# Patent

## Title
Thermostable or thermoactive DNA polymerase molecules with attenuated 3′-5′ exonuclease activity

## Abstract

The present invention provides thermostable or thermoactive DNA polymerases with attenuated 3′-5′ exonuclease activity, methods for their synthesis, methods for their use, kits comprising the polymerases, nucleic acids encoding the polymerases and cells comprising such a nucleic acid. The DNA polymerases of the invention are useful in many recombinant DNA techniques, such as nucleic acid amplification by the polymerase chain reaction. The DNA polymerases of the invention allow higher fidelity replication and amplification of a template DNA sequence, allow less degradation of primers and/or more efficient use of deoxynucleotide triphosphates and are in general more efficient and less costly to make and use.

## Background
This application claims the benefit of priority under 35 U.S.C. §119 (e) of U.S. Provisional Application No. 60/369,815, filed Apr. 2, 2002, the contents of which are hereby incorporated by reference therein.


FIELD OF THE INVENTION
The present invention relates to thermostable or thermoactive DNA polymerases with attenuated 3′-5′ exonuclease (“proofreading”) activity, methods for their synthesis, methods for their use, and kits comprising them. The enzymes are useful in many recombinant DNA techniques, especially nucleic acid amplification by the polymerase chain reaction (PCR).
BACKGROUND OF THE INVENTION
DNA polymerases synthesize DNA molecules in the 5′ to 3′ direction from deoxynucleoside triphosphates (nucleotides) using a complementary template DNA strand and a primer by successively adding nucleotides to the free 3′-hydroxyl group of the growing strand. The template strand determines the order of addition of nucleotides via Watson-Crick base pairing. In cells, DNA polymerases are involved in DNA repair synthesis and replication. See, e.g., Kornberg et al., 1992, DNA Synthesis, W. H. Freeman, New York; Alberts et al., 1994, Molecular Biology of the Cell, 3d ed., Garland Press, New York.
Many molecular cloning techniques and protocols involve the synthesis of DNA in in vitro reactions catalyzed by DNA polymerases. For example, DNA polymerases are used in DNA labelling and DNA sequencing reactions, using either 35S-, 32P-, 33P- or fluorescently-labelled nucleotides. One of the most versatile and widely-used DNA synthesis techniques, the polymerase chain reaction (PCR) technique, is disclosed in U.S. Pat. Nos. 4,683,202; 4,683,195; 4,800,159; and 4,965,188, and discussed in PCR Strategies, 1995 Innis et al. (eds.), Academic Press, Inc., incorporated herein by reference in their entireties.
The best characterized DNA polymerase is Escherichia coli DNA polymerase I (Eco Pol I). Eco Pol I and several DNA polymerases homologous to it have three enzymatic functions: i) a 5′-3′ exonuclease activity, ii) a 3′-5′ exonuclease activity and iii) a DNA synthesis activity. The latter two functions are located toward the carboxy terminus of the protein, within a ‘Klenow’ fragment (Eco Pol I K). Enzyme preparations of Eco Pol I can be treated with subtilisin to yield a Eco Pol I K minus the 5′-3′ exonuclease activity. See Brown et al., 1982, J Biol. Chem. 257: 1965–72; Joyce et al., 1982, J. Biol. Chem. 257: 1958–64; Joyce et al., 1983, Proc Natl Acad Sci USA 80: 1830–34; Klenow et al., 1970, Proc. Natl. Acad. Sci. USA 65: 168–75; Kornberg, 1974; Setlow, P. et al., 1972, J. Biol. Chem. 247: 224–31; Setlow et al., 1972, J. Biol. Chem. 247: 232–40; Steitz et al., 1987, in Protein Engineering, Chap. 20, pp. 227–35 Oxender et al. (eds). Alan R. Liss, New York.
Crystal structure analysis of Eco Pol I K has shown that its peptide chain is folded into two distinct domains, with the smaller domain, of 200 amino acid residues, being the 3′-5′ exonuclease domain and the other domain, of 400 amino acid residues, being the DNA synthesis domain. See Ollis et al., 1985, Nature 313:762–66. The active sites of the 3′-5′ exonuclease and DNA synthesis activities are separated by about 30 angstroms. See id. The DNA synthesis active site binds to double-stranded DNA containing a single-stranded 5′ extension and deoxynucleoside triphosphate (dNTP) whereas the 3′-5′ exonuclease active site binds to single-stranded DNA and deoxynucleoside monophosphate (dNMP). See id. The existence of a conserved 3′-5′ exonuclease active site present in a number of DNA polymerases was predicted by Bernat et al., 1989, Cell 59: 219–28; Blanco et al., 1992, Gene 112: 139–44; Reha-Krantz, 1992, Gene 112: 133–37.
The DNA synthesis domain of Eco Pol I has been cloned, expressed, and characterized independently of the 3′-5′ and 5′-3′ exonuclease domains. As discussed above, the DNA synthesis domain contains approximately 400 amino acids. There is 50-fold less polymerase activity in the DNA synthesis domain than in the Eco Pol I K. See Derbyshire et al., 1993, Nucleic Acids Res. 21:5439–48.
Thermostable and thermoactive DNA polymerases derived from a variety of organisms have been described extensively in the literature. Particular examples include DNA polymerases from a variety of species of the eubacterial genus Thermus, see U.S. Pat. No. 5,466,591, in particular from Thermus aquaticus (Taq DNA polymerase) described in U.S. Pat. Nos. 4,889,818, 5,352,600 and 5,079,352, and the DNA polymerase from the eubacterial species Thermotoga maritima (Tma DNA polymerase) described in U.S. Pat. Nos. 5,374,553 and 5,420,029.
Both E. coli, a mesophile, and T. maritima, a thermophile, are eubacteria. Like E. coli DNA polymerase I, Tma DNA polymerase has both a 5′-3′ exonuclease activity and a 3′-5′ exonuclease activity. In contrast, DNA polymerases from Thermus species, which also are thermophilic eubacteria, possess only 5′-3′ exonuclease activity. A review of thermostable and thermoactive DNA polymerases and their associated activities is found in Abramson, 1995, in PCR Strategies, Innis et al. (eds), Academic Press, Inc. Mutant forms of a number of archae and eubacterial thermostable or thermoactive DNA polymerases that lack a 3′-5′ exonuclease activity are described in U.S. Pat. Nos. 6,015,668, 5,939,301, 5,988,614, 5,882,904, 5,489,523.
While Eco Pol I and Tma DNA polymerase have the same three enzymatic activities, and the same general domain structure, they are very different enzymes. For example, Eco Pol I and Tma DNA polymerase have very different amino acid sequences. In particular, even when gaps are introduced into their sequences to optimize their alignment, the 3′-5′ exonuclease domains of these two proteins are only about 33% identical. Further, the two enzymes exhibit different specific activities and differing resistance to chemical denaturing conditions. As these differences are observed in purified enzymes removed from their natural in vivo environments, they must be caused by differences in the amino acid sequences of the enzymes themselves.
The 3′-5′ exonuclease activity “proofreads” the nascent DNA strand as it is synthesized and preferentially removes nucleotides from it that are mismatched with the template strand, thus increasing the fidelity of DNA synthesis. However, the presence of a robust 3′-5′ exonuclease activity can be problematic for in vitro polymerization reactions, particularly PCR, in which the presence of a 3′-5′ exonuclease activity lowers the efficiency of the amplification. See Barnes, 1994, Proc. Natl. Acad. Sci. USA 91:2216–20.
