymerases are used for DNA amplification techniques, for example polymerase chain reaction (PCR). DNA polymerases, particularly thermostable polymerases, are the key to a large number of techniques in recombinant DNA studies and in medical diagnosis of disease. 
     Due to the importance of Y-family polymerases in biotechnology and medicine, it would be advantageous to identify other thermostable Y-family polymerases and to create chimeric Y-family polymerases in order to optimize polymerase characteristics such as thermostability, fidelity, processivity, and translesion synthesis. 
     SUMMARY 
     Disclosed herein are novel Y-family polymerases:  Acidianus infernus  Dpo4 (SEQ ID NO: 6),  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8),  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10),  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12),  Sulfolobus tengchongensis  Dpo4 (SEQ ID NO: 14),  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41),  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43),  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45),  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47), and  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61). Also encompassed by this disclosure are Y-family polymerase amino acid sequences having at least 95% sequence identity to SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, or SEQ ID NO: 61, as well as conservative variants of SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, or SEQ ID NO: 61, wherein the Y-family polymerase has polymerase activity. Also encompassed by this disclosure are isolated nucleic acid molecules encoding these polymerases, as well as recombinant nucleic acid molecules that include a promoter sequence operably linked to the Y-family polymerase-encoding nucleic acid molecules, and cells transformed with these recombinant nucleic acid molecules. 
     Also disclosed herein are chimeric Y-family polymerases: Dpo4LFDbh (SEQ ID NO: 2), DbhLFDpo4 (SEQ ID NO: 4), AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57), and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59). These chimeric polymerases include the thumb, palm, and finger domains of one Y-family polymerase and the little finger (LF) domain of another Y-family polymerase. Also encompassed by this disclosure are chimeric Y-family polymerase amino acid sequences having at least 95% sequence identity to SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 57, or SEQ ID NO: 59, or conservative variants of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 57, or SEQ ID NO: 59. These chimeric Y-family polymerases retain polymerase activity. Also encompassed are isolated nucleic acid molecules encoding these chimeric polymerases, as well as recombinant nucleic acid molecules that include a promoter sequence operably linked to the Y-polymerase-encoding nucleic acid molecules, and cells transformed with these recombinant nucleic acid molecules. 
     The disclosure also provides a method of generating a chimeric Y-family polymerase. The method includes replacing a first LF domain of a first Y-family polymerase with a second LF domain of a second Y-family polymerase. 
     Also provided is a method of using a Y-family polymerase or a chimeric Y-family polymerase to add a nucleotide to a polynucleotide, the method comprising incubating a polynucleotide with a Y-family polymerase, thereby adding the nucleotide to the polynucleotide. In the disclosed embodiments, the Y-family polymerases or chimeric Y-family polymerase is  Acidianus infernus  Dpo4 (SEQ ID NO: 6),  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8),  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10),  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12),  Sulfolobus tengchongensis  Dpo4 (SEQ ID NO: 14),  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41),  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43),  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45),  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47),  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61), Dpo4LFDbh (SEQ ID NO: 2), DbhLFDpo4 (SEQ ID NO: 4), AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57), and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59). 
     In addition, the disclosure provides a method of identifying a Y-family polymerase. The method includes amplifying a suspected Y-family polymerase DNA molecule with a first degenerate primer and a second degenerate primer, wherein the first degenerate primer hybridizes with a DNA sequence upstream of a known locus of the suspected Y-family polymerase DNA molecule, and wherein the second degenerate primer hybridizes with a DNA sequence downstream of the known locus of the suspected Y-family polymerase DNA molecule; and sequencing the amplified suspected Y-family polymerase DNA molecule, thereby identifying the Y-family polymerase. 
     Also disclosed are methods of amplifying ancient or damaged DNA, and methods of incorporating fluorescent or modified nucleotides into a DNA molecule. The methods include thermocycling a DNA molecule with a first primer, a second primer, and an amount of one of the Y-family polymerase disclosed herein sufficient to amplify the DNA molecule, wherein the first primer hybridizes with a DNA sequence at the 3′-end of the DNA molecule, and the second primer hybridizes with a DNA sequence at the 5′-end of the DNA molecule. 
     The foregoing and other features and advantages will become more apparent from the following detailed description of several embodiments, which proceeds with reference to the accompanying figures. 
    
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         FIG. 1  is a diagram showing the alignment of the Dpo4LFDbh (SEQ ID NO: 2) and DbhLFDpo4 (SEQ ID NO: 4) chimeras. The secondary structures of the finger (˜residues 11-78), thumb (˜residues 164-231), palm (˜residues 1-10 &amp; 79-163), and LF (˜residues 232-353) domains are indicated as boxes (α-helices) and arrows (β-sheets) above the aligned primary amino acid sequence. The primary amino acid sequence of the  Sulfolobus solfataricus  Dpo4 (Sso) is shown in a black typeface, while that of  Sulfolobus acidocaldarius  Dbh (Sac) is shown in a white typeface. Dpo4LFDbh consists of Sso Dpo4 finger, palm and thumb residues and the LF domain from Sac Dbh. DbhLFDpo4 consists of Sac Dbh finger, palm and thumb residues and the LF domain of Sso Dpo4. 
         FIG. 2  is a digital image of a gel showing the ability of Sso Dpo4, Sac Dbh and the Dpo4LFDbh (SEQ ID NO: 2) and DbhLFDpo4 (SEQ ID NO: 4) chimeras to extend a radiolabeled 16-mer primer (5′-CTT GAA AAC ATA GCG A-3′) (SEQ ID NO: 15) annealed to the single-stranded M13 mp18 DNA (7.2 kb) (GenBank Accession No. M77815). The primer/template was fixed at 10 nM and elongation of the primer was assayed over a wide range of enzyme concentrations (0, 10 nM, 50 nM, 100 nM, 1 μM, 2 μM). Reactions contained all four dNTPs (100 μM each) and were performed for 5 minutes at 37° C. Replication products were separated on a 12%/8M Urea polyacrylamide gel and visualized by PhosphorImager analysis. Size markers are given on the left hand side of the figure. 
         FIG. 3  is a digital image of a gel showing the processivity of Sso Dpo4, Sac Dbh and the Dpo4LFDbh (SEQ ID NO: 2) and DbhLFDpo4 (SEQ ID NO: 4) chimeras. Reactions were performed at 60° C. for 3 minutes in the presence of all four dNTPs (100 μM each) and contained 10 nM primer-template and limiting amounts of polymerase. The primer for these assays was a radiolabeled 23-mer (5′-GCG GTG TAG AGA CGA GTG CGG AG-3′) (SEQ ID NO: 16) that was annealed to a 50-mer template (5′-CTC TCA CAA GCA GCC AGG CAA G CT CCG CAC TCG TCT CTA CAC CGC  TCC GC-3′ (SEQ ID NO: 17), where the location of the annealed primer is underlined. The concentration of enzyme in these reactions varied considerably and was determined empirically so as to allow us to compare the size distribution of replication products under conditions where the percentage of primers extended was comparable between the four enzymes. The concentration of enzyme in the 10 μl reaction was as follows: Dbh; 0.2 nM, 0.8 nM and 3.3 nM: DbhLFDpo4; 0.03 nM, 0.17 nM and 0.83 nM: Dpo4; 0.017 nM, 0.08 nM and 0.4 nM; Dpo4LFDbh; 5.5 nM, 7.7 nM and 11 nM. Based upon these assays, both Sso Dpo4 and DbhLFDpo4 are more processive than either Sac Dbh or Dpo4LFDbh. 
         FIG. 4  is a set of three digital images of three gels showing the ability of the Sso Dpo4, Sac Dbh, and the Dpo4LFDbh (SEQ ID NO: 2) and DbhLFDpo4 (SEQ ID NO: 4) chimeras to replicate undamaged DNA and to bypass a synthetic abasic site or a cis-syn cyclobutane pyrimidine dimer. Reactions were performed at 60° C. for 5 minutes (undamaged DNA) or 10 minutes (abasic and CPD-templates) in the presence of all four dNTPs (100 μM each) and contained 10 nM primer template and 1, 10 or 100 nM of enzyme. The local sequence context is given at the left hand side of each panel.  FIG. 4A  is a digital image of a gel showing undamaged DNA.  FIG. 4B  is a digital image of a gel showing abasic site-containing DNA.  FIG. 4C  is a digital image of a gel showing CPD-containing DNA. The complete sequence of the undamaged template was 5′-CTC TCA CAA GCA GCC AGG CAT TCT CCG CAC TCG TCT CTA CAC CGC TCC GC-3′ (SEQ ID NO: 18). The 50-mer cis-syn dimer-containing template was identical, except that it contained a single CPD located at the adjacent Ts indicated in bold font. The 50-mer abasic (N)-containing template was 5′-CTC TCA CAA GCA GCC AGG CAT NCT CCG CAC TCG TCT CTA CAC CGC TCC GC-3′ (SEQ ID NO: 19). All three templates were primed with a radiolabeled 23-mer with the following sequence 5′-GCG GTG TAG AGA CGA GTG CGG AG-3′ (SEQ ID NO: 16) and replication products were separated on a 12%/8M Urea polyacrylamide gel and replication products visualized by PhosphorImager analysis. 
         FIG. 5  is a pair of digital images of gels showing the specificity of Sso Dpo4-, Sac Dbh-, Dpo4LFDbh (SEQ ID NO: 2)-, and DbhLFDpo4 (SEQ ID NO: 4)-dependent nucleotide incorporation on an undamaged template. Standard 10 μl reactions were performed at 37° C. or 60° C. for 2 minutes and contained 10 nM of radiolabeled primer/template; primer: 5′-GTG TCG GGG CGA GTG CGC CG-3′ (SEQ ID NO: 20), template: 5′-CTC TCA CAA GCA GCT AAG CAG  CGG CGC ACT CGC CCC GAC AC C GC-3′ (SEQ ID NO: 21), with the position of the annealed primer underlined, and various amounts of polymerase. Reactions at 37° C. ( FIG. 5A ) contained 30 nM Dbh, 75 nM Dpo4LFDbh, 5 nM Dpo4, and 10 nM DbhLFDpo4 respectively. Those performed at 60° C. ( FIG. 5B ) contained 10 nM Dbh, 25 nM Dpo4LFDbh, 2.5 nM Dpo4 or 5 nM DbhLFDpo4. Products were resolved by denaturing polyacrylamide gel electrophoresis (8 M urea/15% acrylamide) and subsequently visualized using a Molecular Dynamics PhosphorImager. 
         FIG. 6  is a pair of graphs showing the fidelity characteristics of Sso Dpo4, Sac Dbh, Dpo4LFDbh (SEQ ID NO: 2), and DbhLFDpo4 (SEQ ID NO: 4).  FIG. 6A  is a graph showing the ratio of single-base deletion to single-base substitution error rates for each polymerase (from Table 1).  FIG. 6B  is a graph showing a comparison of deletion rates within repetitive versus non-repetitive sequences for each of the polymerases. Error rates are given as deletions per nucleotide copied, and are calculated as described by Bebenek and Kunkel ( Methods. Enzymol.  262:217-32, 1995) to correct for differences in the number of repetitive versus non-repetitive nucleotides in the targets. 
         FIG. 7  is a diagram showing the superposition of the Sso Dpo4 and Sac Dbh LF domains. Although greatest primary amino acid sequence variation occurs in their respective LF domains, after superposition of the catalytic cores of Sso Dpo4 and Sac Dbh polymerases by rotating the Sac Dbh LF finger domain by 62.7° and translating it by 6.2 Å, the α-carbon backbone of the Sso Dpo4 and Sac Dbh LF domains was found to be virtually superimposable. This figure was generated using the program RIBBONS (Carson,  J. Mol. Graphics  5:103-06, 1987). 
         FIG. 8  is an alignment of Sa_ribo (SEQ ID NO: 64), Ss_ribo (SEQ ID NO: 65), and St_ribo (SEQ ID NO: 66) using the Clustal method with a PAM250 residue weight table. Sequences upstream of dpo4-like genes in  Sulfolobus acidocaldarius  (Sa),  Sulfolobus solfataricus  (Ss) and  Sulfolobus tokodaii  (St) are shown. 
         FIG. 9  is an alignment of Sa_hypo (SEQ ID NO: 67), Ss_hypo (SEQ ID NO: 68), and St_hypo (SEQ ID NO: 69) using the Clustal method with a PAM250 residue weight table. Sequences downstream of dpo4-like genes in  Sulfolobus acidocaldarius  (Sa),  Sulfolobus solfataricus  (Ss) and  Sulfolobus tokodaii  (St) are shown. 
         FIG. 10  is a diagrammatic representation of the cloning strategy used to clone the newly-identified Y-family polymerases. Sequences upstream (ribokinase) and downstream (hypothetical) of a dpo4-like gene are illustrated. The upstream consensus region DTTGAGD (SEQ ID NO: 22) and the downstream consensus region YEDVEGG (SEQ ID NO: 25) are also shown. 
         FIG. 11  is a digital image of a gel showing the expression of four of the five newly-identified Y-family polymerases. IPTG was not added to the cultures to induce expression, and the cells were grown overnight. The Y-family polymerase band is indicated by the arrow. Column C is the expression strain without plasmid. Ai:  Acidianus infernus  Dpo4 (SEQ ID NO: 6); Saz:  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8); So:  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10); Ssh:  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12). 
         FIG. 12  is a digital image of a gel showing the expression of four of the five newly-identified Y-family polymerases. 0.01 mM IPTG was added to the cultures to induce expression, and the cells were grown overnight. Column C is the expression strain without plasmid. Ai:  Acidianus infernus  Dpo4 (SEQ ID NO: 6); Saz:  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8); So:  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10); Ssh:  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12). 
         FIG. 13  is a digital image of a gel showing the thermostability of Dpo4. The extract can be enriched by heating the crude cell lysate to 70° C. for 10 minutes. This causes many of the  E. coli  proteins to precipitate. A band of the right molecular weight for the newly-identified Y-family polymerases is visible in all four extracts. The intensity and size of the protein changes in the various extracts and is consistent with the expression in the whole cell extract. The amount loaded corresponds to about 0.5-1.0 μg of the new protein. 
         FIG. 14  is a digital image of a gel showing the results of a polymerase assay. Various amounts of the crude (heat treated) extract were included in replication assays (radiolabeled primer and unlabeled template at 70° C.). All four extracts have polymerase activity. Although polymerase activity from endogenous  E. coli  polymerases cannot be formally excluded,  E. coli  polymerases should not be active at 60° C. Also, the activity of the enzymes varies and roughly corresponds to the amount of protein added to the reaction. The  Sulfolobus shibatae  Dpo4 polymerase (SEQ ID NO: 12) is particularly active. 
         FIG. 15  is a diagram showing the alignment of the newly-identified Y-family polymerases. The alignment was performed using the Clustal method with a PAM250 weight residue weight table. Sa:  Sulfolobus acidocaldarius  Dbh (SEQ ID NO: 70); Ss:  Sulfolobus solfataricus  Dpo4 (SEQ ID NO: 71); St:  Sulfolobus tokodaii  Dpo4 (SEQ ID NO: 72); Ai:  Acidianus infernus  Dpo4 (SEQ ID NO: 6); Saz:  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8); So:  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10); Ssh:  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12); Step:  Sulfolobus tengchongensis  Dpo4 (SEQ ID NO: 14). 
         FIG. 16  is a phylogenetic tree showing the several recently identified members of the Y-polymerase family. Sa:  Sulfolobus acidocaldarius ; Ai:  Acidianus infernus ; Step:  Sulfolobus tengchongensis ; Ss:  Sulfolobus solfataricus ; Ssh:  Sulfolobus shibatae ; St:  Sulfolobus tokodaii ; So:  Sulfurisphaera ohwakuensis ; Saz:  Stygiolobus azoricus.    
         FIG. 17  is a digital image of a gel showing primer extension of undamaged and damaged templates by Dpo4 enzymes. The “undamaged” panel shows primer extension of the SSHTP2/HTU50 primer/template substrate (SEQ ID NOs: 54 and 55) by the various Dpo4 enzymes. The “CPD” panel shows primer extension of the SSHTP2/HMTT50 primer/template substrate (SEQ ID NOs: 54 and 56) containing a TT CPD dimer in the HMTT50 template. The “abasic” panel shows primer extension of the SSHTP2/HTX50 primer/template substrate (SEQ ID NOs: 54 and 56) containing an abasic site in the HTX50 template. Dpo4 is from  Sulfolobus solfataricus ; Ssh:  Sulfolobus shibatae  Dpo4, Ai:  Acidianus infernus  Dpo4; Step:  Sulfolobus tengchongensis  Dpo4; Saz:  Stygiolobus azoricus  Dpo4; and Soh:  Sulfurisphaera ohwakuensis  Dpo4. 
         FIG. 18  is a digital image of a set of gels showing labeled nucleotide incorporation by Dpo4 enzymes during primer extension. The “4 dNTPs” panel shows primer extension in the presence of all four unmodified nucleotides. The “biotin dUTP” panel shows primer extension where dTTP was replaced with biotin-aha-dUTP (Molecular Probes, Eugene Oreg.). The “fluorescein dUTP” panel shows primer extension where dTTP was replaced with fluorescein-aha-dUTP (Molecular Probes, Eugene, Oreg.). The “Alexa fluor dUTP” panel shows primer extension where dTTP was replaced with Alexa Fluor® 647-aha-dUTP (Molecular Probes, Eugene, Oreg.). Lastly, the “Cy5 dCTP” panel shows primer extension where dCTP was replaced with Cy5-dCTP (Amersham Biosciences, Piscatway, N.J.). 
         FIG. 19  is a digital image of a gel showing PCR amplification of the 1.1 kb  Sulfolobus tengchongensis  dpo4 gene. Dpo4 is from  Sulfolobus solfataricus ; Ssh:  Sulfolobus shibatae  Dpo4; Ai:  Acidianus infernus  Dpo4; Step:  Sulfolobus tengchongensis  Dpo4. The gel shows that Sso Dpo4, Ai and Step can all function in a “closed tube” PCR reaction and that the reaction is sufficiently robust to amplify at least a 1.1 kb amplicon. 
         FIG. 20  is a digital image of a gel illustrating primer extension of undamaged and hydantoin containing templates by the Dpo4 enzymes from  Acidianus infernus  (SEQ ID NO: 6),  Sulfolobus shibatae  (SEQ ID NO: 12),  Sulfolobus tengchongensis  (SEQ ID NO: 14), and the AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57) and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59) chimeras. The “undamaged” panel shows primer extension of the SSHydP/HydU22 primer/template substrate by the various Dpo4 enzymes and chimeric enzymes. The “Hydantoin” panel shows primer extension of the SSHydP/ODN primer/template substrate containing a 5-hydroxy-5-methyl hydantoin adduct in the ODN template. 
         FIG. 21  is a digital image of a gel illustrating primer extension of undamaged and hydantoin containing templates by the  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41) and  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43) enzymes. The “undamaged” panel shows primer extension of the SSHydP/HydU22 primer/template substrate by the  Thermoascus aurantiacus  Pol eta and  Thermomyces lanuginosus  Pol eta enzymes. The “Hydantoin” panel shows primer extension of the SSHydP/ODN primer/template substrate containing a 5-hydroxy-5-methyl hydantoin adduct in the ODN template. 
     
    
    
     SEQUENCE LISTING 
     The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing: 
     SEQ ID NOs: 1 and 2 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase chimera Dpo4LFDbh. 
     SEQ ID NOs: 3 and 4 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase chimera DbhLFDpo4. 
     SEQ ID NOs: 5 and 6 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase  Acidianus infernus  Dpo4. 
     SEQ ID NOs: 7 and 8 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase  Stygiolobus azoricus  Dpo4. 
     SEQ ID NOs: 9 and 10 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase  Sulfurisphaera ohwakuensis  Dpo4. 
     SEQ ID NOs: 11 and 12 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase  Sulfolobus shibatae  Dpo4. 
     SEQ ID NOs: 13 and 14 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase  Sulfolobus tengchongensis  Dpo4. 
     SEQ ID NO: 15 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 16 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 17 shows the nucleic acid sequence of an oligonucleotide template. 
     SEQ ID NO: 18 shows the nucleic acid sequence of an oligonucleotide template. 
     SEQ ID NO: 19 shows the nucleic acid sequence of an oligonucleotide abasic (N)-containing template. 
     SEQ ID NO: 20 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 21 shows the nucleic acid sequence of an oligonucleotide template. 
     SEQ ID NO: 22 shows the amino acid sequence of a Y-family polymerase consensus region. 
     SEQ ID NO: 23 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 24 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 25 shows the amino acid sequence of a Y-family polymerase consensus region. 
     SEQ ID NO: 26 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 27 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 28 shows the nucleic acid sequence of a degenerate 5′-primer used in cloning  S. tengchongensis  Dpo4. 
     SEQ ID NO: 29 shows the nucleic acid sequence of a degenerate 3′-primer used in cloning  S. tengchongensis  Dpo4. 
     SEQ ID NO: 30 shows the nucleic acid sequence of a degenerate 5′-primer used in cloning  S. tengchongensis  Dpo4. 
     SEQ ID NO: 31 shows the nucleic acid sequence of a degenerate 3′-primer used in cloning  S. tengchongensis  Dpo4. 
     SEQ ID NO: 32 shows the nucleic acid sequence of a primer (ssdbhbam) used in cloning the  S. acidocaldarius  dbh gene. 
     SEQ ID NO: 33 shows the nucleic acid sequence of a primer (ssdbhbsp) used in cloning the  S. acidocaldarius  dbh gene. 
     SEQ ID NO: 34 shows the nucleic acid sequence of a primer (P2SWDW) used in generating a BalI/MscI restriction site in the  S. acidocaldarius  dbh gene. 
     SEQ ID NO: 35 shows the nucleic acid sequence of a primer (P2SWUP) used in generating a BalI restriction site in the  S. acidocaldarius  dbh gene. 
     SEQ ID NO: 36 shows the nucleic acid sequence of a primer (P1ndeIup) used in cloning DbhLFDpo4. 
     SEQ ID NO: 37 shows the nucleic acid sequence of a primer (P1bal2dw) used in cloning DbhLFDpo4. 
     SEQ ID NO: 38 shows the nucleic acid sequence of the primer P1balIup. 
     SEQ ID NO: 39 shows the nucleic acid sequence of the primer P1bam2dw. 
     SEQ ID NOs: 40 and 41 show the nucleic acid and amino acid sequence, respectively, of  Thermoascus aurantiacus  Pol eta. 
     SEQ ID NOs: 42 and 43 show the nucleic acid and amino acid sequence, respectively, of  Thermomyces lanuginosus  Pol eta. 
     SEQ ID NOs: 44 and 45 show the partial nucleic acid and amino acid sequence, respectively, of  Thermomyces lanuginosus  Pol iota. 
     SEQ ID NOs: 46 and 47 show the partial nucleic acid and amino acid sequence, respectively, of  Thermoascus aurantiacus  Pol iota. 
     SEQ ID NOs: 48-51 show several amino acid sequences used to generate PCR primers for amplifying polymerase eta genes. 
     SEQ ID NO: 52 shows an amino acid sequence used to generate PCR primers for amplifying polymerase iota genes. 
     SEQ ID NO: 53 shows an amino acid sequence used to generate PCR primers for amplifying polymerase iota genes. 
     SEQ ID NO: 54 shows a nucleic acid sequence (SSHTP2) useful as a template for primer extension assays. 
     SEQ ID NO: 55 shows a nucleic acid sequence (HTU50) useful as a template for primer extension assays. 
     SEQ ID NOs: 56 and 57 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase chimera AiLFSte (AiDpo4/SteDpo4LF). 
     SEQ ID NOs: 58 and 59 show the nucleic acid and amino acid sequence, respectively, of Y-family polymerase chimera AiLFDpo4 (AiDpo4/SsoDpo4LF). 
     SEQ ID NOs: 60 and 61 show the partial nucleic acid and amino acid sequence, respectively, of  Thermomyces lanuginosus  Pol kappa. 
     SEQ ID NO: 62 shows the nucleic acid sequence of an oligonucleotide template. 
     SEQ ID NO: 63 shows the nucleic acid sequence of an oligonucleotide primer/probe. 
     SEQ ID NO: 64 shows the amino acid sequence of Sa_ribo. 
     SEQ ID NO: 65 shows the amino acid sequence of Ss_ribo. 
     SEQ ID NO: 66 shows the amino acid sequence of St_ribo. 
     SEQ ID NO: 67 shows the amino acid sequence of Sa_hypo. 
     SEQ ID NO: 68 shows the amino acid sequence of Ss_hypo. 
     SEQ ID NO: 69 shows the amino acid sequence of St_hypo. 
     SEQ ID NO: 70 shows the amino acid sequence of  Sulfolobus acidocaldarius  Dbh. 
     SEQ ID NO: 71 shows the amino acid sequence of  Sulfolobus solfataricus  Dpo4. 
     SEQ ID NO: 72 shows the amino acid sequence of  Sulfolobus tokodaii  Dpo4. 
     SEQ ID NOs: 73-76 show the nucleic acid sequences of several oligonucleotide primers. 
     SEQ ID NO: 77 shows an amino acid sequence used to generate PCR primers for amplifying polymerase kappa genes. 
     SEQ ID NO: 78 shows the nucleic acid sequence of an oligonucleotide primer. 
     SEQ ID NO: 79 shows an amino acid sequence used to generate PCR primers for amplifying polymerase kappa genes. 
     SEQ ID NOs: 80-82 show the nucleic acid sequences of several oligonucleotide primers. 
     DETAILED DESCRIPTION 
     I. Abbreviations 
     Ai:  Acidianus infernus  Dpo4 
     ° C.: degrees Celsius 
     cDNA: complementary DNA 
     CPD: cyclobutane pyrimidine dimer 
     g: gram 
     LF: little finger 
     min: minute(s) 
     ml: milliliter 
     ODN: oligodeoxynucleotide 
     PCR: polymerase chain reaction 
     Sac/Sa:  Sulfolobus acidocaldarius  Dbh 
     Saz:  Stygiolobus azoricus  Dpo4 
     Soh/So:  Sulfurisphaera ohwakuensis  Dpo4 
     Ssh:  Sulfolobus shibatae  Dpo4 
     Sso/Ss:  Sulfolobus solfataricus  Dpo4 
     Sto/St:  Sulfolobus tokodaii  Dpo4 
     Step:  Sulfolobus tengchongensis  Dpo4 
     μg: microgram(s) 
     μl: microliter(s) 
     II. Terms 
     Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin,  Genes VII , published by Oxford University Press, 2000 (ISBN 019879276X); Kendrew et al. (eds.),  The Encyclopedia of Molecular Biology , published by Blackwell Publishers, 1994 (ISBN 0632021829); and Robert A. Meyers (ed.),  Molecular Biology and Biotechnology: a Comprehensive Desk Reference , published by Wiley, John &amp; Sons, Inc., 1995 (ISBN 0471186341); and other similar references. 
     In order to facilitate review of the various embodiments of the invention, the following explanations of specific terms are provided: 
     Animal: Living multi-cellular vertebrate organisms, a category that includes for example, mammals and birds. 
     Amplification: When used in reference to a nucleic acid, any technique that increases the number of copies of a nucleic acid molecule in a sample or specimen. An example of amplification is the polymerase chain reaction, in which a biological sample collected from a subject is contacted with a pair of oligonucleotide primers, under conditions that allow for the hybridization of the primers to nucleic acid template in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid. The product of in vitro amplification can be characterized by electrophoresis, restriction endonuclease cleavage patterns, oligonucleotide hybridization or ligation, and/or nucleic acid sequencing, using standard techniques. Other examples of in vitro amplification techniques include strand displacement amplification (see U.S. Pat. No. 5,744,311); transcription-free isothermal amplification (see U.S. Pat. No. 6,033,881); repair chain reaction amplification (see WO 90/01069); ligase chain reaction amplification (see EP-A-320 308); gap filling ligase chain reaction amplification (see U.S. Pat. No. 5,427,930); coupled ligase detection and PCR (see U.S. Pat. No. 6,027,889); and NASBA™ RNA transcription-free amplification (see U.S. Pat. No. 6,025,134). 
     Antisense, sense, and antigene: Double-stranded DNA (dsDNA) has two strands, a 5′→3′ strand, referred to as the plus strand, and a 3′→5′ strand (the reverse compliment), referred to as the minus strand. Because RNA polymerase adds nucleic acids in a 5′→3′ direction, the minus strand of the DNA serves as the template for the RNA during transcription. Thus, the RNA formed will have a sequence complementary to the minus strand and identical to the plus strand (except that U is substituted for T). 
     Antisense molecules are molecules that are specifically hybridizable or specifically complementary to either RNA or the plus strand of DNA. Sense molecules are molecules that are specifically hybridizable or specifically complementary to the minus strand of DNA. Antigene molecules are either antisense or sense molecules directed to a dsDNA target. 
     Catalytic activity or activity: When used in reference to a polymerase, these terms refer to the enzymatic properties of a polymerase. Catalytic activity includes, for example: enzymatic properties such as the rate of synthesis of nucleic acid polymers; the Km for substrates such as nucleoside triphosphates and template strand; the fidelity of template-directed incorporation of nucleotides, where the frequency of incorporation of non-complementary nucleotides is compared to that of complementary nucleotides; processivity, the number of nucleotides synthesized by a polymerase prior to dissociation from the DNA template; discrimination of the ribose sugar; and stability, for example, at elevated temperatures. “Measurable polymerase activity” refers to polymerase activity, such as one or more of the enzymatic properties of a polymerase (e.g., the catalytic activities described above), that can be detected using methods well know to those of ordinary skill in the art. 
     Polymerases can discriminate between templates, for example, DNA polymerases generally use DNA templates and RNA polymerases generally use RNA templates, whereas reverse transcriptases use both RNA and DNA templates. DNA polymerases also discriminate between deoxyribonucleoside triphosphates and dideoxyribonucleoside triphosphates. Any of these distinct enzymatic properties can be included in the meaning of the term catalytic activity, including any single property, any combination of properties or all of the properties. 
     Chimera: A nucleic acid sequence, amino acid sequence, or protein that comprises a nucleic acid sequence, amino acid sequence, or protein from two or more sources, for example amino acid sequence from two or more different species. In general, chimeric sequences are the result of genetic engineering. 
     Chimeric Y-family polymerases can be created by replacing a portion of a native Y-family polymerase with an orthologous portion of another Y-family polymerase. Specific, non-limiting examples of chimeric Y-family polymerases include DbhLFDpo4, Dpo4LFDbh, AiLFSte (AiDpo4/SteDpo4LF), and AiLFDpo4 (AiDpo4/SsoDpo4LF). Other chimeric Y-family polymerases can be created using the Y-family polymerases disclosed herein, for example  Acidianus infernus  Dpo4,  Stygiolobus azoricus  Dpo4,  Sulfurisphaera ohwakuensis  Dpo4,  Sulfolobus shibatae  Dpo4, or  Sulfolobus tengchongensis  Dpo4. In some chimeric Y-family polymerases, the LF domain of one Y-family polymerase has been substituted for the LF domain of another Y-family polymerase. In other chimeric Y-family polymerases, the finger domain of one Y-family polymerase has been substituted for the finger domain of another Y-family polymerase. In still other chimeric Y-family polymerases, both substitutions have been made. 
     DNA (deoxyribonucleic acid): A long chain polymer which comprises the genetic material of most living organisms (some viruses have genes comprising ribonucleic acid (RNA)). The repeating units in DNA polymers are four different nucleotides, each of which comprises one of the four bases, adenine, guanine, cytosine and thymine bound to a deoxyribose sugar to which a phosphate group is attached. Triplets of nucleotides (referred to as codons) code for each amino acid in a polypeptide. The term codon is also used for the corresponding (and complementary) sequences of three nucleotides in the mRNA into which the DNA sequence is transcribed. 
     Unless otherwise specified, any reference to a DNA molecule is intended to include the reverse complement of that DNA molecule. Except where single-strandedness is required by the text herein, DNA molecules, though written to depict only a single strand, encompass both strands of a double-stranded DNA molecule. Thus, a reference to the nucleic acid molecule that encodes a specific protein, or a fragment thereof, encompasses both the sense strand and its reverse complement. Thus, for instance, it is appropriate to generate probes or primers from the reverse complement sequence of the disclosed nucleic acid molecules. 
     Deletion: The removal of a sequence of DNA, the regions on either side being joined together. 
     Encode: A polynucleotide is said to “encode” a polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, it can be transcribed and/or translated to produce the mRNA for and/or the polypeptide or a fragment thereof. The anti-sense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom. 
     Fidelity: When used in reference to a polymerase, fidelity refers to the accuracy of template-directed incorporation of complementary bases in a synthesized DNA strand relative to the template strand. Fidelity is measured based on the frequency of incorporation of incorrect bases in the newly-synthesized nucleic acid strand. The incorporation of incorrect bases can result in point mutations, insertions or deletions. Fidelity can be calculated according to the procedures described in Tindall and Kunkel ( Biochemistry  27:6008-13, 1988). Methods for determining fidelity are well known in the art. A polymerase can exhibit high fidelity or low fidelity. As used herein, the term “high fidelity” is intended to mean a frequency of accurate base incorporation that exceeds a predetermined value. Similarly, the term “low fidelity” is intended to mean a frequency of accurate base incorporation that is lower than a predetermined value. The predetermined value can be, for example, a desired frequency of accurate base incorporation or the fidelity of a known polymerase. 
     As used herein, the term “altered fidelity” refers to the fidelity of a chimeric polymerase that differs from the fidelity of one or both of the parent polymerases from which the chimeric polymerase is derived. The altered fidelity can either be higher or lower than the fidelity of a parent polymerase. Thus, chimeric polymerases with altered fidelity can be classified as high fidelity polymerases or low fidelity polymerases. Altered fidelity can be determined by assaying the parent and chimeric polymerases and comparing their activities using any assay that measures the accuracy of template directed incorporation of complementary bases. Such methods are known to those skilled in the art. 
     Finger domain: Although they share little primary amino acid sequence homology with DNA polymerases from other families, structural studies of two archaeal DinB-like polymerases, Sac Dbh and Sso Dpo4, and of the catalytic core of  Saccharomyces cerevisiae  Polη (also referred to herein as “Pol eta”) reveal they are topologically similar to classical polymerases in that they resemble a right hand and possess “finger”, “palm” and “thumb” sub-domains. In addition, they possess a unique domain that has been termed the “little finger” (LF; Ling et al.,  Cell  107:91-102, 2001), “wrist” (Silvian et al.,  Nat. Struct. Biol.  8:984-89, 2001) or “PAD: polymerase associated domain” (Trincao et al.,  Mol. Cell.  8:417-26, 2001). 
     In one specific, non-limiting example, the finger domain of Dpo4 is represented by amino acids 11-78 of the Dpo4 amino acid sequence. In another specific, non-limiting example, the finger domain of Dbh is represented by amino acids 11-78 of the Dbh amino acid sequence. 
     Functional fragments and variants of a polypeptide: Included are those fragments and variants that maintain one or more functions of the parent polypeptide. It is recognized that the gene or cDNA encoding a polypeptide can be considerably mutated without materially altering one or more of the polypeptide&#39;s functions. First, the genetic code is well-known to be degenerate, and thus different codons encode the same amino acids. Second, even where an amino acid substitution is introduced, the mutation can be conservative and have no material impact on the essential functions of a protein. See Stryer,  Biochemistry  3rd Ed., (c) 1988. Third, part of a polypeptide chain can be deleted without impairing or eliminating all of its functions. Fourth, insertions or additions can be made in the polypeptide chain for example, adding epitope tags, without impairing or eliminating its functions (Ausubel et al.  Short Protocols in Molecular Biology,  4 th  ed., John Wiley &amp; Sons, Inc., 1999). Other modifications that can be made without materially impairing one or more functions of a polypeptide include, for example, in vivo or in vitro chemical and biochemical modifications or the incorporation of unusual amino acids. Such modifications include, for example, acetylation, carboxylation, phosphorylation, glycosylation, ubiquination, labeling, e.g., with radionucleides, and various enzymatic modifications, as will be readily appreciated by those well skilled in the art. A variety of methods for labeling polypeptides and labels useful for such purposes is well known in the art, and include radioactive isotopes such as  32 P, ligands which bind to or are bound by labeled specific binding partners (e.g., antibodies), fluorophores, chemiluminescent agents, enzymes, and antiligands. Functional fragments and variants can be of varying length. For example, some fragments have at least 10, 25, 50, 75, 100, or 200 amino acid residues. 
     A functional fragment or variant of a thermostable Y-family polymerase is defined herein as a polypeptide which retains measurable polymerase activity. 
     Heterologous: A type of sequence that is not normally (i.e. in the wild-type sequence) found adjacent to a second sequence. In one embodiment, the sequence is from a different genetic source, such as a virus or organism, than the second sequence. 