Attempts have been made to avoid the deleterious effects of 3′-5′ exonuclease activity by using a DNA polymerase enzyme that lacks a 3′-5′ exonuclease activity. Taq polymerase naturally lacks this activity. Other DNA polymerases have been genetically engineered to eliminate it. See, e.g., U.S. Pat. Nos. 6,015,668, 5,939,301, 5,988,614, 5,882,904 and 5,489,523. These enzymes work in applications where higher fidelity of replication is unnecessary, for example, in a PCR used to amplify a template for DNA sequencing reactions, size analysis, restriction enzyme analysis or probe-based analyses.
However, other polymerization reactions, e.g., PCR to amplify a DNA fragment for cloning, require a higher level of fidelity. In an effort to reduce the problems associated with the 3′-5′ exonuclease activity while retaining its benefits, mixtures of two different DNA polymerases have been used. One polymerase in the mix has a wild-type level of 3′-5′ exonuclease activity. The other lacks this activity. The ratio of the two polymerases is manipulated to produce the desired ratio of 3′-5′ exonuclease to DNA polymerase activities. See Cheng et al., 1994, Proc. Natl. Acad. Sci. USA 91:5695–99; Barnes, 1994, Proc. Natl. Acad. Sci. USA 91:2216–20; Cheng, 1995, “Longer PCR Amplifications” in PCR Strategies (Innis et al., eds), Academic Press, San Diego 313–24; Cheng et al., 1995, PCR Meth. Applic. 4:294–98; U.S. Pat. Nos. 5,512,462, 5,436,149 and 5,556,772 and PCT Pat. App. Pub. WO 94/26766. While this blending technique can be used to achieve the desired amount of 3′-5′ exonuclease activity, it is expensive, time consuming, and must be optimized on a batch-by-batch basis. It requires the DNA polymerase activities and 3′-5′ exonuclease activities of each enzyme preparation to be carefully calibrated so that the two polymerases can be mixed in the right amounts to produce the desired ratio of 3′-5′ exonuclease activity to DNA polymerase activity. Thus, there is a need in the art for a rapid and economical method of producing a DNA polymerase reagent with a desired level of 3′-5′ exonuclease activity and a desired ratio of 3′-5′ exonuclease to DNA polymerase activities.
SUMMARY OF THE INVENTION
The present invention describes the surprising generation of a thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity. The attenuated 3′-5′ exonuclease activity makes such enzymes useful in a wide range of polymerization reactions.
In one aspect, the present invention provides an isolated thermostable or thermoactive DNA polymerase exhibiting attenuated 3′-5′ exonuclease activity. In one embodiment, the thermostable or thermoactive polymerase is a modified thermostable or thermoactive DNA polymerase. In another embodiment, the modified thermostable DNA polymerase is a mutant thermostable DNA polymerase. In another embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.1% and about 65% of that of a corresponding unmodified thermostable or thermoactive DNA polymerase, wherein exonuclease activity is determined using the Standard Assay described in Example 3. In another embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 1% and about 30% of that of a corresponding unmodified thermostable or thermoactive DNA polymerase. In another embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 3% and about 20% of that of a corresponding unmodified thermostable or thermoactive DNA polymerase. In another embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 3% and about 10% of that of a corresponding unmodified thermostable or thermoactive DNA polymerase. In another embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 3% and about 5% of that of a corresponding unmodified thermostable or thermoactive DNA polymerase.
In another aspect, the present invention provides an isolated thermostable or thermoactive DNA polymerase having 6.5 units or less, but more than 0, units (U)/pmol 3′-5′ exonuclease activity, measured using the Standard Assay described below in Example 3. In one embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.4 and 3.0 U/pmol. In another embodiment, the modified thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.4 and 1.6 U/pmol.
In another aspect, the present invention provides an isolated thermostable or thermoactive DNA polymerase, wherein the thermostable or thermoactive DNA polymerase has a 5′-3′ DNA polymerase activity and a 3′-5′ exonuclease activity and the ratio of the polymerase activity to the exonuclease activity is greater than 1. In one embodiment, the thermostable or thermoactive DNA polymerase has a ratio of 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity between about 3.0 and 50. In another embodiment, the thermostable or thermoactive DNA polymerase has a ratio of 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity between about 6.0 and 25.0.
In another aspect, the thermostable or thermoactive DNA polymerase has an attenuated 3′-5′ exonuclease activity. In one embodiment, the thermostable or thermoactive DNA polymerase is a modified thermostable or thermoactive DNA polymerase. In another embodiment, the modified thermostable DNA polymerase is a mutant thermostable DNA polymerase.
In another aspect, the invention provides a modified thermostable or thermoactive DNA polymerase wherein either the ssDNA or the dsDNA 3′-5′ exonuclease activity is preferentially attenuated. In one embodiment, the modified thermostable DNA polymerase is a mutant thermostable DNA polymerase.
In another aspect, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a thermophilic eubacterium in the genus Thermotoga. In yet another aspect, the thermophilic eubacterium is Thermotoga maritima (Tma). In another aspect, the thermophilic eubacterium is Thermotoga neapolitana. 
In one aspect, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a thermophilic eubacterium in the genus Thermosipho. In one embodiment, the thermophilic eubacterium is Thermosipho africanus. 
In another aspect, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a thermophilic eubacterium in the genus Aquifex. In one embodiment, the thermophilic eubacterium is Aquifex pyrophilus. In another embodiment, the thermophilic eubacterium is Aquifex aeolieus. 
In another aspect, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a thermophilic archae in the genus Thermococcus. In one embodiment, the thermophilic archae is Thermococcus barossi. In another embodiment, the thermophilic archae is Thermococcus litoralis. In another embodiment, the thermophilic archae is Thermococcus gorgonarius (“Tgo”).
In another aspect, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a thermophilic archae in the genus Pyrococcus. In one embodiment, the thermophilic archae is Pyrococcus furiosus. In another embodiment, the thermophilic archae is Pyrococcus sp. GB-D. In another embodiment, the thermophilic archae is Pyrococcus woesei. In another embodiment, the thermophilic archae is Pyrococcus abyssi. 
In another aspect, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a thermophilic archae in the genus Pyrodictium. In one embodiment, the thermophilic archae is Pyrodictium abyssi. In another embodiment, the thermophilic archae is Pyrodictium occultum. 
In another aspect, the invention provides an isolated thermostable or thermoactive DNA polymerase comprising a 3′-5′ exonuclease domain and exhibiting an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, wherein said 3′-5′ exonuclease domain comprises the sequence motif:

    
    
        (a) An EXO I motif having the formula DX1EX2X3SX4, wherein
        
            D is an aspartate residue,
            X1 is any amino acid residue, or no residue,
            E is a glutamate residue,
            X2 is any amino acid residue,
            X3 is any amino acid residue,
            S is a serine residue, and
            X4 is any amino acid residue, or
        
        
        (b) An EXO II motif having the formula X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO:1), wherein
        
            X5 is any amino acid residue,
            X6 is any amino acid residue,
            X7 is a cysteine or a leucine residue,
            X8 is any amino acid residue,
            X9 is a phenylalanine or a tyrosine residue,
            X10 is any amino acid residue,
            X11 is any amino acid residue,
            X12 is any amino acid residue,
            X13 is an isoleucine or valine residue, and
            X14 is a leucine or phenylalanine residue, or
        
        
        (c) An EXO IIa motif having the formula DX15X16X17X18X19YX20X21X22X23 (SEQ ID NO:2), wherein
        
            D is an aspartate residue,
            X15 is a proline, an alanine, a leucine or a threonine residue,
            X16 is a leucine or a methionine residue,
            X17 is a leucine or an isoleucine residue,
            X18 is any amino acid residue,
            X19 is an alanine or a serine residue,
            Y is a tyrosine residue,
            X20 is a leucine, an isoleucine or a valine residue,
            X21 is a leucine or a tryptophan residue,
            X22 is an aspartate residue, an asparagine residue, a glutamate residue or a glutamine residue, and
            X23 is a proline or a serine residue, or
        
        
        (d) An EXO III motif having the formula
        
            X24X25X26X27X28X29X30X31X32X33X34X35X36 (SEQ ID NO:3), wherein
            X24 is a proline or an alanine residue,
            X25 is any amino acid residue,
            X26 is a glutamate, an aspartate or a proline residue,
            X27 is a lysine, an arginine or glutamate residue,
            X28 is any amino acid residue,
            X29 is any amino acid residue,
            X30 is a glutamate, an arginine or an asparagine residue,
            X31 is any amino acid residue,
            X32 is a serine, an alanine or cysteine residue,
            X33 is any amino acid residue,
            X34 is a glutamate or a threonine residue,
            X35 is any amino acid residue, and
            X36 is an alanine residue.
        
        
    
    


In another aspect, the invention provides an isolated thermostable or thermoactive DNA polymerase comprising a 3′-5′ exonuclease domain and having a 5′-3′ polymerase activity and an attenuated 3′-5′ exonuclease activity wherein the ratio of said 5′-3′ polymerase activity in U/pmol, measured using the polymerase assay in Example 3, to said 3′-5′ exonuclease activity in U/pmol, measured as described using the Standard Assay in Example 3, is between about 1 and 100 and said 3′-5′ exonuclease domain comprises the sequence motif

    
    
        (a) An EXO I motif having the formula DX1EX2X3SX4, wherein
        
            D is an aspartate residue,
            X1 is any amino acid residue, or no residue,
            E is a glutamate residue,
            X2 is any amino acid residue,
            X3 is any amino acid residue,
            S is a serine residue, and
            X4 is any amino acid residue, or
        
        
        (b) An EXO II motif having the formula X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO:1), wherein
        
            X5 is any amino acid residue,
            X6 is any amino acid residue,
            X7 is a cysteine or a leucine residue,
            X8 is any amino acid residue,
            X9 is a phenylalanine or a tyrosine residue,
            X10 is any amino acid residue,
            X11 is any amino acid residue,
            X12 is any amino acid residue,
            X13 is an isoleucine or valine residue, and
            X14 is a leucine or phenylalanine residue, or
        
        
        (c) An EXO IIa motif having the formula DX15X16X17X18X19YX20X21X22X23 (SEQ ID NO:2), wherein
        
            D is an aspartate residue,
            X15 is a proline, an alanine, a leucine or a threonine residue,
            X16 is a leucine or a methionine residue,
            X17 is a leucine or an isoleucine residue,
            X18 is any amino acid residue,
            X19 is an alanine or a serine residue,
            Y is a tyrosine residue,
            X20 is a leucine, an isoleucine or a valine residue,
            X21 is a leucine or a tryptophan residue,
            X22 is an aspartate residue, an asparagine residue, a glutamate residue or a glutamine residue, and
            X23 is a proline or a serine residue, or
        
        
        (d) An EXO m motif having the formula
        
            X24X25X26X27X28X29X30X31X32X33X34X35X36 (SEQ ID NO:3), wherein
            X24 is a proline or an alanine residue,
            X25 is any amino acid residue,
            X26 is a glutamate, an aspartate or a proline residue,
            X27 is a lysine, an arginine or glutamate residue,
            X28 is any amino acid residue,
            X29 is any amino acid residue,
            X30 is a glutamate, an arginine or an asparagine residue,
            X31 is any amino acid residue,
            X32 is a serine, an alanine or cysteine residue,
            X33 is any amino acid residue,
            X34 is a glutamate or a threonine residue,
            X35 is any amino acid residue, and
            X36 is an alanine residue.
        
        
    
    


In yet another aspect, the invention provides a modified thermostable or thermoactive DNA polymerase wherein said modified polymerase comprises a 3′-5′ exonuclease domain, has about 0.1% to 65% of the 3′-5′ exonuclease activity of the thermostable DNA polymerase before modification and said 3′-5′ exonuclease domain comprises the sequence motif

    
    
        (a) An EXO I motif having the formula DX1EX2X3SX4, wherein
        
            D is an aspartate residue,
            X1 is any amino acid residue, or no residue,
            E is a glutamate residue,
            X2 is any amino acid residue,
            X3 is any amino acid residue,
            S is a serine residue, and
            X4 is any amino acid residue, or
        
        
        (b) An EXO II motif having the formula X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO:1), wherein
        
            X5 is any amino acid residue,
            X6 is any amino acid residue,
            X7 is a cysteine or a leucine residue,
            X8 is any amino acid residue,
            X9 is a phenylalanine or a tyrosine residue,
            X10 is any amino acid residue,
            X11 is any amino acid residue,
            X12 is any amino acid residue,
            X13 is an isoleucine or valine residue, and
            X14 is a leucine or phenylalanine residue, or
        
        
        (c) An EXO IIa motif having the formula DX15X16X17X18X19YX20X21X22X23 (SEQ ID NO:2), wherein
        