     Hybridization: Oligonucleotides and their analogs hybridize by hydrogen bonding, which includes Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary bases. Generally, nucleic acid consists of nitrogenous bases that are either pyrimidines (cytosine (C), uracil (U), and thymine (T)) or purines (adenine (A) and guanine (G)). These nitrogenous bases form hydrogen bonds between a pyrimidine and a purine, and the bonding of the pyrimidine to the purine is referred to as base pairing. More specifically, A will hydrogen bond to T or U, and G will bond to C. Complementary refers to the base pairing that occurs between to distinct nucleic acid sequences or two distinct regions of the same nucleic acid sequence. 
     Isolated: A biological component (such as a nucleic acid molecule, protein or organelle) that has been substantially separated or purified away from other biological components in the cell of the organism in which the component naturally occurs, i.e., other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles. Nucleic acids and proteins that have been isolated include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids. 
     Little finger domain: Although they share little primary amino acid sequence homology with DNA polymerases from other families, structural studies of two archaeal DinB-like polymerases, Dbh and Dpo4, and of the catalytic core of  Saccharomyces cerevisiae  Polη reveal they are topologically similar to classical polymerases in that they resemble a right hand and possess “fingers”, “palm” and “thumb” sub-domains. In addition, they possess a unique domain that has been termed the “little finger” (LF; Ling et al.,  Cell  107:91-102, 2001), “wrist” (Silvian et al.,  Nat. Struct. Biol.  8:984-89, 2001) or “PAD: polymerase associated domain” (Trincao et al.,  Mol. Cell.  8:417-26, 2001). 
     The LF domain is the least conserved of the four domains in the Y-family polymerases, and the variable LF domain plays a major role in determining the enzymatic and biological properties of each individual Y-family member. 
     In one specific, non-limiting example, the LF domain of the chimeras and Y-family polymerases disclosed herein is found at codons 245-353 (DbhLFDpo4), 244-353 (Dpo4LFDbh), 245-354 ( Acidianus infernus  Dpo4), 245-350 ( Stygiolobus azoricus  Dpo4), 244-351 ( Sulfurisphaera ohwakuensis  Dpo4), 244-352 ( Sulfolobus shibatae  Dpo4), and 244-351 ( Sulfolobus tengchongensis  Dpo4). The LF domain is connected to the thumb domain of the proteins by a 14 amino acid linker protein. Thus the LF domain and linker region that connects it to the thumb domain of the chimeras and Y-family polymerases disclosed herein are found at codons 231-353 (DbhLFDpo4), 230-353 (Dpo4LFDbh), 231-354 ( Acidianus infernus  Dpo4), 231-350 ( Stygiolobus azoricus  Dpo4), 230-351 ( Sulfurisphaera ohwakuensis  Dpo4), 230-352 ( Sulfolobus shibatae  Dpo4), and 230-351 ( Sulfolobus tengchongensis  Dpo4). 
     Label: A biomolecule attached covalently or noncovalently to a detectable label or reporter molecule. Typical labels include radioactive isotopes, enzyme substrates, co-factors, ligands, chemiluminescent or fluorescent agents, haptens, and enzymes. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed, for example, in Sambrook et al. (ed.),  Molecular Cloning: A Laboratory Manual,  2 nd  ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989 and Ausubel et al.  Short Protocols in Molecular Biology,  4 th  ed., John Wiley &amp; Sons, Inc., 1999. For example, ATP can be labeled in any one of its three phosphate groups with radioisotopes such as  32 P or  33 P, or in its sugar moiety with a radioisotope such as  35 S. 
     Linker region: A segment of DNA or amino acid sequence connecting domains. In one specific, non-limiting example, the LF domain of a Y-family polymerase is joined to the thumb domain by a 14 amino acid linker region. In another specific, non-limiting example, the LF domain of Dpo4 is joined to the thumb domain by a linker region comprising amino acids 230-244. 
     Mammal: This term includes both human and non-human mammals. Similarly, the term subject includes both human and veterinary subjects. 
     Nucleotide: This term includes, but is not limited to, a monomer that includes a base linked to a sugar, such as a pyrimidine, purine or synthetic analogs thereof, or a base linked to an amino acid, as in a peptide nucleic acid (PNA). A nucleotide is one monomer in a polynucleotide. A nucleotide sequence refers to the sequence of bases in a polynucleotide. 
     Oligonucleotide: A plurality of joined nucleotides joined by native phosphodiester bonds, between about 6 and about 300 nucleotides in length. An oligonucleotide analog refers to moieties that function similarly to oligonucleotides but have non-naturally occurring portions. For example, oligonucleotide analogs can contain non-naturally occurring portions, such as altered sugar moieties or inter-sugar linkages, such as a phosphorothioate oligodeoxynucleotide. Functional analogs of naturally occurring polynucleotides can bind to RNA or DNA, and include peptide nucleic acid (PNA) molecules. 
     Particular oligonucleotides and oligonucleotide analogs can include linear sequences up to about 200 nucleotides in length, for example a sequence (such as DNA or RNA) that is at least 6 bases, for example at least 8, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100 or even 200 bases long, or from about 6 to about 50 bases, for example about 10-25 bases, such as 12, 15 or 20 bases. 
     Open reading frame: A series of nucleotide triplets (codons) coding for amino acids without any internal termination codons. These sequences are usually translatable into a peptide. 
     Polymerase: An enzyme that polymerizes nucleoside triphosphates. Polymerases use a template nucleic acid strand to synthesize a complementary nucleic acid strand. The template strand and synthesized nucleic acid strand can independently be either DNA or RNA. Polymerases can include, for example, DNA polymerases such as  Escherichia coli  DNA polymerase I and  Thermus aquaticus  (Taq) DNA polymerase I, DNA-dependent RNA polymerases and reverse transcriptases. A polymerase need not contain all of the amino acids found in a native enzyme, but only those which are sufficient to allow the polymerase to carry out a desired catalytic activity. Catalytic activities include, for example, 5′-3′ polymerization, 5′-3′ exonuclease, and 3′-5′ exonuclease activities. 
     Polypeptide: A polymer in which the monomers are amino acid residues which are joined together through amide bonds. When the amino acids are alpha-amino acids, either the L-optical isomer or the D-optical isomer can be used, the L-isomers being preferred. The term polypeptide or protein as used herein encompasses any amino acid sequence and includes modified sequences such as glycoproteins. The term polypeptide is specifically intended to cover naturally occurring proteins, as well as those that are recombinantly or synthetically produced. 
     The term polypeptide fragment refers to a portion of a polypeptide which exhibits at least one useful epitope. The phrase “functional fragments of a polypeptide” refers to all fragments of a polypeptide that retain an activity, or a measurable portion of an activity, of the polypeptide from which the fragment is derived. Fragments, for example, can vary in size from a polypeptide fragment as small as an epitope capable of binding an antibody molecule to a large polypeptide capable of participating in the characteristic induction or programming of phenotypic changes within a cell. An epitope is a region of a polypeptide capable of binding an immunoglobulin generated in response to contact with an antigen. Thus, smaller peptides containing the biological activity of insulin, or conservative variants of the insulin, are thus included as being of use. 
     The term substantially purified polypeptide as used herein refers to a polypeptide that is substantially free of other proteins, lipids, carbohydrates or other materials with which it is naturally associated. In one embodiment, the polypeptide is at least 50%, for example at least 80% free of other proteins, lipids, carbohydrates or other materials with which it is naturally associated. In another embodiment, the polypeptide is at least 90% free of other proteins, lipids, carbohydrates or other materials with which it is naturally associated. In yet another embodiment, the polypeptide is at least 95% free of other proteins, lipids, carbohydrates or other materials with which it is naturally associated. 
     Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another: 
     1) Alanine (A), Serine (S), Threonine (T); 
     2) Aspartic acid (D), Glutamic acid (E); 
     3) Asparagine (N), Glutamine (Q); 
     4) Arginine (R), Lysine (K); 
     5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 
     6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). 
     Variations in the cDNA sequence that result in amino acid changes, whether conservative or not, are usually minimized in order to preserve the functional and immunologic identity of the encoded protein. The immunologic identity of the protein may be assessed by determining whether it is recognized by an antibody; a variant that is recognized by such an antibody is immunologically conserved. Any cDNA sequence variant will preferably introduce no more than twenty, and preferably fewer than ten amino acid substitutions into the encoded polypeptide. Variant amino acid sequences may, for example, be 80%, 90% or even 95% or 98% identical to the native amino acid sequence. Programs and algorithms for determining percentage identity can be found at the NCBI website. 
     Probes and primers: Nucleic acid probes and primers can be readily prepared based on the nucleic acid molecules provided in this invention. A probe comprises an isolated nucleic acid attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, enzyme substrates, co-factors, ligands, chemiluminescent or fluorescent agents, haptens, and enzymes. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed, for example, in Sambrook et al. (ed.),  Molecular Cloning: A Laboratory Manual,  2 nd  ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989 and Ausubel et al.  Short Protocols in Molecular Biology,  4 th  ed., John Wiley &amp; Sons, Inc., 1999. 
     Primers are short nucleic acid molecules, preferably DNA oligonucleotides 10 nucleotides or more in length. More preferably, longer DNA oligonucleotides can be about 15, 17, 20, or 23 nucleotides or more in length. Primers can be annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, and then the primer extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the PCR or other nucleic-acid amplification methods known in the art. 
     Methods for preparing and using nucleic acid primers and probes are described, for example, in Sambrook et al. (ed.),  Molecular Cloning: A Laboratory Manual,  2 nd  ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; Ausubel et al.  Short Protocols in Molecular Biology,  4 th  ed., John Wiley &amp; Sons, Inc., 1999; and Innis et al.  PCR Protocols, A Guide to Methods and Applications , Academic Press, Inc., San Diego, Calif., 1990. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, © 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). One of ordinary skill in the art will appreciate that the specificity of a particular probe or primer increases with its length. Thus, for example, a primer comprising 30 consecutive nucleotides of a Y-family polymerase-encoding nucleotide will anneal to a target sequence, such as a Y-family polymerase gene homolog from the gene family contained within a human genomic DNA library, with a higher specificity than a corresponding primer of only 15 nucleotides. Thus, in order to obtain greater specificity, probes and primers can be selected that comprise at least 17, 20, 23, 25, 30, 35, 40, 45, 50 or more consecutive nucleotides of Y-family polymerase nucleotide sequences. 
     Processivity: The ability of an enzyme to repetitively continue its catalytic function without dissociating from its substrate. 
     Protein: A biological molecule expressed by a gene and comprised of amino acids. 
     Purified: The term purified does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified protein preparation is one in which the protein referred to is more pure than the protein in its natural environment within a cell. 
     Recombinant: A nucleic acid that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. 
     Sequence identity: The similarity between two nucleic acid sequences, or two amino acid sequences, is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are. Homologs or orthologs of a Y-family polymerase protein, and the corresponding cDNA sequence, will possess a relatively high degree of sequence identity when aligned using standard methods. This homology will be more significant when the orthologous proteins or cDNAs are derived from species which are more closely related (e.g., human and chimpanzee sequences), compared to species more distantly related (e.g., human and  C. elegans  sequences). 
     Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith &amp; Waterman  Adv. Appl. Math.  2:482, 1981; Needleman &amp; Wunsch  J. Mol. Biol.  48:443-53, 1970; Pearson &amp; Lipman  Proc. Natl. Acad. Sci. USA  85:2444-48, 1988; Higgins &amp; Sharp  Gene,  73:237-44, 1988; Higgins &amp; Sharp  CABIOS  5:151-53, 1989; Corpet et al.,  Nuc. Acids Res.  16:10881-90, 1988; Huang et al.,  Computer Appls. in the Biosciences  8:155-65, 1992; and Pearson et al.,  Meth. Mol. Bio.  24:307-31, 1994. Altschul et al. ( J. Mol. Biol.  215:403-10, 1990) present a detailed consideration of sequence alignment methods and homology calculations. 
     The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al.  J. Mol. Biol.  215:403-10, 1990) is available from several sources, including the National Center for Biotechnology Information (NCBI, Bethesda, Md.) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. It can be accessed at the NCBI website, together with a description of how to determine sequence identity using this program. 
     An alternative indication that two nucleic acid molecules are closely related is that the two molecules hybridize to each other under stringent conditions. Stringent conditions are sequence-dependent and are different under different environmental parameters. Generally, stringent conditions are selected to be about 5° C. to 20° C. lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH. The T m  is the temperature (under defined ionic strength and pH) at which 50% of the target sequence remains hybridized to a perfectly matched probe or complementary strand. Conditions for nucleic acid hybridization and calculation of stringencies can be found in Sambrook et al. (ed.),  Molecular Cloning: A Laboratory Manual,  2 nd  ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, and Tijssen  Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes  Part I, Chapter 2, Elsevier, New York, 1993. 
     Nucleic acid sequences that do not show a high degree of identity can nevertheless encode similar amino acid sequences, due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid molecules that all encode substantially the same protein. 
     Thermostability: an enzyme that is thermostable is relatively unaffected by relatively high temperatures. In one specific, non-limiting example, a polymerase with a high degree of thermostability is unaffected by a temperature of at least 80° C., for example, 82° C., 85° C., 88° C., 90° C., 92° C., 95° C., or even higher temperatures. 
     Transfected: A process by which a nucleic acid molecule is introduced into cell, for instance by molecular biology techniques, resulting in a transfected cell. As used herein, the term transfection encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transduction with viral vectors, transfection with plasmid vectors, and introduction of DNA by electroporation, lipofection, and particle gun acceleration. 
     Translesion synthesis: Translesion synthesis is an important cellular mechanism to overcome replication blockage by DNA damage. To copy damaged DNA templates during replication, specialized DNA polymerases are required. In one specific, non-limiting example, a Y-family polymerase is used for translesion synthesis. 
     Translesion synthesis can be error-free or error-prone. From  E. coli  to humans, error-prone translesion synthesis constitutes a major mechanism of DNA damage-induced mutagenesis. As a response to DNA damage during replication, translesion synthesis contributes to cell survival and induced mutagenesis. 
     Vector: A nucleic acid molecule as introduced into a host cell, thereby producing a transfected host cell. Recombinant DNA vectors are vectors having recombinant DNA. A vector can include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication. A vector can also include one or more selectable marker genes and other genetic elements known in the art. Viral vectors are recombinant DNA vectors having at least some nucleic acid sequences derived from one or more viruses. 
     Y-family polymerase: Based on phylogenetic relationships, DNA polymerases can be broadly classified into five families. The A-family is typified by  E. coli  polymerase I; the B-family by  E. coli  polymerase II; the C-family by the  E. coli  polymerase III α-catalytic subunit; the D-family by archeal polymerases; and the X-family by eukaryotic polymerase β. Recently, a large number of new DNA polymerases have been identified, which although sharing significant amino acid sequence and similarity amongst themselves, exhibit little homology to any of the five previously identified polymerase families. This new family of polymerases has been described in the literature as the UmuC/DinB/Rev1/Rad30 superfamily. At the present time, these enzymes are best characterized in terms of their low-fidelity synthesis on undamaged DNA and their ability to bypass DNA lesions in vitro which normally block replication by members of the A-, B-, C-, D-, or X-family of polymerases. This family of polymerases has been re-named the Y-family of polymerases. 
     Many Y-family polymerases are known in the art. For a more thorough discussion of Y-family polymerases, see Ohmori et al.,  Mol. Cell.  8:7-8, 2001, which is herein incorporated by reference. In specific, non-limiting examples, a Y-family polymerase is Sac Dbh, Sso Dpo4, Dpo4LFDbh, DbhLFDpo4, AiLFSte (AiDpo4/SteDpo4LF), AiLFDpo4 (AiDpo4/SsoDpo4LF),  Acidianus infernus  Dpo4,  Stygiolobus azoricus  Dpo4,  Sulfurisphaera ohwakuensis  Dpo4,  Sulfolobus shibatae  Dpo4,  Sulfolobus tengchongensis  Dpo4,  Thermoascus aurantiacus  Pol eta,  Thermomyces lanuginosus  Pol eta,  Thermomyces lanuginosus  Pol iota,  Thermoascus aurantiacus  Pol iota,  Thermomyces lanuginosus  Pol kappa, or  Thermoascus aurantiacus  Pol kappa. 
     Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Hence “comprising A or B” means including A, or B, or A and B. It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. 
     III. Overview of Several Embodiments 