            D is an aspartate residue,
            X15 is a proline, an alanine, a leucine or a threonine residue,
            X16 is a leucine or a methionine residue,
            X17 is a leucine or an isoleucine residue,
            X18 is any amino acid residue,
            X19 is an alanine or a serine residue,
            Y is a tyrosine residue,
            X20 is a leucine, an isoleucine or a valine residue,
            X21 is a leucine or a tryptophan residue,
            X22 is an aspartate residue, an asparagine residue, a glutamate residue or a glutamine residue, and
            X23 is a proline or a serine residue, or
        
        
        (d) An EXO m motif having the formula
        
            X24X25X26X27X28X29X30X31X32X33X34X35X36 (SEQ ID NO:3), wherein
            X24 is a proline or an alanine residue,
            X25 is any amino acid residue,
            X26 is a glutamate, an aspartate or a proline residue,
            X27 is a lysine, an arginine or glutamate residue,
            X28 is any amino acid residue,
            X29 is any amino acid residue,
            X30 is a glutamate, an arginine or an asparagine residue,
            X31 is any amino acid residue,
            X32 is a serine, an alanine or cysteine residue,
            X33 is any amino acid residue,
            X34 is a glutamate or a threonine residue,
            X35 is any amino acid residue, and
            X36 is an alanine residue.
        
        
    
    


In one aspect, the 3′-5′ exonuclease domain of an isolated thermostable or thermoactive DNA polymerase of the invention comprises an EXO I, EXO II, EXO IIa, or EXO III domain having any combination of particular amino acid residues consistent with the above formulae.
In another aspect, the 3′-5′ exonuclease domain of an isolated thermostable or thermoactive DNA polymerase of the the invention comprises at least two, three or each of said sequence motifs (a), (b), (c) and (d), in an amino-terminal to carboxy-terminal order.
In another aspect, a modified thermostable or thermoactive DNA polymerase of the invention comprises a 3′-5′ exonuclease domain and exhibits an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, wherein said 3′-5′ exonuclease domain has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain that is underlined in FIG. 1A (SEQ ID NO:85).
In another aspect, a modified thermostable or thermoactive DNA polymerase of the invention comprises a 3′-5′ exonuclease domain and exhibits an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, wherein said modified DNA polymerase has greater than about 80% but less than 100% sequence identity to the sequence of FIG. 1A (SEQ ID NO:85).
In another aspect, a modified thermostable or thermoactive DNA polymerase of the invention comprises a 3′-5′ exonuclease domain and exhibits an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, wherein said 3′-5′ exonuclease domain has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Tne DNA polymerase. In one embodiment, the 3′-5′ exonuclease domain of the unmodified Tne DNA polymerase comprises the sequence shown in FIG. 2 (SEQ ID NO:88).
In another aspect, a modified thermostable or thermoactive DNA polymerase of the invention comprises a 3′-5′ exonuclease domain and exhibits an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, wherein said DNA polymerase has greater than about 80% but less than 100% sequence identity to the amino acid sequence of an unmodified Tne DNA polymerase. The amino acid sequence of an unmodified Tne DNA polymerase can, for example, comprise the amino acid sequence of a Tne polymerase provided in U.S. Pat. No. 5,948,614.
In another aspect, a modified thermostable or thermoactive DNA polymerase of the invention comprises a 3′-5′ exonuclease domain and exhibits an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, wherein said 3′-5′ exonuclease domain has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Taf DNA polymerase. In one embodiment, the 3′-5′ exonuclease domain of the unmodified Taf DNA polymerase comprises the sequence shown in FIG. 3 (SEQ ID NO:89).
In another aspect, a modified thermostable or thermoactive DNA polymerase of the invention comprises a 3′-5′ exonuclease domain and exhibits an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, wherein said DNA polymerase has greater than about 80% but less than 100% sequence identity to the amino acid sequence of an unmodified Taf DNA polymerase. The amino acid sequence of the unmodified Taf DNA polymerase can, for example, comprise the amino acid sequence of a Taf DNA polymerase provided in U.S. Pat. No. 5,968,799.
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO I motif wherein

    
    
        DX1EX2X3SX4, wherein
        D is an aspartate residue,
        X1 is any amino acid residue, or no residue,
        E is a glutamate residue,
        X2 is a threonine residue,
        X3 is any amino acid residue,
        S is a serine residue, and
        X4 is any amino acid residue (SEQ ID NO:4);

or wherein

        D is an aspartate residue,
        X1 is any amino acid residue, or no residue,
        E is a glutamate residue,
        X2 is a threonine residue,
        X3 is a threonine residue,
        S is a serine residue, and
        X4 is a leucine residue (SEQ ID NO:5);

or wherein

        D is an aspartate residue,
        X1 is any amino acid residue, or no residue,
        E is a glutamate residue,
        X2 is a threonine residue,
        X3 is any amino acid residue,
        S is a serine residue, and
        X4 is a leucine residue (SEQ ID NO:6);

or wherein

        D is an aspartate residue,
        X1 is any amino acid residue, or no residue,
        E is a glutamate residue,
        X2 is any amino acid residue,
        X3 is any amino acid residue,
        S is a serine residue, and
        X4 is a leucine residue (SEQ ID NO:7);

or wherein

        D is an aspartate residue,
        X1 is any amino acid residue, or no residue,
        E is a glutamate residue,
        X2 is any amino acid residue,
        X3 is a threonine residue,
        S is a serine residue, and
        X4 is a leucine residue (SEQ ID NO:8);

or wherein

        D is an aspartate residue,
        X1 is a leucine residue,
        E is a glutamate residue,
        X2 a threonine residue,
        X3 is a serine residue,
        S is a serine residue, and
        X4 is a leucine residue (SEQ ID NO:9).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is any amino acid residue,
        X6 is any amino acid residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is any amino acid residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:10);

or wherein

        X5 is an uncharged polar residue,
        X6 is any amino acid residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is any amino acid residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:11);

or wherein

        X5 is an uncharged polar residue,
        X6 is an uncharged polar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is any amino acid residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:12);

or wherein

        X5 is an uncharged polar residue,
        X6 is an uncharged polar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an acidic residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:13);

or wherein

        X5 is an uncharged polar residue,
        X6 is an uncharged polar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an acidic residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or a phenylalanine residue (SEQ ID NO:14);

or wherein

        X5 is a glutamine residue,
        X6 is an asparagine residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an aspartate residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine residue (SEQ ID NO:15);

or wherein

        X5 is a glutamine residue,
        X6 is an asparagine residue,
        X7 is a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine residue,
        X10 is an aspartate residue,
        X11 is a tyrosine residue,
        X12 is a lysine residue,
        X13 is a valine residue and
        X14 is a leucine residue (SEQ ID NO:16).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein X5 is a nonpolar residue, such as an alanine residue. In one embodiment, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein X8 is a lysine residue. In another embodiment, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein wherein X5 is a nonpolar residue and X8 is a lysine residue.
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is a nonpolar residue,
        X6 is an uncharged polar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an acidic residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:17);

or wherein

        X5 is an alanine residue,
        X6 is an uncharged polar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an acidic residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:18);

or wherein

        X5 is an alanine residue,
        X6 is an asparagine residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an aspartate residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine residue (SEQ ID NO:19).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is an alanine residue,
        X6 is an asparagine residue,
        X7 is a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine residue,
        X10 is an aspartate residue,
        X11 is a tyrosine residue,
        X12 is a lysine residue,
        X13 is a valine residue and
        X14 is a leucine residue (SEQ ID NO:20).
    
    


In one embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of the 3′-5′ exonuclease domain depicted in FIG. 4A modified by a Q384A mutation (SEQ ID NO:96). In another embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 4A modified by a Q384A mutation (SEQ ID NO:97).
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein X6 is a nonpolar amino acid residue.
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is an uncharged polar residue,
        X6 is nonpolar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an acidic residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:21);

or wherein

        X5 is a glutamine residue,
        X6 is an alanine residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an aspartate residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine residue (SEQ ID NO:22).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is a glutamine residue,
        X6 is an alanine residue,
        X7 is a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine residue,
        X10 is an aspartate residue,
        X11 is a tyrosine residue,
        X12 is a lysine residue,
        X13 is a valine residue and
        X14 is a leucine residue (SEQ ID NO:23).
    
    


In one embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of the 3′-5′ exonuclease domain depicted in FIG. 4A modified by a N385A mutation (SEQ ID NO:98). In another embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 4A modified by a N385A mutation (SEQ ID NO:99).
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein X10 is a glutamate residue.
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is an uncharged polar residue,
        X6 is an uncharged polar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is a glutamate residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:24);

or wherein

        X5 is a glutamine residue,
        X6 is an asparagine residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is a glutamate residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine residue (SEQ ID NO:25).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is a glutamine residue,
        X6 is an asparagine residue,
        X7 is a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine residue,
        X10 is a glutamate residue,
        X11 is a tyrosine residue,
        X12 is a lysine residue,
        X13 is a valine residue and
        X14 is a leucine residue (SEQ ID NO:26).
    
    


In one embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of the 3′-5′ exonuclease domain depicted in FIG. 4A modified by a D389E mutation (SEQ ID NO: 159). In another embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 4A modified by a D389E mutation (SEQ ID NO:175).
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein X10 is a glutamate residue.
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein X5 is a nonpolar residue and X6 is a nonpolar residue.
In another aspect, the 3′-5′ exonuclease domain of a themostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is a nonpolar residue,
        X6 is a nonpolar residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an acidic residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine amino acid residue (SEQ ID NO:27);

or wherein

        X5 is an alanine residue,
        X6 is an alanine residue,
        X7 is a cysteine or a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine or a tyrosine residue,
        X10 is an aspartate residue,
        X11 is any amino acid residue,
        X12 is any amino acid residue,
        X13 is an isoleucine or a valine residue and
        X14 is a leucine or phenylalanine residue (SEQ ID NO:28).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO II motif wherein

    
    
        X5 is an alanine residue,
        X6 is an alanine residue,
        X7 is a leucine residue,
        X8 is a lysine residue,
        X9 is a phenylalanine residue,
        X10 is an aspartate residue,
        X11 is a tyrosine residue,
        X12 is a lysine residue,
        X13 is a valine residue and
        X14 is a leucine residue (SEQ ID NO:29).
    
    


In one embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of the 3′-5′ exonuclease domain depicted in FIG. 4A modified by a Q384A N385A double mutation (SEQ ID NO:100). In another embodiment, such a thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 4A modified by a Q384A N385A double mutation (SEQ ID NO:101).
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO IIA motif wherein

    
    
        D is an aspartate residue,
        X15 is a threonine residue,
        X16 is a methionine residue,
        X17 is an isoleucine residue,
        X18 is an alanine residue,
        X19 is an alanine residue,
        Y is a tyrosine residue,
        X20 is a leucine residue,
        X21 is a leucine residue,
        X22 is a glutamate residue, and
        X23 is a proline residue (SEQ ID NO:30).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO III motif as above wherein X35 is an acidic amino acid residue.
In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO III motif wherein

    
    
        X24 is a proline residue,
        X25 is a valine, leucine or isoleucine residue,
        X26 is a glutamate, an aspartate or a proline residue,
        X27 is a lysine, an arginine residue,
        X28 is an alanine or a valine residue,
        X29 is an alanine or a valine residue,
        X30 is a glutamate, or an asparagine residue,
        X31 is an uncharged polar amino acid residue,
        X32 is a serine or cysteine residue,
        X33 is a cysteine or glycine residue,
        X34 is a glutamate or a threonine residue,
        X35 is an aspartate residue, and
        X36 is an alanine residue (SEQ ID NO:31)

or wherein

        X24 is a proline residue,
        X25 is a valine residue,
        X26 is a glutamate residue,
        X27 is a lysine residue,
        X28 is an alanine residue,
        X29 is an alanine residue,
        X30 is an asparagine residue,
        X31 is a tyrosine residue,
        X32 is a serine residue,
        X33 is a cysteine residue,
        X34 is a glutamate residue,
        X35 is an aspartate residue, and
        X36 is an alanine residue (SEQ ID NO:32).
    
    


In another aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO III motif wherein X31 is a nonpolar residue. In one embodiment, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO III motif wherein X31 is a nonpolar residue and X35 is an acidic residue.
In one aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO III motif wherein

    
    
        X24 is a proline residue,
        X25 is a valine, leucine or isoleucine residue,
        X26 is a glutamate, an aspartate or a proline residue,
        X27 is a lysine or an arginine residue,
        X28 is an alanine or a valine residue,
        X29 is an alanine or a valine residue,
        X30 is a glutamate or an asparagine residue,
        X31 is a nonpolar residue,
        X32 is a serine or cysteine residue,
        X33 is a cysteine or a glycine residue,
        X34 is a glutamate or a threonine residue,
        X35 is an aspartate residue, and
        X36 is an alanine residue (SEQ ID NO:33).
    
    


In one aspect, the 3′-5′ exonuclease domain of a thermostable or thermoactive DNA polymerase of the invention comprises an EXO III motif wherein

    
    
        X24 is a proline residue,
        X25 is a valine residue,
        X26 is a glutamate residue,
        X27 is a lysine residue,
        X28 is an alanine residue,
        X29 is an alanine residue,
        X30 is an asparagine residue,
        X31 is an alanine residue,
        X32 is a serine residue,
        X33 is a cysteine residue,
        X34 is a glutamate residue,
        X35 is an aspartate residue, and
        X36 is an alanine residue (SEQ ID NO:34).
    