     Provided herein are novel Y-family polymerases and chimeras that are particularly well adapted for the PCR amplification of ancient or degraded DNA samples, such as from an ancient biological sample, mitochondrial DNA or forensic samples (e.g., paraffin-embedded samples). The Y-family polymerases (and chimeras) disclosed herein can enhance PCR-based recovery of forensic DNA samples or ancient DNAs from extinct organisms by promoting replication past DNA lesions refractory to standard DNA polymerases. A number of replication-blocking DNA lesions are known to accumulate in unprotected (or poorly preserved) DNA as it ages, for instance, due to exposure to oxygen, background radiation, and other genotoxic agents. These types of lesions are thus prevalent in old forensic DNA samples and ancient DNA samples, making standard PCR-based analysis difficult. Inclusion of a lesion-bypassing Y-family polymerase along with a conventional thermostable polymerase in a PCR protocol designed to amplify old DNA samples can greatly increase recoverability, accuracy and length of products. Exemplary Y-family polymerases include  Acidianus infernus  Dpo4 (SEQ ID NO: 6),  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8),  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10),  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12),  Sulfolobus tengchongensis  Dpo4 (SEQ ID NO: 14),  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41),  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43),  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45),  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47),  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61), as well as the Dpo4LFDbh (SEQ ID NO: 2), DbhLFDpo4 (SEQ ID NO: 4), AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57), and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59) chimeras. 
     In one embodiment, a Y-family polymerase is used independently to amplify damaged DNA. In another embodiment, a Y-family polymerase is combined with a standard thermostable polymerase, so as to promote bypass replication of inhibitory DNA lesions within the target molecule by the Y-family polymerase during the first one, a few or several rounds of thermocycling. Thereafter, the standard thermostable polymerase substantially or wholly takes over to complete the amplification process. Exemplary ratios of Y-family polymerase to standard thermostable polymerase include at least 1:1, such as at least 1:2, 1:5, 1:10, 1:25, 1:50, 1:100, 1:250, 1:500, and 1:1000, and such as at least 2:1, 5:1, 10:1, 25:1, 50:1, 100:1, 250:1, 500:1, and 1000:1. 
     In a specific, non-limiting example, one of the Dpo4 polymerases described herein (e.g.,  Acidianus infernus  Dpo4 (SEQ ID NO: 6),  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8),  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10),  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12), or  Sulfolobus tengchongensis  Dpo4 (SEQ ID NO: 14)) is used for a typical PCR protocol in place of a standard high-fidelity polymerase, such as Taq polymerase. The DNA is denatured, and a long first extension cycle is employed at approximately 60° C. (for instance, about 57° C. to about 63° C.) for approximately 30-60 minutes. After this extension cycle, a PCR thermocycling protocol is carried out as usual. Alternatively, this long extension step can be carried out at lower temperatures (for instance about 45° C. to about 55° C.) when one or more of the eukaryotic Y-family polymerases disclosed herein (e.g.,  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41),  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43),  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45),  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47), or  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61)) is used for the long extension step. In another specific, non-limiting example, a chimeric Y-family polymerase is used (e.g., Dpo4LFDbh (SEQ ID NO: 2), DbhLFDpo4 (SEQ ID NO: 4), AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57), or AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59)). In yet another specific, non-limiting example, a mixture of two or more of the Y-family polymerases (and/or chimeras) is used. 
     In a further, non-limiting example, Taq polymerase (or any other relatively high-fidelity polymerase) is added to the reaction mixture following the first extension cycle (which used the Y-family polymerase), and then a PCR thermocycling protocol is carried out as usual. In some embodiments, several PCR cycles are carried out with the Y-family polymerase(s) alone before a high-fidelity polymerase (or mixture of thereof) is added, for example 3-7 cycles (for instance 5 cycles) of 5-15 minutes each (for instance 10 minutes each). In yet a further, non-limiting example, a high-fidelity polymerase (e.g., Taq polymerase) and a Y-family polymerase are added to the reaction tube prior to the first extension cycle, and the entire PCR reaction is completed in a single “closed” reaction. The Taq polymerase (or another relatively high-fidelity polymerase) will compete with the Y-family polymerase for primer extension, but when it encounters a lesion in the template, it will terminate synthesis and fall off, allowing the Y-family polymerase to access the damaged DNA. Thus, the Y-family polymerases (and/or chimeras) disclosed herein, alone, or in combination with any other PCR enzyme, can amplify DNA targets that were previously “unamplifiable” or marginally amplifiable using conventional PCR methods. 
     In other embodiments, the Y-family polymerases (and chimeras) disclosed herein are used for making labeled DNA probes for molecular biology, either at high or low temperatures. The Y-family polymerases described herein are able to incorporate several different labeled DNA nucleotides into DNA during replication or primer extension. Thus, the novel Y-family polymerases disclosed herein provide a good substitute for Taq and other relatively high-fidelity polymerases in applications utilizing, for example, fluorescent nucleoside triphosphate derivatives or other labels. Such applications include, but are not limited to, production of fluorescent nucleic acid probes for DNA or RNA hybridization blots, DNA sequencing, flow sorting, fluorescence in situ hybridization, and microarray analysis. 
     In general, labeled nucleic acid molecules may be amplified using techniques well known to one of skill in the art, but a fluorescent derivative is substituted for an unmodified dNTP. The derivative can either be 100% substituted (i.e., all fluorescent or otherwise modified or labeled nucleotides), or used in a ratio (e.g., 1:100 of unmodified dNTP versus fluorescent dNTP), to generate an optimal fluorescent amplification product. In addition, many amplification techniques are automated and rely heavily on computer analyzed hybridization of fluorescent probes to specific genes or markers. By generating a probe with higher specific fluorescence, as is possible using the Y-family polymerases/chimeras described herein, the sensitivity of such assays is increased. 
     Furthermore, in addition to amplifying nucleotides while incorporating fluorescent or other labels, the Y-family polymerases/chimeras disclosed herein are also useful for amplifying a variety of other modified nucleotides and DNA analogues, for example, dinucleotide triphosphates, non-canonical base pairs (such as mispairs), as well as base analogues incorporated in the damaged or opposite strand to monitor structural and dynamic changes in the DNA. This approach also can be used to incorporate non-natural DNA nucleotides to expand the genetic “alphabet.” 
     In still other embodiments, the biochemical characteristics of the Y-family polymerases disclosed herein can be altered, enhanced, or augmented to tailor their activities to suit specific applications by constructing chimeric proteins or using directed-evolution techniques. Exemplary chimeras include Dpo4LFDbh (SEQ ID NO: 2), DbhLFDpo4 (SEQ ID NO: 4), AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57), and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59). Dpo4 has been crystallized in a ternary complex with DNA and incoming nucleoside triphosphate. Therefore, the domain architecture of the enzyme is known, as are the residues likely to be important for DNA binding and substrate specificity. For example, the LF domain is important for DNA binding, whereas residues in the “fingers” domain are important for substrate specificity (Ling et al.,  Cell  107:91-102, 2001; Silvian et al.,  Nat. Struct. Biol.  8:984-89, 2001). 
     In the case of the LF domain, generation of such chimeras is demonstrated herein by swapping the LF of the poorly processive Dbh enzyme with the more processive Dpo4 enzyme, which creates a chimeric enzyme more Dpo4-like in its lesion bypass and processivity. Based upon the amino acid alignments of the various polymerases, it is clear where the “breakpoints” between the various sub-domains of the polymerase lie. For example, the LF domain of the Y-family polymerases disclosed herein starts at codons 245 ( Sulfolobus acidocaldarius  Dbh); 244 ( Sulfolobus solfataricus  Dpo4); 245 ( Acidianus infernus  Dpo4); 245 ( Stygiolobus azoricus  Dpo4); 244 ( Sulfurisphaera ohwakuensis  Dpo4); 244 ( Sulfolobus shibatae  Dpo4), and 244 ( Sulfolobus tengchongensis  Dpo4). Thus, one specific example involves replacing the LF domain of the  Acidianus infernus  Dpo4 enzyme, which is less processive than  Sulfolobus solfataricus  Dpo4 or the  Sulfolobus tengchongensis  Dpo4, with the littler finger domain from either  Sulfolobus solfataricus  Dpo4 or  Sulfolobus tengchongensis  Dpo4, thereby creating a more robust polymerase. Similarly, the  Stygiolobus azoricus  Dpo4 and  Sulfurisphaera ohwakuensis  Dpo4 enzymes are poorly processive (like  Sulfolobus acidocaldarius  Dbh), but their activity is increased dramatically if the LF domain of either of these two enzymes is swapped with that from  Sulfolobus solfataricus  or  Sulfolobus tengchongensis.    
     The same approach can be utilized to domain-swap the “fingers” domain. The  Acidianus infernus  Dpo4 enzyme has many beneficial properties (e.g., it is thermostable and performs well in PCR), but it does not bypass lesions as well as  Sulfolobus solfataricus  Dpo4 or  Sulfolobus tengchongensis  Dpo4. Thus, the  Acidianus infernus  fingers domain can be swapped with, for example, that from  Sulfolobus solfataricus  Dpo4 or  Sulfolobus tengchongensis  Dpo4 in order to create an enzyme that bypasses lesions well. In addition, a “DNA shuffling” approach can be used to create a better polymerase, or a polymerase with specific desired characteristics. This technique uses randomly sheared DNA from homologous organisms to generate chimeras with enhanced properties. 
     Another approach to modify the Y-family polymerases described herein is called “compartmentalized self-replication”. In this technique, a Y-family polymerase gene (e.g., a Dpo4 gene) is used as a template for self replication in PCR. For example, to “evolve” a polymerase that is better at bypassing a CPD, primers are designed to the Y-family polymerase gene in question that contain a CPD in the oligonucleotide. Enzymes that have evolved to bypass the CPD better are more efficiently amplified and then cloned and isolated. Several cycles are performed until the enzyme is much better at CPD bypass. Examples of this method can be found in, for example, Ghadassy et al. ( Nat. Biotechnol.  22:755-59, 2004), which is incorporated by reference in its entirety. In addition to the Dpo4 polymerase, this approach can be used to perform compartmentalized self-replication of the fungal Pol eta, Pol iota and Pol kappa polymerases described herein. 
     Other applications for which the Y-family polymerases and chimeras disclosed herein are useful include, but are not limited to, labeling or tagging DNA, real-time PCR, detection of SNPs, mismatches or DNA lesions, mutagenic PCR, directed-evolution methods, and expanding the DNA “alphabet” utilizing non-natural nucleotides. In addition, any fragment of any of the Y-family polymerases disclosed herein can be used as part of a fusion protein. 
     IV. Chimeric Y-Family Polymerases 
     Although they share little primary amino acid sequence homology with DNA polymerases from other families, structural studies of two archaeal DinB-like polymerases, Dbh and Dpo4, and of the catalytic core of  Saccharomyces cerevisiae  Polη, reveal that they are topologically similar to classical polymerases in that they resemble a right hand and possess “fingers,” “palm” and “thumb” sub-domains. In addition these polymerases possess a unique domain that has been termed the “little finger” (Ling et al.,  Cell  107:91-102, 2001), “wrist” (Silvian et al.,  Nat. Struct. Biol.  8:984-89, 2001) or “PAD” (polymerase associated domain) (Trincao et al.,  Mol. Cell.  8:417-26, 2001) domain. The thumb and finger domains are smaller than those found in high-fidelity polymerases, and in the ternary complex of Dpo4 with DNA and an incoming nucleotide, the primer-template is held between the thumb and little finger (LF) domains and buttresses against the finger domain (Ling et al.,  Cell  107:91-102, 2001). The importance of the LF-DNA contact is highlighted by the fact that a proteolytic fragment of Dpo4 which retains the fingers, palm and thumb sub-domains, but lacks the LF domain, is much less active than the full-length polymerase (Ling et al.,  Cell  107:91-102, 2001). Interestingly, the LF domain is the least conserved of the four domains in the Y-family polymerases, and it is hypothesized that such divergence may, in part, contribute to the assorted biochemical properties reported in the literature for the various Y-family polymerases (Ling et al.,  Cell  107:91-102, 2001). 
     To further investigate the role that the LF domain contributes to the overall enzymatic properties of Y-family polymerases, the fact that both structural and biochemical data are available for two closely related archaeal DinB-like polymerases, Dbh and Dpo4, was taken advantage of. Dbh (DinB homolog) was identified and cloned by Kulaeva et al. using degenerate PCR primers designed against the  E. coli  umuC and dinB genes ( Mutat. Res.  357:245-53, 1996). The genomic DNA used in those studies was from an archaeal strain obtained from the American Type Culture Collection (ATCC, Manassas, Va.) that was originally believed to be  Sulfolobus solfataricus  P1. However, the entire genome of  Sulfolobus acidocaldarius  has recently been determined and the ˜2.5 kb dbh-containing sequence reported by Kulaeva et al. matches perfectly with the genomic sequence from  S. acidocaldarius . Dbh therefore originates from  S. acidocaldarius , not  S. solfataricus  P1. DNA polymerase IV (Dpo4) was identified in the genome of  Sulfolobus solfataricus  P2, through BLAST searches (Altschul et al.,  J. Mol. Biol.  215:403-10, 1990) of the complete P2 genome (She et al.,  Proc. Natl. Acad. Sci. USA  98:7835-40, 2001), using the dbh gene as a search query (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001). Overall, the Dbh and Dpo4 proteins share 54% identity, yet the two polymerases exhibit different enzymatic properties (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001; Gruz et al.,  J. Biol. Chem.  276:47394-401, 2001; Potapova, et al.,  J. Biol. Chem.  277:28157-66, 2002). Dpo4 is thermostable and exhibits robust polymerase activity. At high enzyme to template ratios it can synthesize more than 1 kb of DNA, thereby allowing it to substitute for Taq polymerase in PCR assays (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001). In addition, the lesion bypass properties of Dpo4 are somewhat like that of the eukaryotic translesion polymerases, in that Dpo4 can bypass thymine-thymine cyclobutane pyrimidine dimers (CPDs) (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001; Ling et al.,  Nature  424:1083-87, 2003; McCulloch et al.,  Nature  428:97-100, 2004) and abasic sites (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16; Kokoska et al.,  J. Biol. Chem.  278:50537-45, 2003). In contrast, Dbh is a much more distributive polymerase when replicating undamaged DNA, and is unable to incorporate a base opposite a CPD and bypasses an abasic site with very low efficiency (Gruz et al.,  J. Biol. Chem.  276:47394-401, 2001; Potapova, et al.,  J. Biol. Chem.  277:28157-66, 2002; Zhou et al.,  Mol. Cell.  8:427-37, 2001). 
     Structural studies of the two polymerases reveal that, in addition to sharing high sequence homology, the fingers, palm and thumb domains of the proteins are virtually superimposable. Without being bound by theory, this suggests that the different enzymatic properties of the two enzymes lie more in their sequence-divergent and structurally mobile LF domains. For example, in the Dpo4-DNA complex, the linker connecting the thumb and LF domains interacts only with DNA (Ling et al.,  Cell  107:91-102, 2001). In the apo-form of Dbh, however, this linker is hydrogen bonded to the β-sheets in the palm domain, as well as the β-sheets in the LF domain, thereby pinning the LF domain to the catalytic core (Silvian et al.,  Nat. Struct. Biol.  8:984-89, 2001). In order for Dbh to bind substrate, this linker has to peel off from the palm domain to allow the LF domain to reorient. 
     To investigate the role that the LF domain plays in determining the enzymatic properties of Y-family polymerases in general, Dbh-Dpo4 chimeras were constructed in which the LF domains and the preceding linker have been interchanged ( FIG. 1 ). Exemplary chimeras include Dpo4LFDbh (SEQ ID NO: 2), DbhLFDpo4 (SEQ ID NO: 4), AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57), and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59). Studies revealed that by replacing Dpo4&#39;s LF domain with that from Dbh, the enzyme became more “Dbh-like.” Conversely, by replacing Dbh&#39;s LF with that of Dpo4, the enzyme became more “Dpo4-like”, indicating that the LF domain is a major factor in determining the physical and enzymatic properties of each polymerase. These observations are discussed herein in light of the crystal structure of Dbh and of various Dpo4-DNA complexes. 
     V. Cloning Novel Y-Family Polymerases 
     In addition, disclosed herein are several novel Y-family polymerases, including:  Acidianus infernus  Dpo4 (SEQ ID NO: 6),  Stygiolobus azoricus  Dpo4 (SEQ ID NO: 8),  Sulfurisphaera ohwakuensis  Dpo4 (SEQ ID NO: 10),  Sulfolobus shibatae  Dpo4 (SEQ ID NO: 12), and  Sulfolobus tengchongensis  Dpo4 (SEQ ID NO: 14). Not only do these enzymes each have unique physical and enzymatic properties useful in, for instance, research and medical applications, but each of these Y-family polymerases also can be used to make chimeric Y-family polymerases that have still more unique physical and enzymatic properties. 
     By mutating or replacing the LF domains of these and other Y-family polymerases, polymerases can be created with the characteristics needed for a particular application. For example, altering the LF domain using the methods disclosed herein, a polymerase can be created that has a particular thermostability, fidelity, processivity, or ability to carry out translesion synthesis. 
     In addition to mutating or replacing the LF domain, the finger domain can be mutated or replaced with another Y-family polymerase finger domain. The finger domain is important as it makes a “substrate-lid.” Some of the Y-family polymerases have a more open or closed active site and may or may not be able to accommodate a variety of lesions or nucleoside analogs. Mutant or chimeric Y-family polymerases can also be created in which both the finger and LF domains have been mutated or replaced with domains from other Y-family polymerases. 
     Furthermore, processivity of the Y-family polymerases can be increased by modifying the PCNA binding site on the polymerase. PCNA is a “sliding-clamp” that helps to hold the polymerase on to DNA. The appropriate binding sites can be engineered into the chimeras so as to increase processivity at high temperature. 
     Several additional newly-identified Y-family polymerases are disclosed herein as well, for example  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41),  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43),  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45),  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47), and  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61). Because the functions and properties of human and yeast Pol eta are so well conserved, these enzymes have properties similar to other Pol eta family members. In addition, because these newly-identified Y-family polymerases originate in organisms that grow at relatively high temperatures (for example, approximately 45-50° C.), they are good candidate polymerases for protocols requiring thermostability. 
     These newly-identified Pol eta, Pol iota and Pol kappa polymerases can be used to form chimeric molecules with each other, as well as with other fungal or yeast Pol eta, iota and kappa genes. Using an approach similar to that described for the other Y-family polymerases described herein, one or more domains, for example a LF domain, can be swapped between the Pol eta (or iota/kappa) polymerases in order to create chimeric polymerase with a desired processivity and/or thermostability. 
     The following examples are provided to illustrate certain particular features and/or embodiments. These examples should not be construed to limit the invention to the particular features or embodiments described. 
     EXAMPLES 
     Example 1 
     Chimeric Y-Family Polymerases 
     This example describes the design and construction of chimeric Y-family polymerases. 
     Overproduction of  Sulfolobus acidocaldarius  Dbh 
     The dbh gene from  Sulfolobus acidocaldarius  was PCR-amplified from pOS21 (Kulaeva et al.,  Mutat. Res.  357:245-53, 1996) with two oligonucleotides, ssdbhbam: 5′-CGC GGA TCC TTA AAT GTC GAA GAA ATC AGA TAA ATT TG-3′ (SEQ ID NO: 32) and ssdbhbsp: 5′-CAT GTC ATG ATA GTG ATA TTC GTT GAT TTT G-3′ (SEQ ID NO: 33) containing a BamHI and BspHI restriction enzyme site respectively. The ˜1050 bp PCR fragment was digested with BamHI and BspHI and the fragment gel purified before cloning into pET16b (Novagen, Madison, Wis.) digested with NcoI and BamHI. The sequence of the dbh gene in the recombinant plasmid, called pJM349, was verified and subsequently introduced into  E. coli  strain RW382, a ΔumuDC595::cat derivative of BL21(λDE3) (McDonald et al.,  Proc. Natl. Acad. Sci. USA  95:1478-83, 1998). 
     Generation of DbhLFDpo4 and Dpo4LFDbh Chimeras 
     Native  Sulfolobus acidocaldarius  Dbh is a 354 amino acid protein with an estimated pI of 9.37.  Sulfolobus solfataricus  Dpo4 is two amino acids shorter and has an estimated pI of 9.11. Alignment of the two primary amino acid sequences reveals that although both proteins originate from related Sulfolobaceae, they only share 54% identity overall. Interestingly, most identity is found in the fingers, palm and thumb sub-domains of the polymerases, which are 59% identical. In contrast, the LF domain is least conserved, with only 41% primary amino acid sequence identity ( FIG. 1 ). To investigate the role that the LF domain plays in the enzymatic properties of Y-family polymerases, chimeric proteins were constructed in which the respective LF domains and the flexible linker that tethers it to the thumb domain were interchanged ( FIG. 1 ). 
     The first step toward generating Dbh/Dpo4 chimeras was to introduce a unique restriction enzyme site at the junction of the LF domain in Dpo4. This was achieved by site-directed mutagenesis (Quick Change, Stratagene, La Jolla, Calif.) of Leu228 (CTA→CTG) and Ala229 (GCT→GCC) codons, so as to produce a novel BalI/MscI restriction enzyme site within the Dpo4 gene. The BalI/MscI restriction site was generated in the Dpo4 over-expressing plasmid, p1914 (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001) using oligonucleotides P2SWDW: 5′-CTC GTC TCT GGC CAG AGA GAT CAA ATA TTT AGC C-3′ (SEQ ID NO: 34) and P2SWUP: 5′-TTG ATC TCT CTG GCC AGA GAC GAG TAT AAC GAG CC-3′ (SEQ ID NO: 35) and gave rise to plasmid p1941. Chimeras were subsequently generated by domain swapping as follows: an ˜700 bp NdeI-BalI/MscI fragment was amplified using pJM349 (Dbh) DNA as a template with primers P1ndeIup: 5′-GGG GGG CAT ATG ATA GTG ATA TTC GTT GAT-3′ (SEQ ID NO: 36) and P1bal2dw: 5′-GGG GGG ATT CTT GGC CAA CTT TAG TAG ATA TAA GGC TAA GGC-3′ (SEQ ID NO: 37) (NdeI and BalI/MscI restriction sites are underlined). The amplicon was then digested with NdeI and BalI/MscI and cloned into the similarly digested plasmid, p1941. The resulting plasmid, called p1947, therefore expresses a chimeric polymerase consisting of the thumb, finger and palm domains of Dbh, and the LF domain of the Dpo4 polymerase (DbhLFDpo4; SEQ ID NO: 4) ( FIG. 1 ). 
     A second plasmid, p1946, expressing the thumb, finger and palm domains of Dpo4 and the LF domain of the Dbh polymerase (Dpo4LFDbh; SEQ ID NO: 2) ( FIG. 1 ) was obtained by amplification of a dbh fragment from pJM349 with oligonucleotides P1balIup: 5′-GGG AAG T TG GCC A GA AAT AAA TAT AGT-3′ (SEQ ID NO: 38) and P1bam2dw: 5′-CCC CCC  GGA TCC  TTA AAT GTC GAA GAA ATC AGA-3′ (SEQ ID NO: 39) containing BalI/MscI and BamHI sites respectively (underlined). The amplicon was digested with BamHI and BalI/MscI and cloned into the similarly digested p1941 plasmid. The sequence of the chimeric Dpo4LFDbh and DbhLFDpo4 genes in p1946 and p1947, respectively, were verified and the plasmids were subsequently introduced into RW382. 
     Generation of AiLFSte (AiDpo4/SteDpo4LF) and AiLFDpo4 (AiDpo4/SsoDpo4LF) Chimeras 
     The AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57) and AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59) chimeras consist of the finger, thumb and palm domain from the  Acidianus infernus  Dpo4 and LF domain from the  Sulfolobus tengchongensis  Dpo4 or the  Sulfolobus solfataricus  Dpo4, respectively. These chimeras were prepared in a manner similar to the Dbh/Dpo4 chimeras described herein. Briefly, a BalI/MscI restriction site was generated in the  Acidianus infernus  dpo4 gene using oligonucleotides Ai_FMsc711: 5′-TAT TCT C TG GCC A AC AAT ACC TAT GCT GAA CCG-3′ (SEQ ID NO: 73) and Ai_RMsc667: 5′-GGT ATT GT T GGC C AG AGA ATA CAA GTA ACT AGC-3′ (SEQ ID NO: 74), and generated in the  Sulfolobus tengchongensis  dpo4 gene using oligonucleotides Ste_FMsc708b: 5′-TTC TCG C TG GCC A GA GAT GAA TAT TTT GAA CCA-3′ (SEQ ID NO: 75) and Ste_RMsc644: 5′-TTC ATC TCT GGC CAG CGA GAA TAA GTA ATT AGC-3′ (SEQ ID NO: 76). The LF domain of the  Acidianus infernus  dpo4 gene was then replaced from the BalI/MscI site to the BamHI site with either the  Sulfolobus tengchongensis  dpo4 BalI/MscI to BamHI LF domain fragment, or the  Sulfolobus solfataricus  dpo4 BalI/MscI to BamHI LF domain fragment to create the AiLFSte (AiDpo4/SteDpo4LF) (SEQ ID NO: 57) or the AiLFDpo4 (AiDpo4/SsoDpo4LF) (SEQ ID NO: 59) chimeras. 
     Purification of Dpo4, Dbh, and Chimeric Proteins 
     The protocol utilized to purify all of the polymerases was based upon that described for  Sulfolobus solfataricus  Dpo4 (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001), but includes several modifications. Although all of the recombinant genes are under the control of an IPTG-inducible T7 promoter (in the parental pET vector), significant expression of the recombinant proteins was found in the absence of induction. Furthermore, the Sulfolobaceae proteins are very stable in  E. coli  and significant quantities of the recombinant proteins was recovered by simply harvesting uninduced stationary phase overnight cultures of RW382 harboring the Dpo4/Dbh-expressing plasmids. Soluble cell extracts were made, but the heat-denaturation step that removes significant quantities of the thermolabile  E. coli  proteins was reduced from 85° C. to 75° C. for 5 min. Each polymerase was purified to homogeneity in three chromatographic steps using HiTrapQ, Hydroxylapatite and Mono S columns, except that the phosphate buffer used in the HiTrapQ column was replaced by a 20 mM HEPES buffer at pH 7.0, containing 100 mM NaCl, 1 mM DTT and 0.1 mM EDTA. 
     DNA Templates for In Vitro Primer Extension Assays 
     Most of the synthetic oligonucleotides used in the in vitro replication assays were synthesized by Lofstrand Laboratories (Gaithersburg, Md.) using standard techniques and were gel purified prior to use. Where utilized, the synthetic abasic site (dSpacer) was purchased from Glen Research (Sterling, Va.) and was incorporated into oligonucleotide templates using standard protocols by Lofstrand Laboratories (Gaithersburg, Md.). The exception was the cis-syn cyclobutane pyrimidine dimer-containing oligonucleotide that was synthesized and purified by Phoenix Biotechnologies (Huntsville, Ala.). Primers were 5′-labeled with [γ- 32 P]ATP (5000 Ci/mmole; 1 Ci=37 GBq) (Amersham Biosciences, Piscatway, N.J.) using T4 polynucleotide kinase (Invitrogen, Carlsbad, Calif.). The sequence of each primer/template is given in the legend of the respective figure in which it was used. Single-stranded M13 mp18 DNA was purchased from Invitrogen (Carlsbad, Calif.). 
     In Vitro Primer Extension Assays 
     Radiolabeled primer-template DNAs were prepared by annealing the 5′-[ 32 P]-labeled primer to the unlabeled template DNA at a molar ratio of 1:1.5. Standard 10 μl reactions contained 40 mM Tris.HCl at pH 8.0, 5 mM MgCl 2 , 100 μM of each ultrapure dNTP (Amersham Biosciences, Piscatway, N.J.), 10 mM DTT, 250 μg/ml BSA, 2.5% glycerol, and 10 nM primer-template DNA. The concentration of polymerase added varied and is given in the respective figure legend. After incubation at 37° C. or 60° C. for various times, reactions were terminated by the addition of 10 μl of 95% formamide/10 mM EDTA and the samples heated to 100° C. for 5 min and briefly chilled on ice. Reaction mixtures (5 μl) were subjected to polyacrylamide/8 M Urea gel electrophoresis and replication products visualized by PhosphorImager analysis. 
     Forward Mutation Assay 
     Reaction mixtures (30 μl) contained 1 nM gel-purified M13 mp2 gapped DNA substrate, 40 mM Tris.HCl (pH 9.0 at 22° C.), 5 mM MgCl 2 , 10 mM dithiothreitol, 7.5 μg bovine serum albumin, 2.5% glycerol and 1 mM each of dATP, dGTP, dCTP and dTTP. Polymerization reactions were initiated by adding 20 nM Dpo4LFDbh or 1.5 nM DbhLFDpo4, incubated at 70° C. for 1 hour and terminated by adding EDTA to 15 mM. DNA products were analyzed by agarose gel electrophoresis and assayed for the frequency of lacZ mutants as described by Bebenek et al. ( Methods Enzymol.  262:217-32, 1995) and Kokoska et al. ( J. Biol. Chem.  277:19633-38, 2002). DNA samples from independent lacZ mutant phage were sequenced to identify the sequence changes generated during gap-filling synthesis. Error rates were calculated as described by Bebenek et al. ( Methods Enzymol.  262:217-32, 1995) and Kokoska et al. ( J. Biol. Chem.  277:19633-38, 2002). 
     Size Distribution of Replication Products Synthesized by Native and Chimeric Dpo4 and Dbh Polymerases 
     In vitro replication reactions with Y-family polymerases have clearly established that they are less processive than high-fidelity replicative polymerases. However, the absolute number of nucleotides incorporated per DNA binding event varies considerably among Y-family polymerases. For example, recent studies suggest that archaeal Dpo4 is more processive than human Polη (Kokoska et al.,  J. Biol. Chem.  278:50537-45, 2003). Indeed, when replicating circular M13 DNA at high enzyme to template ratios, Dpo4 synthesizes replication products that are several hundred nucleotides in length ( FIG. 2 ). Under the same assay conditions, Dbh-dependent replication products are much shorter. Moreover, in contrast to Dpo4, adding a large molar excess of Dbh to the reaction does not dramatically change the size distribution of replication products on the circular M13 primer/template. The size distribution of replication products appears to be largely dependent upon the LF domain. Replacing the native LF domain of Dbh with that of Dpo4 leads to a dramatic increase in the size of the overall length of the replication products. Conversely, replacing the native LF domain of Dpo4 with that of Dbh reduces the size distribution of replication products from several hundred nucleotides at a 20-fold molar excess, to ˜50 nucleotides or less at the same enzyme to template ratio ( FIG. 2 ). Similar results were obtained in experiments performed at 60° C. with a shorter linear DNA template and a large molar excess of substrate over enzyme, so as to more accurately measure processivity of each enzyme during a single extension reaction ( FIG. 3 ). Under reaction conditions where primer usage is minimal, full-length replication products are only observed in the presence of Dpo4 and the chimeric DbhLFDpo4, whereas those generated by either Dbh or Dpo4LFDbh, are considerably shorter. Based upon these observations, the respective LF domain of Dpo4/Dbh is the major factor determining the overall processivity of the two enzymes. Such conclusions are consistent with the crystallized ternary structure of Dpo4-DNA and incoming nucleotide, which revealed that Dpo4&#39;s LF domain in conjunction with the thumb domain wraps around DNA and helps hold the polymerase on to the primer-terminus (Ling et al.,  Cell  107:91-102, 2001). 
     Effect of LF Domain Swapping on Translesion DNA Synthesis of CPD and Abasic Sites 
     Previous studies have shown that although Dpo4 is phylogenetically located in the DinB branch of the Y-family polymerases, it actually has enzymatic properties that are reminiscent of Polη-like enzymes, in that it can bypass cis-syn cyclobutane pyrimidine dimers (CPDs). The efficiency of Dpo4-dependent bypass of a CPD has been estimated to be approximately one tenth of that of human Polη (McCulloch et al.,  Nature  428:97-100, 2004). The reduced ability of Dpo4 to bypass a CPD compared to Polη appears to be largely due to stearic clashes between the 5′-T of the CPD and Dpo4, when the enzyme attempts to incorporate a nucleotide opposite the covalently linked 3′-T of the CPD (Ling et al.,  Nature  424:1083-87, 2003). Nevertheless, the ability of Dpo4 to bypass a CPD is greater than that of the related Pol IV (Tang et al.,  Nature  404:1014-18, 2000), Pol kappa (Johnson et al.,  Proc. Natl. Acad. Sci. USA  97:3838-43, 2000; Ohashi et al.,  Genes  &amp;  Dev.  14:1589-94, 2000; Zhang et al.,  Nucleic Acids Res.  28:4138-46, 2000) or Dbh polymerases ( FIG. 4 ), which have little ability to incorporate a base opposite the 3′-T of the dimer. Likewise, Dpo4 can bypass a synthetic abasic site (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001; Kokoska et al.,  J. Biol. Chem.  278:50537-45, 2003) ( FIG. 4 ), yet Dbh only does so at high enzyme to template ratios and high levels of dNTPs (Potapova et al.,  J. Biol. Chem.  277:28157-66, 2002) ( FIG. 4 ). Similar to the results above with undamaged DNAs ( FIG. 2  &amp;  FIG. 3 ), lesion bypass appears to depend upon the LF domain of the protein. While Dpo4 bypasses both CPDs and an abasic site, Dbh and the Dpo4LFDbh chimera showed only a limited ability to incorporate a base opposite either lesion even when they were present at a 10-fold excess of enzyme to template ( FIG. 4 ). In contrast, replacing the Dbh LF domain with that of Dpo4 allowed the chimera to bypass an abasic site and a CPD, albeit with somewhat lower efficiency than wild-type Dpo4 ( FIG. 4 ). These observations suggest that like Dpo4, the active site of Dbh can accommodate both adducts, but that the efficiency with which the chimeras bypass these lesions is largely determined by their LF domain. 
     Effects of LF Domain Swapping on Fidelity 
     Since the processivity and lesion-bypassing properties of the chimeras is strongly influenced by the LF domain, determining if the LF might also effect the fidelity of the enzymes when replicating undamaged DNA was also investigated. To examine this possibility, the pattern of insertion of each of the four nucleotides opposite template Guanine by Dpo4, Dbh and the LF chimeras in primer extension assays that were performed at 37° C. or 60° C. were analyzed. Similar to the temperature-dependent increase in catalytic activity reported for Dbh (Potapova et al.,  J. Biol. Chem.  277:28157-66, 2002), all four polymerases are more active at 60° C. as compared to 37° C. Using amounts of each enzyme yielding roughly similar levels of primer extension, it was found that at both temperatures, Dbh favors incorporation of correct dCMP rather than any of the three incorrect nucleotides, whereas Dpo4 extends the radiolabeled primer by one or more bases in the presence of either correct dCTP or any of the three incorrect dNTPs ( FIG. 5 ). This difference in insertion specificity largely depends on the LF domain because Dpo4LFDbh gave a pattern similar to wild-type Dbh, whereas DbhLFDpo4 was more similar to Dpo4 than to Dbh. These qualitative misinsertion results at a single template nucleotide suggest that the LF domain can influence the fidelity with which Y-family polymerases replicate undamaged DNA. 
     To test this hypothesis quantitatively and at a large number of template positions, the effects of LF domain swapping on fidelity during synthesis of a 407-base single-stranded gap in M13 mp2 DNA that contains the lacZ α-complementation gene sequence was determined. Base substitution, addition and deletion error rates for the two chimeric polymerases to those previously reported for Dpo4 using the same assay were compared (Kokoska et al.,  J. Biol. Chem.  277:19633-38, 2002). Owing to an inability to fill the lacZ gapped substrate with Dbh under any condition examined, for comparison to the other three enzymes, the error rates for Dbh obtained using a 203-base substrate containing the HSV-tk target gene were used (Potapova et al.,  J. Biol. Chem.  277:28157-66, 2002). Although the lacZ and HSV-tk gene sequences are not identical, both mutational targets score many different types of errors in numerous sequence contexts, such that overall average error rates are representative when considering major classes of events, as described herein. Results of the fidelity assays for all four polymerases are shown in Table 1. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Fidelity of Dpo4, DbhLFDpo4, Dpo4LFDbh and Dbh polymerases. 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Dpo4 
                 DbhLFDpo4 
                 Dpo4LFDbh 
                 Dbh 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                 Total plaques 
                 6253 
                 1782 
                 4574 
                   