    


In another aspect, the invention provides a chimeric thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity, said polymerase comprising an amino terminal portion and a carboxy terminal portion, with the amino terminal portion derived from the amino terminal portion of a first DNA polymerase and the carboxy terminal portion derived from a second DNA polymerase. In one embodiment, said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity comprises an amino terminal portion derived from the amino terminal portion of a first thermostable or thermoactive DNA polymerase and a carboxy terminal portion derived from a second thermostable or thermoactive DNA polymerase, said second polymerase preferably being one that exhibits 3′-5′ exonuclease activity. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, said amino terminal and/or carboxy terminal portion is derived from a DNA polymerase from a Thermus species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, said amino terminal and/or carboxy terminal portion is derived from a DNA polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal and/or carboxy terminal portion or another portion is derived from a DNA polymerase from a Thermus species and the other terminal portion or another portion is derived from a DNA polymerase from a Thermotoga species; for example, in one embodiment, the amino terminal portion is derived from a DNA polymerase from a Thermus species and the carboxy terminal portion is derived from a DNA polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal portion is derived from a Thermus species and comprises a 5′-3′ exonuclease domain and the carboxy terminal portion is derived from a Thermotoga species and comprises a 3′-5′ exonuclease domain and a polymerase domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal portion is derived from a Thermus species and comprises a 5′-3′ exonuclease domain and has greater than about 80% sequence identity with a corresponding amino terminal portion the DNA polymerase from the Thermus species and said carboxy terminal portion has greater than about 80% but less than 100% sequence identity with a corresponding carboxy terminal portion of the DNA polymerase from the Thermotoga species. In another embodiment, said Thermus species is Thermus sp. Z05 and said Thermotoga species is Thermotoga maritima. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 4 (SEQ ID NO:90) modified by one or more of the mutations indicated in the figure. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 5 (SEQ ID NO:107) modified by one or more of the mutations indicated in the figure. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity comprises an amino terminal portion, a middle portion, and a carboxy terminal portion. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal portion comprises a 5′-3′ exonuclease domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the middle portion comprises a 3′-5′ exonuclease domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the carboxy terminal portion comprises a polymerase domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the carboxy terminal portion and the amino terminal portion are derived from a polymerase from a Thermus species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminus and/or the carboxy terminus have greater than 80% sequence identity with a corresponding amino and/or carboxy terminus portion of a polymerase from a Thermus species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the middle portion is derived from a polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the middle portion has greater than 80%, but less than 100%, sequence identity to the corresponding polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, an amino portion and a carboxy portion are derived from a polymerase from a Thermus species and a middle portion is derived from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the Thermus species is Thermus sp. Z05 and the Thermotoga species is Thermotoga maritima. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 6 (SEQ ID NO:130) modified by one or more of the mutations indicated in the figure. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 7 (SEQ ID NO:148) modified by one or more of the mutations indicated in the figure.
In another aspect, an isolated thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Tma DNA polymerase. In one embodiment, an isolated thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, has greater than about 80% but less than 100% sequence identity to an unmodified Tma DNA polymerase. The amino acid sequence of the unmodified Tma DNA polymerase can, for example, comprise the amino acid sequence of FIG. 1A (SEQ ID NO:85).
In another aspect, an isolated thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Tne DNA polymerase. In one embodiment, the 3′-5′ exonuclease domain of the unmodified Tne DNA polymerase comprises the sequence shown in FIG. 2 (SEQ ID NO:88). In another embodiment, an isolated thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, has greater than about 80% but less than 100% sequence identity to an unmodified Tne DNA polymerase. The amino acid sequence of the unmodified Tne DNA polymerase can, for example, comprise the amino acid sequence of a Tne polymerase provided in U.S. Pat. No. 5,948,614.
In another aspect, an isolated thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Taf DNA polymerase. In one embodiment, the 3′-5′ exonuclease domain of the unmodified Taf DNA polymerase comprises the sequence shown in FIG. 3 (SEQ ID NO:89). In another embodiment, an isolated thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay of Example 3, below, has greater than about 80% but less than 100% sequence identity to an unmodified Taf DNA polymerase. The amino acid sequence of the unmodified Taf DNA polymerase can, for example, comprise the amino acid sequence of a Taf DNA polymerase provided in U.S. Pat. No. 5,968,799.
In another aspect, the invention provides an isolated thermostable or thermoactive DNA polymerase having a 3′-5′ exonuclease domain exhibiting attenuated 3′-5′ activity wherein the ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol, wherein both enzymatic activities are determined as described in Example 3, below, is between about 1 and 100 and the 3′-5′ exonuclease domain has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Tma DNA polymerase. In one embodiment, the invention provides an isolated thermostable or thermoactive DNA polymerase having greater than about 80% but less than 100% sequence identity to an unmodified Tma DNA polymerase wherein the ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol, wherein both enzymatic activities are determined as described in Example 3, below, is between about 1 and 100. The amino acid sequence of the unmodified Tma DNA polymerase can, for example, comprise the amino acid sequence of FIG. 1A (SEQ ID NO:85).
In another aspect, an isolated thermostable or thermoactive DNA polymerase of the invention has a 3′-5′ exonuclease domain and exhibits attenuated 3′-5′ activity wherein the ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol, both enzymatic activities being measured as described in Example 3, below, is between about 1 and 100 and the 3′-5′ exonuclease domain has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Tne DNA polymerase. In one embodiment, the 3′-5′ exonuclease domain of the unmodified Tne DNA polymerase comprises the sequence shown in FIG. 2 (SEQ ID NO:88). In another embodiment, an isolated thermostable or thermoactive DNA polymerase of the invention exhibits attenuated 3′-5′ activity wherein the ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol is between about 1 and 100 as measured using the assays described in Example 3, and the polymerase has greater than about 80% but less than 100% sequence identity to an unmodified Tne DNA polymerase. The amino acid sequence of the unmodified Tne DNA polymerase can, for example, comprise the amino acid sequence of a Tne polymerase provided in U.S. Pat. No. 5,948,614.