               
               
                 Total mutants 
                 975 
                 233 
                 2077 
               
               
                 Frequency 
                 1.56 × 10 −1   
                 1.31 × 10 −1   
                 4.54 × 10 −1   
                 1.7 × 10 −1   
               
               
                 Mutants 
                 182 
                 78 
                 68 
                 46 
               
               
                 sequenced 
               
               
                 Total bases 
                 50050 
                 21450 
                 18700 
                 7682 
               
               
                 sequenced 
               
               
                 Total seq changes 
                 476 
                 154 
                 140 
                 290 
               
               
                 Changes/mutant 
                 2.6 
                 2.0 
                 2.1 
                 6.3 
               
               
                 # of substitutions 
                 326 
                 102 
                 37 
                 42 
               
               
                 # 1 bp deletions 
                 116 
                 41 
                 91 
                 228 
               
               
                 # 1 bp additions 
                 9 
                 5 
                 1 
                 3 
               
               
                 Other 
                 25 
                 6 
                 11 
                 7 
               
               
                 Rate of 
                 6.5 × 10 −3   
                 4.8 × 10 −3   
                 2.0 × 10 −3   
                 5.5 × 10 −3   
               
               
                 substitutions 
               
               
                 Rate 1 bp 
                 2.3 × 10 −3   
                 1.9 × 10 −3   
                 4.9 × 10 −3   
                 3.0 × 10 −2   
               
               
                 deletions 
               
               
                   
               
            
           
         
       
     