In another aspect, an isolated thermostable or thermoactive DNA polymerase of the invention has a 3′-5′ exonuclease domain and exhibits attenuated 3′-5′ activity wherein the ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol, measured using the assays described in Example 3, below, is between about 1 and 100 and the 3′-5′ exonuclease domain has greater than about 80% but less than 100% sequence identity to the 3′-5′ exonuclease domain of an unmodified Taf DNA polymerase. In one embodiment, the 3′-5′ exonuclease domain of the unmodified Taf DNA polymerase comprises the sequence shown in FIG. 3 (SEQ ID NO:89). In another embodiment, an isolated thermostable or thermoactive DNA polymerase of the invention exhibits attenuated 3′-5′ activity wherein the ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol is between about 1 and 100, measured using the assays described in Example 3, below, and the polymerase has greater than about 80% but less than 100% sequence identity to an unmodified Taf DNA polymerase.comprise the amino acid sequence of a Taf DNA polymerase provided in U.S. Pat. No. 5,968,799.
In another aspect, the present invention provides for a mixture of thermostable or thermoactive DNA polymerases comprising a thermostable or thermoactive DNA polymerase of the invention exhibiting attenuated 3′-5′ exonuclease activity. In one embodiment, such a mixture has a 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, measured using the Standard Assay described in Example 3, below. In another embodiment, such a mixture has a ratio of 5′-3′ polymerase activity in U/pmol to 3′-5′ exonuclease activity in U/pmol that is between about 1 and 100, measured using the assays described in Example 3, below.
In another aspect, the present invention provides nucleic acids comprising a sequence that encodes a thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity. In one embodiment the present invention provides plasmids comprising a sequence that encodes a thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity. In another embodiment, the plasmid is an expression vector. In another embodiment, the expression vector allows expression of the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity in a microorganism. In another embodiment, the microorganism is a bacterium. In another embodiment, the bacterium is Escherichia coli. 
In another aspect, the instant invention provides cells engineered to contain and/or express a nucleic acid comprising a sequence that encodes a thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity. In one embodiment, the cell comprises a plasmid comprising a sequence that encodes the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity. In another embodiment, the plasmid is an expression vector that allows expression of the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity in the cell. In another embodiment, the cell is a microorganism. In another embodiment, the microorganism is a bacterium, such as Escherichia coli. 
In another aspect, the present invention provides methods of producing a thermostable or thermoactive DNA polymerase of the invention with attenuated 3′-5′ exonuclease activity comprising the steps of incubating a cell capable of expressing a nucleic acid encoding the thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity under conditions that allow expression of the thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity and separating the thermoactive DNA polymerases with attenuated 3′-5′ exonuclease activity from the cell. In one embodiment, the cell is a microorganism. In another embodiment, the microorganism is a bacterium. In another embodiment, the bacterium is Escherichia coli. In another embodiment, the cell comprises an expression vector comprising the thermoactive DNA polymerases with attenuated 3′-5′ exonuclease activity.
In another aspect, the present invention provides methods of replicating a DNA molecule comprising the steps of incubating the DNA molecule with a thermostable or thermoactive DNA polymerase of the invention under conditions that allow the thermostable or thermoactive DNA polymerase to replicate the DNA molecule. The DNA molecule can be any kind of DNA molecule, e.g., a cDNA molecule, a genomic DNA molecule, a single-stranded DNA molecule or a double-stranded DNA molecule. In one embodiment, the thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is used to amplify the DNA molecule, e.g., via PCR. In another embodiment, a thermostable or thermoactive DNA polymerase with a desired level of 3′-5′ exonuclease activity is selected to suit the conditions of a particular application, e.g., the type and concentration of metal ion, the type and concentration of salt, the length of the target nucleic acid and/or whether the target molecule is, e.g., a single-stranded DNA, a double-stranded DNA or an RNA.
In another aspect, the instant invention provides a method of selecting a thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity, comprising the steps of assaying the 3′-5′ exonuclease activity of a thermostable or thermoactive DNA polymerase and selecting the polymerase if it has an attenuated 3′-5′ exonuclease activity. In one embodiment, the thermostable or thermoactive DNA polymerase is a modified thermostable or thermoactive DNA polymerase. In another embodiment, the modified thermostable or thermoactive DNA polymerase is a mutant thermostable or thermoactive DNA polymerase. In another embodiment, the thermostable or thermoactive DNA polymerase is selected if it has a level of 3′-5′ exonuclease activity that is between about 0.1% and about 65% of the level of 3′-5′ exonuclease activity of a reference polymerase, measured using the Standard Assay of Example 3, below. In another embodiment, the thermostable or thermoactive DNA polymerase is selected if it has a level of 3′-5′ exonuclease activity that is between about 1.0% and about 30% of the level of 3′-5′ exonuclease activity of the reference polymerase. In another embodiment, the thermostable or thermoactive DNA polymerase is selected if it has a level of 3′-5′ exonuclease activity that is between about 3.0% and about 20% of the level of 3′-5′ exonuclease activity of the reference polymerase. In another embodiment, the thermostable or thermoactive DNA polymerase is selected if it has a level of 3′-5′ exonuclease activity that is between about 3.0% and about 10% of the level of 3′-5′ exonuclease activity of the reference polymerase. In another embodiment, the thermostable or thermoactive DNA polymerase is selected if it has a level of 3′-5′ exonuclease activity that is between about 3.0% and about 5% of the level of 3′-5′ exonuclease activity of the reference polymerase. In another embodiment, the thermostable or thermoactive DNA polymerase is selected if it has a level of activity of between 6.5 or less, but greater than 0, units/pmol, as measured using the Standard Assay of Example 3. In another embodiment, the mutant thermostable or thermoactive DNA polymerase is selected if it has a ratio of 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity of between about 1 and 100, wherein the enzymatic activities are measured using the assays described in Example 3, below.
In another aspect, the instant invention provides kits comprising at least one thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity. In one embodiment, the kit further comprises a reagent useful for replicating a DNA molecule. In another embodiment, the reagent is useful for replicating a DNA molecule in a PCR amplification. In another embodiment, the reagent is a buffer. In another embodiment, the reagent is a primer. In another embodiment, the reagent is a deoxyribonucleotide. In another embodiment, the reagent is a dideoxyribonucleotide.