     As reported by Kokoska et al. ( J. Biol. Chem.  277:19633-38, 2002), Dpo4 has low fidelity and an average error rate for single-base deletions about 3-fold lower than for single base substitutions ( FIG. 6A ). When averaged for all 12 mispairs at many different template locations, the overall single-base substitution error rate of Dbh is similar to that of Dpo4 (Table 1; from Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001). However, Dbh is 13-fold less accurate than Dpo4 for single base deletions (Table 1), such that the ratio of single-base deletions to single-base substitutions ( FIG. 6A ) is much higher for Dbh (5.5 to 1) than for Dpo4 (0.35:1). Moreover, Dbh generates single-base deletions within repetitive sequence tracts at a rate that is about 8-fold higher than for single-base deletions of non-repeated nucleotides ( FIG. 6B ). In contrast, the Dpo4 rates for deleting iterated and non-iterated nucleotides differ by less than 2-fold. These results suggest that, despite their sequence homology and structural similarities, Dpo4 and Dbh differ in single-base deletion fidelity, with Dbh being particularly prone to deleting nucleotides in mononucleotide runs. 
     In this analysis, swapping the LF domains had little effect on the overall average single-base substitution error rates of Dpo4 and Dbh (Table 1). This does not exclude an effect of the LF on error rates for specific base substitutions at specific sites (as suggested by the data in  FIG. 5 ). When the Dpo4 LF is swapped into Dbh, the ratio of the deletion to substitution rate is more similar to that of Dpo4 than Dbh (Table 1 and  FIG. 6A ), as are the error rates for deleting iterated and non-iterated bases (Table 1 and  FIG. 6B ). In contrast, when the Dbh LF is swapped into Dpo4, the ratio of deletion to substitution rate is higher (Table 1 and  FIG. 6A ), and the rate of deleting iterated bases is about 3-fold higher than the rate of deletion of non-iterated bases (Table 1 and  FIG. 6B ). The LF domains of Dpo4 and Dbh differentially influence error rates, primarily for deletion of single nucleotides, within repetitive sequences. 
     Structural Aspects of the LF Domain that Lead to DNA Binding and Translocation 
     Data presented herein shows that the LF domain of the polymerase has a significant effect on the processivity, fidelity and lesion-bypassing potential of the Y-family polymerases. By generating chimeras in which the LF domain of the Dpo4 and Dbh polymerases were interchanged, it was demonstrated that certain biochemical characteristics of the recombinant chimeras are similar to the polymerase from which the LF originated. For example, DbhLFDpo4 is similar to native Dpo4 in its processivity and ability to bypass a CPD or an abasic site. Conversely, swapping Dpo4&#39;s LF domain with that of Dbh (Dpo4LFDbh) reduces the catalytic activity of the enzyme on undamaged DNA and its ability to bypass a CPD and abasic site ( FIGS. 2 ,  3  &amp;  4 ). The fidelity results with undamaged DNA templates ( FIG. 6 ; Table 1) indicate that error rates for single nucleotide deletions within repetitive sequences are differentially influenced by the identity of the LF domain. Dpo4LFDbh, which deletes single nucleotides within repetitive sequences at higher rates than Dpo4 is quite distributive ( FIG. 3 ) and is unable to generate long DNA chains in reactions involving multiple cycles of DNA binding-synthesis-dissociation ( FIG. 2 ). This correlation is noteworthy in light of extensive evidence with polymerases in other families (Bebenek et al.,  Cold Spring Harb. Symp. Quant. Biol.  65:81-91, 2000), suggesting that single-base deletion intermediates in repetitive sequences arise as the polymerase dissociates and/or reassociates with the primer-template. This suggests that for Y-family polymerases with generally low-fidelity for single-base deletion errors (Kokoska et al.,  J. Biol. Chem.  277:19633-38, 2002, and references therein), LF domain-specific interactions with the duplex primer-template region that control enzyme processivity, can also influence DNA strand alignment. 
     Alignment of the primary amino acid sequence of the Dpo4 and Dbh LF domains (residues 245-352 and 244-354, respectively) reveals that they are much less conserved than their catalytic cores (41% versus 59%), yet superposition of the LF domains in the Dpo4-DNA and apo-Dbh structures shows that the alpha-carbon backbone of the two domains is nearly indistinguishable ( FIG. 7 ). However, despite their overall structural similarity, the LF domains of Dbh and Dpo4 differ in their surface curvature and electropotential. In particular, the LF domain of Dpo4 is more positively charged, especially at key residues shown to contact the DNA backbone in the Dpo4 ternary complex structures. These subtle changes, combined with the slightly different curvature of the surface, may alter the ability of the domain to interact with DNA. In addition, the linker region (residues 232-245) that connects the LF and thumb domains of each polymerase is highly variable and has a very different electrostatic potential. The 14 amino acid Dbh linker has an estimated pI of 8.6, but the corresponding region in Dpo4 is much more basic (estimated pI of 10), which may alter the interactions with a DNA substrate. Furthermore, the Dbh linker appears to be sandwiched between the β-sheets of both the palm and LF domains. This particular conformation would make it difficult for the LF to dissociate from the catalytic core of Dbh and to subsequently interact with DNA. In the absence of a crystal structure of apo-Dpo4, the possibility that in the absence of a DNA substrate, Dpo4 may also retract its LF domain in the same manner as Dbh, cannot be excluded. 
     Several structures of Dpo4 in a ternary complex with undamaged (Ling et al.,  Cell  107:91-102, 2001) and lesion-containing DNA (Ling et al.,  Nature  424:1083-87, 2003; Ling et al.,  Mol. Cell.  13:751-62, 2004; Ling et al.,  PNAS  101:2265-69, 2004) have been solved. Comparison of these structures reveal that tertiary structures are very similar in nature with only modest variations in their finger, palm and thumb domains. There is, however, substantial movement in the LF domain to accommodate the various types of DNA lesions encountered. One of these structures (Ab-5) (Ling et al.,  Mol. Cell.  13:751-62, 2004), which depicts an abortive complex of Dpo4 attempting to replicate an abasic lesion, reveals that the Dpo4 LF undergoes a rotation of 54° and a 4.1 Å translation, similar in magnitude to the movement that would be required for the Dbh LF to dissociate from the catalytic core and to bind substrate. In the Ab-5 structure, the DNA template makes a “U-turn” and the base 3′ to the abasic lesion becomes the template for replication. These observations suggest that the LF domain not only helps the polymerase bind to DNA, but physical movement of the domain also facilitates DNA translocation along the primer-template. Such observations are therefore in good agreement with findings that the LF domain plays an important role in determining the processivity of the polymerase ( FIG. 4 ). 
     By making chimeras in which the LF domains of two closely related archaeal Y-family polymerases were interchanged, a hitherto pivotal role of the LF domain in determining the enzymatic properties of the enzymes has been uncovered. This includes effects on their processivity, ability to bypass template lesions, and their capacity to generate base-pair substitutions versus single-base deletions during low-fidelity DNA synthesis of undamaged DNA. The LF domain of Y-family polymerases is the least conserved among their four structural domains, but like the two diverged LF domains from Dpo4 and Dbh, they undoubtedly share common structural features. Therefore, just like Dpo4 or Dbh polymerases, subtle amino acid variations in the LF domains of the various polymerases likely contributes to a wide variety of enzymatic properties previously attributed to Y-family polymerases. 
     Example 2 
     Cloning of a Y-Family Polymerases from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , and  Sulfolobus tengchongensis    
     This example describes the cloning of Y-family polymerases from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , and  Sulfolobus tengchongensis . One of ordinary skill in the art will recognize that similar methods can be used to clone Y-family polymerases from other Archaea. 
     A set of degenerate primers were generated and used to obtain sequences 5′- and 3′- to dpo4 from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , and  Sulfolobus tengchongensis . The degenerate primers are based on conserved sequences upstream ( FIG. 8 ) and downstream ( FIG. 9 ) of dpo4-like genes in  Sulfolobus acidocaldarius, Sulfolobus solfataricus  and  Sulfolobus tokodaii . The consensus or “majority” amino acid sequence upstream and downstream of Dpo4 based on these three sequences is shown in  FIGS. 8 and 9 . To obtain an approximately 500 bp fragment of a 5′-section from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , or  Sulfolobus tengchongensis , the following degenerate primers were used to amplify the consensus region DTTGAGD (SEQ ID NO: 22; see  FIG. 8 ): 5′-CCG GAA TTC  GAY ACI ACI GGI GCI GGI GAY-3′ (SEQ ID NO: 23) and 5′-GCC G CT CGA G TC IAD RWA IGC YTC RTC IAY ISW IRY-3′ (SEQ ID NO: 24) ( FIG. 10 ). To obtain an approximately 1100 bp fragment of a 3′-section from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , or  Sulfolobus tengchongensis , the following degenerate primers were generated to amplify the consensus region YEDVEGG (SEQ ID NO: 25; see FIG.  9 ): 5′-CCG GAA TTC  RYI WSI RTI GAY GAR GCI TWY HTI GA-3′ (SEQ ID NO: 26) and 5′-GCC G CT CGA G TA YGA RGA YGT IGA RGG IGG-3′ (SEQ ID NO: 27) ( FIG. 10 ). 
     The primers were incubated with DNA obtained from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , or  Sulfolobus tengchongensis , and PCR amplification performed using standard methods. Briefly, the samples were thermocycled using the following reaction conditions: 95° C. for 30 seconds, 50° C. for 1 minute, 71° C. for 2 minutes, for a total of 55 cycles. The reaction mix included 500 Rx, 200-300 ng of DNA, 0.4 μM primer, and 3 mM MgCl2. The resulting PCR amplification products were sequenced, and gene specific primers designed to the start and end of the Dpo4-like gene from each organism. The primers designed also included restriction sites for sub-cloning the gene into an expression vector. They have an NdeI site at the start of the gene and a BamHI site at the 3′-end, so as to clone into pET22 derivatives. 
     Using the PCR conditions described above, the full-length Y-family polymerase gene from  Acidianus infernus  (SEQ ID NO: 5),  Stygiolobus azoricus  (SEQ ID NO: 7),  Sulfurisphaera ohwakuensis  (SEQ ID NO: 9),  Sulfolobus shibatae  (SEQ ID NO: 11), and  Sulfolobus tengchongensis  (SEQ ID NO: 13) was re-amplified with a high fidelity PCR polymerase. An amino acid alignment of the polymerases is shown in  FIG. 15 . 
     Example 3 
     Cloning of Y-Family Polymerases from  Thermoascus aurantiacus  and  Thermomyces lanuginosus    
     This example describes the cloning of Y-family polymerases from  Thermoascus aurantiacus  and  Thermomyces lanuginosus.    
     Additional newly-identified Y-family polymerases are disclosed herein, including  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41),  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43),  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45),  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47), and  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61). Because the functions and properties of human and yeast Pol eta are so well conserved, these enzymes have properties similar to other Pol eta family members. In addition, because these newly-identified Y-family polymerases originate in organisms that grow at relatively high temperatures (for example, approximately 45-50° C.), they are good candidate polymerases for protocols requiring or benefiting from thermostability. For example, the  Thermoascus aurantiacus  polymerases function optimally at approximately 49-52° C. and have a maximum operating temperature of about 61° C., while the  Thermomyces lanuginosus  polymerases function optimally at approximately 45-50° C. and have a maximum operating temperature of about 60° C. An example of the activity of the  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41) and  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43) polymerases is shown in Example 9. 
     These newly-identified Pol eta, Pol iota and Pol kappa polymerases can be used to form chimeric molecules with each other, as well as with other fungal or yeast Pol eta, iota and kappa genes. Using an approach similar to that described for the other Y-family polymerases described herein, one or more domains, for example a LF domain, can be swapped between the Pol eta (or iota/kappa) polymerases in order to create chimeric polymerase with a desired processivity and/or thermostability. 
     The  Thermoascus aurantiacus  Pol eta (SEQ ID NO: 41) and  Thermomyces lanuginosus  Pol eta (SEQ ID NO: 43) polymerases were isolated using degenerate PCR primers based on other fungal polymerase eta genes from  Aspergillus fumigatus, Aspergillus nidulans, Coccidioides posadasii, Gibberella zeae, Magnaporthe grisea , and  Neurospora crassa . The first degenerate primers that successfully PCR amplified a piece of these genes were based on the following two amino acid sequences: (D/N)(A/C)F(F/Y)AQCE (SEQ ID NO: 48) and DEVF(I/M)DL (SEQ ID NO: 49). Amino acids shown in the parentheses are alternative sequences used to generate the degenerate primers. Additional gene-specific PCR primers and additional degenerate PCR primers were designed, including primers based on the following amino acid sequences: GGKLG(E/D)Q (SEQ ID NO: 50) and GFEDG(V/T/I)(T/S/N) (SEQ ID NO: 51). Inverse PCR was employed to obtain the complete 5′-end of the  Thermomyces lanuginosus  gene. Inverse PCR was also used to obtain a portion of the  Thermoascus aurantiacus  3′-end. Flanking sequence PCR was employed to complete the beginning and end of these genes. 
     The  Thermomyces lanuginosus  Pol iota (SEQ ID NO: 45) and  Thermoascus aurantiacus  Pol iota (SEQ ID NO: 47) polymerases were isolated using degenerate PCR primers based on other fungal polymerase iota genes from  Aspergillus fumigatus, Aspergillus nidulans, Coccidioides posadasii, Gibberella zeae, Magnaporthe grisea , and  Neurospora crassa . The first degenerate primers that successfully PCR amplified a piece of these genes were based on the following two amino acid sequences: DYDCFYA (SEQ ID NO: 52) and GEDLT(RKP)F (SEQ ID NO: 53). Amino acids shown in the parentheses are alternative sequences used to generate the degenerate primers. Additional sequences of the  Thermomyces lanuginosus  Pol iota gene and the  Thermoascus aurantiacus  Pol iota gene were obtained by performing flanking-sequence PCR as described by Sørensen et al. ( J. Virol.  67:7118-24, 1993). The functions and properties of human and  Drosophila  polymerase iota are very different (e.g., human DNA polymerase iota bypasses a CPD inefficiently and with low-fidelity, whereas  Drosophila  Pol iota does so efficiently and accurately), and it is likely that  Thermomyces lanuginosus  Pol iota and  Thermoascus aurantiacus  Pol iota have properties similar to either lower eukaryotes (e.g.,  Drosophila ) or higher eukaryotes (e.g., humans and mice). In addition, like other Y-family polymerases, they are good candidates for protocols requiring thermostability. 
     The  Thermomyces lanuginosus  Pol kappa (SEQ ID NO: 61) polymerase (partial) was isolated by performing degenerate PCR using primers that were based on the following two amino acid sequences: GVLTTCNY (SEQ ID NO: 77) [Funkappa_FRIDegen3 5′-CCG GAA TTC GGI GTI YTI ACI ACI TGY AAY TAY-3′ (SEQ ID NO: 78)] and NKPNGQ(FY) (SEQ ID NO: 79) [Funkappa_RXhDegen2 5′-GCC GCT CGA GRW AYT GIC CRT TIG GYT TRT T-3′ (SEQ ID NO: 80)]. Amino acids shown in the parentheses are alternative sequences used to generate the degenerate primers. 
     Example 4 
     Cloning Other Y-Family Polymerase Sequences 
     This example describes methods that can be used to identify Y-family polymerases from other organisms, such as other Archaea, for example, members of the phyla Crenarchaeota. As described herein in Example 2,  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , and  Sulfolobus tengchongensis  Y-family polymerases were cloned using degenerate primers that recognize a consensus sequence upstream and downstream of dpo4. Using identical or similar methods, additional Y-family polymerases can be identified. 
     For example, using the two-step PCR approach described in Example 2, Y-family polymerases can be cloned from other organisms. Briefly, DNA of the desired organism is PCR amplified in the presence of SEQ ID NOs: 23 and 24 or SEQ ID NOs: 26 and 27 to obtain sequences 5′- and 3′- to the Y-family polymerase, respectively, using the PCR conditions described in Example 2. Based on the sequence of each of the resulting two products, gene-specific primers are designed to the start and end of the Dpo4-like gene. The primers can also include restriction sites for sub-cloning the gene into an expression vector. Using standard PCR conditions, a full-length Y-family polymerase gene is re-amplified using a high fidelity PCR polymerase. 
     A one-step PCR approach can also be used to clone other Y-family polymerases. Briefly, DNA of the desired Archaea organism is PCR amplified in the presence of two primers, for example, SEQ ID NOs: 23 and 27, under standard PCR conditions, such as those described in Example 2. 
     DNA does not need to be isolated from an organism prior to PCR amplification. In some examples, the organism is incubated directly with the PCR primers, dNTPs, and other PCR reagents. In other examples, isolated DNA is incubated with the PCR primers, dNTPs, and other PCR reagents. 
     One skilled in the art will understand that degenerate primers that vary from SEQ ID NOs: 23, 24, 26, and 27 can also be used to practice the methods disclosed herein. For example, other degenerate primers that vary from SEQ ID NOs: 23, 24, 26, and 27 by one, two, three, four, or more nucleic acid residues, can still retain the ability to amplify a consensus sequence. 
     Example 5 
     Expression of Y-Family Polymerase Sequences 
     This example describes the expression of Y-family polymerases and chimeras. 
     The newly-identified Y-family polymerase genes were expressed from an IPTG-inducible promoter. As expression of Dpo4 is “leaky” and significant amounts of the protein accumulate by simply growing cells overnight without, the newly-identified Y-family polymerases were also grown in this fashion. The  Acidianus infernus  (two separate cultures) and  Sulfolobus shibatae  cultures gave strong signals ( FIG. 11 ; “M,” marker and “C,” strain without plasmid). Expression in the  Stygiolobus azoricus  and  Sulfurisphaera ohwakuensis  cultures was lower, but was increased by induction with IPTG ( FIG. 12 ). 
     Example 6 
     Partial Purification Via Heat Denaturation of  E. coli  Proteins 
     This example describes the partial purification of Y-family polymerases using heat denaturation. 
     Dpo4-like enzymes are thermostable and when expressed in  E. coli , cell extracts can be enriched for the thermostable polymerase by simply heating a crude cell lysate to 70° C. for 10 minutes. This causes many of the endogenous  E. coli  proteins to denature and precipitate. The denatured proteins can be removed by centrifugation, leaving the desired thermostable polymerase in solution. 
     Following heat treatment and centrifugation, the  Acidianus infernus, Sulfolobus shibatae , and  Sulfolobus tengchongensis , extracts were applied to a 10 ml Hydroxyapatite Bio-Gel HTP Gel column (Bio-Rad, Hercules, Calif.), and were eluted in a 10 mM to 500 mM KHPO4 (pH 7.5) gradient. The three peak Dpo4-like containing fractions were pooled and applied to a 50 mL HiPrep 26/10 desalting column (Amersham Biosciences, Piscatway, N.J.) and eluted with 20 mM NaCl, 20 mM Tris pH 7.5, 0.1 mM EDTA and 1 mM DTT. Six fractions containing the Dpo4-like enzyme were then loaded onto an 8.5 ml SP Sepharose HP column (Amersham Biosciences, Piscatway, N.J.) and eluted with a 20 mM to 1M NaCl gradient. A band of the right molecular weight for the corresponding new Y-family polymerases was visible in all four extracts ( FIG. 13 ). The intensity and size of the polymerase changes in the various extracts and is consistent with the level of overall expression in the whole cell extract. The amount loaded corresponds to about 0.5-1.0 μg of the polymerase. 
     Several fractions containing pure Dpo4-like enzymes were pooled, concentrated and 10% glycerol added to a final concentration before samples were frozen for long-term storage at −80° C. Purification of the Dpo4-like enzymes from  Stygiolobus azoricus  and  Sulfurisphaera ohwakuensis  was identical to that described above, except that an additional HiLoad 26/60 Superdex 75 column (Amersham Biosciences, Piscatway, N.J.) was utilized as the final step of purification prior to pooling samples, adding glycerol and freezing for long term storage. 
     Example 7 
     Polymerase Assays 
     This example describes the polymerase activity of isolated Y-family polymerases (Dpo4), such as from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis , and  Sulfolobus shibatae.    
     Various amounts of the heat treated extract were included in replication assays (see Example 1). Purified  Sulfolobus solfataricus  Dpo4 was used as a standard. All four extracts have polymerase activity as measured by this assay ( FIG. 14 ). This activity is roughly proportional to the amount of protein added to the reaction. The  Sulfolobus shibatae  Dpo4-polymerase is particularly active ( FIG. 14 ). 
     Additional examples of the polymerase activity of  Acidianus infernus  Dpo4,  Sulfolobus shibatae  Dpo4,  Sulfolobus tengchongensis  Dpo4,  Thermoascus aurantiacus  Pol eta,  Thermomyces lanuginosus  Pol eta, and the AiLFSte (AiDpo4/SteDpo4LF) and AiLFDpo4 (AiDpo4/SsoDpo4LF) chimeras are shown in Example 9. 
     Example 8 
     Functional Characteristics of the Novel Y-Family Polymerases 
     This example describes some of the functional characteristics of the newly-isolated Y-family polymerases, such as  Acidianus infernus  Dpo4,  Stygiolobus azoricus  Dpo4 , Sulfurisphaera ohwakuensis  Dpo4,  Sulfolobus shibatae  Dpo4, and  Sulfolobus tengchongensis  Dpo4. 
     Y-family polymerases are characterized by their ability to bypass lesions in DNA that would otherwise block replication by high fidelity DNA polymerases. They are ubiquitous and are found in all kingdoms of life: bacteria, archaea and eukaryotes. Y-family polymerase from thermostable organisms are of particular interest because the enzymes isolated from such species tend to be more stable, easy to work with, and may have more utility in assays at higher temperature, such as PCR. 
     Two thermostable Y-family polymerases (Dbh and Dpo4 from Sulfolobaceae) have been identified. Both belong to the DinB branch of the Y-family, have been crystallized and have been extensively studied. As disclosed herein, five additional novel DinB-like genes from five different crenarchaeota have been identified using a degenerate PCR approach:  Acidianus infernus  dpo4 (SEQ ID NO: 6),  Stygiolobus azoricus  dpo4 (SEQ ID NO: 8),  Sulfurisphaera ohwakuensis  dpo4 (SEQ ID NO: 10),  Sulfolobus shibatae  dpo4 (SEQ ID NO: 12), and  Sulfolobus tengchongensis  dpo4 (SEQ ID NO: 14). As described herein in Example 1, the novel DinB-like genes were over-expressed in  E. coli  and the proteins purified employing a similar protocol to that which was described for  Sulfolobus solfataricus  Dpo4 (Boudsocq et al.,  Nucleic Acids Res.  29:4607-16, 2001), with several modifications. First, the crude protein extracts were heat-treated at 70° C. for 10 minutes and centrifuged to remove a majority of the heat labile  E. coli  proteins. Subsequently, the protein extracts were subjected to HPLC, first over a hydroxylapetite column and then over an SP Sepharose column and gel filtration column as a final “polishing” step. Each of the five purified DinB-like proteins is capable of inserting nucleotides to the 3′-hydroxyl of a DNA primer/template duplex at 60° C., demonstrating that they are thermostable DNA polymerases. 
     Functional characteristics of the five novel DinB-like enzymes were evaluated using the following methods: 
     Primer Extension Assay 
     Three template DNA molecules were designed for primer extension experiments. The first, designated HTU50, has the sequence 5′-CTC TCA CAA GCA GCC AGG CAN NCT CCG CAC TCG TCT CTA CAC CGC TCC GC-3′ (SEQ ID NO: 55) and contains no damaged bases (i.e., NN=TT). The second template, designated HMTT50, has a sequence identical to that of HTU50, except that it contains a thymine-thymine cyclobutane pyrimidine dimer at positions 21-22 (i.e., NN=a TT CPD). The third template, designated HTX50, also has a sequence identical to that of HTU50, except that it contains thymine paired with an abasic site (X) at positions 21-22 (i.e., NN=TX). The primer designated SSHTP2 has the sequence 5′-GCG GTG TAG AGA CGA GTG CGG AG-3′ (SEQ ID NO: 54) and was 5′-end-labeled with  32 P (Lofstrand Laboratories, Gaithersburg, Md.). 
     Ten pmol of the  32 P-labeled SSHTP2 primer was annealed with an excess (20 pmol) of one of the three templates by heating the mixture to 95° C. for five minutes in 100 μl of 1× annealing buffer (400 mM Tris pH 8.0, 50 mM MgCl 2 , 5 μg/ml BSA and 14.2 mM 2-mercaptoethanol) and allowing the mixture to slowly cool to room temperature. Primer extension reactions were carried out using 10 nM labeled primer/template in 10 μl reactions containing 1× replication buffer (200 mM Tris pH 8.0, 25 mM MgCl 2 , 1.25 mg/ml BSA, and 12.5% glycerol), 100 μM each dNTP, and various concentrations of polymerase. Dilutions of polymerase were made in 1× dilution buffer (25 mM Tris pH 7.9, 0.5 mM EDTA, 1 mM dithiothreitol, 0.05% NP-40, and 25% glycerol). For the lesion primer extension experiment, 10 nM of each Dpo4 polymerase was used and the reactions were incubated at 60° C. for 10 minutes. For the labeled nucleotide primer extension experiment 0.2 nM of each Dpo4 protein was used, while 1 μl of a 1 to 1000 dilution of Taq was used. In the reactions containing labeled nucleotides, 100 μM of the labeled dUTP nucleotides (biotin-aha-dUTP, fluorescein-aha-dUTP or Alexa Fluor® 647-aha-dUTP (Molecular Probes, Eugene, Oreg.)) or 100 μM of the Cy5-dCTP nucleotide (Amersham Biosciences, Piscatway, N.J.) replaced either dTTP or dCTP, respectively. The labeled nucleotide reactions were incubated at 60° C. for three minutes. To stop the reactions, 10 μl of 2× loading dye (95% formamide, 10 mM EDTA, 0.1% xylene cyanol and 0.1% bromophenol blue) was added and the reactions were incubated at 95° C. for five minutes and briefly chilled before loading 5 μl onto a 12% acrylamide/7 M urea sequencing gel. 
       FIG. 17  shows a set of gels that illustrate primer extension of undamaged and damaged templates by the Dpo4 enzymes from  Acidianus infernus, Stygiolobus azoricus, Sulfurisphaera ohwakuensis, Sulfolobus shibatae , and  Sulfolobus tengchongensis , with purified  Sulfolobus solfataricus  Dpo4 as a standard. The “undamaged” panel shows primer extension of the SSHTP2/HTU50 primer/template substrate by the various Dpo4 enzymes. The “CPD” panel shows primer extension of the SSHTP2/HMTT50 primer/template substrate containing a TT CPD dimer in the HMTT50 template. The “abasic” panel shows primer extension of the SSHTP2/HTX50 primer/template substrate containing an abasic site in the HTX50 template. 
     Under the assay conditions used, Ssh (Dpo4 from  Sulfolobus shibatae ), Ai (Dpo4 from  Acidianus infernus ), and Step (Dpo4 from  Sulfolobus tengchongensis ) have properties similar to Sso (purified Dpo4 from  Sulfolobus solfataricus ) in their ability to efficiently extend primers to the very end of the undamaged DNA template. Soh (Dpo4 from  Sulfurisphaera ohwakuensis ) is less active, and Saz (Dpo4 from  Stygiolobus azoricus ) is much more distributive and only extends the primer by 2-3 nucleotides. On a CPD template, Ssh and Step are able to bypass the lesion, but to a lesser extent than Sso Dpo4. Ai, Saz and Soh are unable to bypass a CPD lesion. On an abasic template, Ssh and Step are able to bypass the lesion with a roughly similar efficiency as Sso Dpo4, whereas Ai, Saz and Soh are unable to bypass the lesion. Therefore, the novel polymerases have DNA polymerase activity, and while the enzymatic properties of the enzymes are similar (particularly for Ssh and Step), each enzyme has its own unique properties. 
     Both the Ssh and Ste polymerases are comparable to Sso Dpo4 in activity with regard to processivity. The Ai polymerase is somewhat less processive than the Sso Dpo4, while the Saz and Soh polymerases are significantly less active and less processive than Sso Dpo4. The properties of the Saz and Soh polymerases are, in fact, more similar to Dbh than to Dpo4, and these properties may be due to certain amino acids in their structural LF domain. Furthermore, like Sso Dpo4, the Ssh, Step and Ai polymerases are capable of replication past DNA lesions, such as abasic sites and CPD lesions. The ability to bypass such lesions is confined to Y-family polymerases, since these lesions usually block/terminate replication by other non-Y-family polymerases, such as human DNA polymerases alpha (Masutani et al.,  EMBO J.  19:3100-09, 2000) or delta (McCulloch et al.,  Nucleic Acids Res.  32:4665-75, 2004). 
       FIG. 18  shows a set of gels that illustrate labeled nucleotide incorporation by Dpo4 enzymes from  Acidianus infernus, Sulfolobus shibatae , and  Sulfolobus tengchongensis , with purified  Sulfolobus solfataricus  Dpo4 and Taq polymerase as standards, during primer extension. The “4 dNTPs” panel shows primer extension in the presence of all four unmodified nucleotides. The “biotin dUTP” panel shows primer extension where dTTP was replaced with biotin-aha-dUTP (Molecular Probes, Eugene, Oreg.). The “fluorescein dUTP” panel shows primer extension where dTTP was replaced with fluorescein-aha-dUTP (Molecular Probes, Eugene, Oreg.). The “Alexa fluor dUTP” panel shows primer extension where dTTP was replaced with Alexa Fluor® 647-aha-dUTP (Molecular Probes, Eugene, Oreg.). Lastly, the “Cy5 dCTP” panel shows primer extension where dCTP was replaced with Cy5-dCTP (Amersham Biosciences, Piscatway, N.J.). 
     These gels show that purified Sso Dpo4, Ssh, Ai, and Step enzymes can all utilize the modified nucleoside triphosphates. Under the assay conditions used, Ai is the least efficient of the enzymes at incorporating modified nucleoside triphosphates. Sso and Ssh are similar to Taq, with Step being somewhat better than Taq when using biotin dUTP and fluorescein dUTP. Although the primer was extended by Sso, Ssh, Ai, and Step in the presence of Cy5-dCTP, there was a strong pause when encountering the adjacent Gs (5-6 bases from the 3′-end of the primer), indicating that the Dpo4 enzymes extend tandem Cy5-dCTPs, whereas Taq does not have this pause. 
     The Ssh, Ai, and Ste polymerases were able to incorporate several different labeled DNA nucleotides into DNA during replication. For all four of the labeled nucleotides, Step Dpo4 was significantly more active than Taq in insertion of the labeled nucleotide and extension from the labeled nucleotide. In the Alexa Fluor® dUTP reactions, Sso Dpo4, Ssh Dpo4 and Step Dpo4 were all better than Taq at completing extension of the primer. However, Taq was better that the Dpo4 polymerases at completing extension of the primer in the Cy5 reactions. Thus, the novel Dpo4 enzymes disclosed herein provide a good substitute for Taq polymerase in applications utilizing, for example, fluorescent nucleoside triphosphate derivatives. 
     PCR Reactions 
     Fifty microliter PCR reactions were carried out using 200 nM of each of the Dpo4 enzymes from  Acidianus infernus, Sulfolobus shibatae , and  Sulfolobus tengchongensis  (with purified  Sulfolobus solfataricus  Dpo4 as a standard), or 2.5 units of Taq DNA polymerase (also as a standard; New England Biolabs, Beverly, Mass.) in 1× ThermoPol reaction buffer (20 mM Tris pH 8.8, 10 mM KCl, 10 mM (NH 4 ) 2 SO 4 , 2 mM MgSO 4  and 0.1% Triton X-100; New England Biolabs, Beverly, Mass.), using 1 μM of primers (Ste_FNde5 [5′-A AAA ACC AAA AGT TAT ATG CAT ATG AT-3′ (SEQ ID NO: 81)] and Ste_RBam1089 [5′-TTA CCT CAA GGA TCC TAA GGA AAT TG-3′ (SEQ ID NO: 82)]), 200 μM each of all four dNTPs and 10 ng of the circular plasmid pJM548 containing the 1.1 kb  Sulfolobus tengchongensis  Dpo4 gene. Thermocycling was performed as follows: 3 minutes at 85° C. followed, by 35 cycles of 85° C. for 30 seconds (denaturation step) and 60° C. for 7 minutes (annealing and elongation steps). 
     Two microliters of the 50 μl reactions were electrophoresed through a 0.9% agarose gel and stained with ethidium bromide ( FIG. 19 ). The gel shows that, under the assay conditions used, Sso Dpo4, Ai and Step can all function in a “closed tube” PCR reaction, and that the reaction is sufficiently robust to amplify at least a 1.1 kb amplicon. Using the  Sulfolobus tengchongensis  Dpo4 gene as a template demonstrates that each of the enzymes can amplify DNA roughly the size of their own gene. This is useful for compartmentalized self replication, which can be utilized to modify the properties of the enzymes. 
     Example 9 
     Using Y-Family Polymerases to Amplify Ancient or Damaged DNA 
     This example illustrates the ability of the Y-family polymerases disclosed herein, such as  Acidianus infernus  Dpo4,  Sulfolobus shibatae  Dpo4,  Sulfolobus tengchongensis  Dpo4 , Thermoascus aurantiacus  Pol eta,  Thermomyces lanuginosus  Pol eta, and the AiLFSte (AiDpo4/SteDpo4LF) and AiLFDpo4 (AiDpo4/SsoDpo4LF) chimeras, to amplify ancient or damaged DNA. 
     Ancient DNA and/or forensic samples often have lesions that are refractory to PCR amplification by Taq (or any other high-fidelity DNA polymerase). As unprotected DNA ages, a number of replication-blocking DNA lesions accumulate due to exposure to oxygen, background radiation, and other genotoxic agents. Thus, these types of lesions are common in forensic and ancient DNA samples, making PCR-based analysis difficult. One such lesion is 5-hydroxy-5-methyl hydantoin, which is prevalent in ancient DNA. Inclusion of a lesion-bypassing Dpo4 polymerase along with a conventional thermostable polymerase in a PCR protocol designed to amplify old DNA or forensic DNA samples greatly increases recoverability, accuracy and length of amplification products. 
     The ability of  Acidianus infernus  Dpo4,  Sulfolobus shibatae  Dpo4,  Sulfolobus tengchongensis  Dpo4 , Thermoascus aurantiacus  Pol eta,  Thermomyces lanuginosus  Pol eta, and the AiLFSte (AiDpo4/SteDpo4LF) and AiLFDpo4 (AiDpo4/SsoDpo4LF) chimeras to amplify ancient or damaged DNA were evaluated using the following method: 
     Primer Extension Assay 
     Two template DNA molecules were designed for primer extension experiments. The first, designated HydU22, has the sequence 5′-CAC TTC GGA NCG TGA CTG ATC T-3′ (SEQ ID NO: 62) and contains no damaged bases (i.e., N=T). The second template, designated ODN, has a sequence identical to that of HydU22, except that it contains a 5-hydroxy-5-methyl hydantoin adduct at position 10 (i.e., N=a hydantoin adduct). The primer designated SSHydP has the sequence 5′-AGA TCA GTC ACG-3′ (SEQ ID NO: 63) and was 5′-end-labeled with  32 P (Lofstrand Laboratories, Gaithersburg, Md.). 
     Ten pmol of the  32 P-labeled SSHydP primer was annealed with an excess (20 pmol) of one of the two templates by heating the mixture to 95° C. for five minutes in 100 μl of 1× annealing buffer (400 mM Tris pH 8.0, 50 mM MgCl 2 , 5 μg/ml BSA and 14.2 mM 2-mercaptoethanol) and allowing the mixture to slowly cool to room temperature. Primer extension reactions were carried out using 10 nM labeled primer/template in 10 μl reactions containing 1× replication buffer (200 mM Tris pH 8.0, 25 mM MgCl 2 , 1.25 mg/ml BSA, and 12.5% glycerol), 100 μM each dNTP and the following concentrations of polymerase: Taq (standard), 1 μl of a 1 to 600 dilution; Sso Dpo4 (standard), 0.33 nM; Step Dpo4, 0.75 nM; Ssh Dpo4, 1 nM; Ai Dpo4 0.5 nM; AiLFDpo4 (AiDpo4/SsoDpo4LF) chimera, 1.25 nM; AiLFSte (AiDpo4/SteDpo4LF) chimera, 1.25 nM;  Thermoascus aurantiacus  Pol eta and  Thermomyces lanuginosus  Pol eta, 100 ng of a 1 to 10 dilution of a soluble  E. coli  extract in which the eta polymerases were over-produced. Dilutions of polymerase were made in 1× dilution buffer (25 mM Tris pH 7.9, 0.5 mM EDTA, 1 mM dithiothreitol, 0.05% NP-40, and 25% glycerol). The reactions were incubated at 37° C. for 10 minutes. To stop the reactions, 10 μl of 2× loading dye (95% formamide, 10 mM EDTA, 0.1% xylene cyanol and 0.1% bromophenol blue) was added and the reactions were incubated at 95° C. for five minutes and briefly chilled before loading 5 μl onto a 12% acrylamide/7 M urea sequencing gel. 
       FIG. 20  shows a pair of gels that illustrate primer extension of undamaged and hydantoin containing templates by the Dpo4 enzymes from  Acidianus infernus, Sulfolobus shibatae, Sulfolobus tengchongensis , and the AiLFSte (AiDpo4/SteDpo4LF) and AiLFDpo4 (AiDpo4/SsoDpo4LF) chimeras. The “undamaged” panel shows primer extension of the SSHydP/HydU22 primer/template substrate by the various Dpo4 enzymes and chimeric enzymes. The “Hydantoin” panel shows primer extension of the SSHydP/ODN primer/template substrate containing a 5-hydroxy-5-methyl hydantoin adduct in the ODN template. 
       FIG. 20  reveals that under the assay conditions used, Sso (purified Dpo4 from  Sulfolobus solfataricus ), Step (Dpo4 from  Sulfolobus tengchongensis ), Ssh (Dpo4 from  Sulfolobus shibatae ), Ai (Dpo4 from  Acidianus infernus ), Ai/Sso (the AiLFDpo4 chimeric), and Ai/Step (the AiLFSte chimeric) are able to bypass the hydantoin lesion with roughly similar efficiency, while Taq DNA polymerase is significantly less able to bypass this lesion. Ai Dpo4 exhibits a reduced processivity, both on the undamaged and the hydantoin containing template, relative to the other Dpo4 enzymes. However, the chimeric enzymes, in which the Ai LF domain has been replaced with either the LF domain from Sso or Step, have a much enhanced processivity on both the undamaged and the hydantoin containing template, relative to native Ai Dpo4. 
       FIG. 21  shows a pair of gels that illustrate primer extension of undamaged and hydantoin containing templates by the  Thermoascus aurantiacus  Pol eta and  Thermomyces lanuginosus  Pol eta enzymes. The “undamaged” panel shows primer extension of the SSHydP/HydU22 primer/template substrate by the  Thermoascus aurantiacus  Pol eta and  Thermomyces lanuginosus  Pol eta enzymes. The “Hydantoin” panel shows primer extension of the SSHydP/ODN primer/template substrate containing a 5-hydroxy-5-methyl hydantoin adduct in the ODN template.  FIG. 21  reveals that under the assay conditions used, Ta (Pol eta from  Thermoascus aurantiacus ) and T1 (Pol eta from  Thermomyces lanuginosus ) are both DNA polymerases and, similar to the Dpo4 enzymes, are both capable of bypass replication past a hydantoin lesion. 
     This disclosure provides thermostable Y-family polymerases, in particular several novel Y-family polymerases and chimeras made therefrom, as well as methods of identifying other Y-family polymerases and methods of generating other chimeric Y-family polymerases. It will be apparent that the precise details of the methods described may be varied or modified without departing from the spirit of the described invention. We claim all such modifications and variations that fall within the scope and spirit of the claims below.