In another aspect, the invention provides mixtures of DNA polymerases comprising a first thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity and a second thermostable or thermoactive DNA polymerase. In one embodiment, the second thermostable or thermoactive DNA polymerase has less 3′-5′ exonuclease activity than the first thermostable or thermoactive DNA polymerase. In another embodiment, the second thermostable or thermoactive DNA polymerase has essentially no 3′-5′ exonuclease activity. In another embodiment, the second thermostable or thermoactive DNA polymerase has more 3′-5′ exonuclease activity than the first thermostable or thermoactive DNA polymerase. In another embodiment, the mixture has a 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, units/pmol, measured using the Standard Assay of Example 3, below.
In another aspect, the instant invention provides methods of replicating a DNA molecule using a mixture of thermostable or thermoactive DNA polymerases comprising the steps of incubating the DNA molecule with a first polymerase with an attenuated 3′-5′ exonuclease activity and a second thermostable or thermoactive DNA polymerase under conditions that allow the DNA polymerases to replicate the DNA molecule. In one embodiment, the DNA is replicated using the mixture of polymerase in a PCR amplification.
The compositions and methods of the invention offer several advantages over previously available compositions and methods. The thermostable or thermoactive DNA polymerases of the invention are superior to thermostable or thermoactive DNA polymerases without 3′-5′ exonuclease activity because the polymerases of the invention allow for higher fidelity replication and amplification of a template DNA sequence. The thermostable or thermoactive DNA polymerases of the invention are superior to thermostable or thermoactive DNA polymerases with robust 3′-5′ exonuclease activities because the polymerases of the invention allow for less degradation of the template to be replicated, less degradation of the primers and/or more efficient use of dNTPs and other reaction components by reducing the occurrence of counterproductive “idling” reactions. The mutant thermostable or thermoactive DNA polymerases of the invention are superior to mixtures of thermostable or thermoactive DNA polymerases with and without 3′-5′ exonuclease activities because the polymerases of the invention require less handling and less calibrating and therefore are more efficient and less costly to make and use. Also, surprisingly, it has been found that PCR requires less of the polymerases of the invention than of the mixture of enzymes used previously. The mixtures of thermostable or thermoactive enzymes of the present invention are superior to the mixtures previously available because they allow for a finer control over the ratio of template dependent 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity and because they allow for mixtures to be created wherein the level of ssDNA exonuclease and dsDNA exonuclease activities are independently modulated.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1A presents the amino acid sequence of the Thermotoga maritima (Tma) DNA polymerase (SEQ ID NO:85). The 3′-5′ exonuclease domain lies within about amino acid residues 292 to 487 (SEQ ID NO:86), which residues are underlined. FIG. 1B presents the nucleic acid sequence (SEQ ID NO:87) that encodes the amino acid sequence of FIG. 1A.
FIG. 2 presents an amino acid sequence from the region of the 3′-5′ exonuclease domain of Thermotoga neapolitana (Tne) DNA polymerase (SEQ ID NO:88).
FIG. 3 presents an amino acid sequence from the region of the 3′-5′ exonuclease domain of Thermosipho africanus (Taf) DNA polymerase (SEQ ID NO:89).
FIG. 4A presents the amino acid sequence of the chimeric thermostable DNA polymerase CS5 (SEQ ID NO:90). The 3′-5′ exonuclease domain extends from about residue 292 to about residue 487, which residues are underlined (SEQ ID NO:91). Residues 1–291 (SEQ ID NO:92) are derived from Z05 DNA polymerase and residues 292–893 (SEQ ID NO:93) are derived from Tma DNA polymerase, as indicated by the arrows. Amino acid residue substitutions introduced during the second round of mutagenesis appear directly above the residues they replaced, which are indicated in bold: L329A (3′-5′ exonuclease domain, SEQ ID NO:94; entire protein, SEQ ID NO:95), Q384A (3′-5′ exonuclease domain, SEQ ID NO:96; entire protein, SEQ ID NO:97), N385A (3′-5′ exonuclease domain, SEQ ID NO:98; entire protein, SEQ ID NO:99), Q384A N385A (3′-5′ exonuclease domain, SEQ ID NO:100; entire protein, SEQ ID NO:101), D389E (3′-5′ exonuclease domain, SEQ ID NO:102; entire protein, SEQ ID NO:103), and Y464A (3′-5′ exonuclease domain, SEQ ID NO:104; entire protein, SEQ ID NO:105). FIG. 4B presents the nucleic acid sequence that encodes CS5 (SEQ ID NO:106).
FIG. 5A presents the amino acid sequence of the chimeric thermostable DNA polymerase CS6 (SEQ ID NO:107). The 3′-5′ exonuclease domain extends from about residue 292 to about residue 487, which residues are underlined (SEQ ID NO:108). Residues 1–291 (SEQ ID NO:109) are derived from Z05 DNA polymerase and residues 292–893 (SEQ ID NO:110) are derived from Tma DNA polymerase, as indicated by the arrows, except that residues 323–325 have been replaced with the sequence ALA. Amino acid residue substitutions introduced during the first round of mutagenesis appear directly above the residues they replaced, which are indicated in bold: DEE (3′-5′ exonuclease domain, SEQ ID NO:111; entire protein, SEQ ID NO:112), DDE (3′-5′ exonuclease domain, SEQ ID NO:113; entire protein, SEQ ID NO:114), DKE (3′-5′ exonuclease domain, SEQ ID NO:115; entire protein, SEQ ID NO:116), DNE (3′-5′ exonuclease domain, SEQ ID NO:117; entire protein, SEQ ID NO:118), DQE (3′-5′ exonuclease domain, SEQ ID NO:119; entire protein, SEQ ID NO:120), DHE (3′-5′ exonuclease domain, SEQ ID NO:121; entire protein, SEQ ID NO:122), DLD (3′-5′ exonuclease domain, SEQ ID NO:123; entire protein, SEQ ID NO:124), ELD (3′-5′ exonuclease domain, SEQ ID NO:125; entire protein, SEQ ID NO:126), ELE (3′-5′ exonuclease domain, SEQ ID NO:127; entire protein, SEQ ID NO:128). FIG. 5B presents the nucleic acid sequence that encodes CS6 (SEQ ID NO:129).
FIG. 6A presents the amino acid sequence (SEQ ID NO:130) of the chimeric thermostable DNA polymerase CS7. The 3′-5′ exonuclease domain extends from about residue 292 to about residue 487, which residues are underlined (SEQ ID NO:131). Residues 1–291 (SEQ ID NO:132) and 485–894 (SEQ ID NO:133) are derived from Z05 DNA polymerase and residues 292–484 (SEQ ID NO:134) are derived from Tma DNA polymerase, as indicated by the arrows. Amino acid residue substitutions analogous to those introduced into CS5 during the second round of mutagenesis appear directly above the residues they replace, which are indicated in bold:L329A (3′-5′ exonuclease domain, SEQ ID NO:135; entire protein, SEQ ID NO:136), Q384A (3′-5′ exonuclease domain, SEQ ID NO:137; entire protein, SEQ ID NO:138), N385A (3′-5′ exonuclease domain, SEQ ID NO:139; entire protein, SEQ ID NO:140), Q384A N385A (3′-5′ exonuclease domain, SEQ ID NO:141; entire protein, SEQ ID NO:142), D389E (3′-5′ exonuclease domain, SEQ ID NO:143; entire protein, SEQ ID NO:144), and Y464A (3′-5′ exonuclease domain, SEQ ID NO:145; entire protein, SEQ ID NO:146). FIG. 6B presents the nucleic acid sequence that encodes CS7 (SEQ ID NO:147).
FIG. 7A presents the amino acid sequence of the chimeric thermostable DNA polymerase CS8 (SEQ ID NO:148). The 3′-5′ exonuclease domain extends from about residue 292 to about residue 487, which residues are underlined (SEQ ID NO:149). Residues 1–291 (SEQ ID NO:150) and 485–894 (SEQ ID NO:151) are derived from Z05 DNA polymerase and residues 292–484 (SEQ ID NO:152) are derived from Tma DNA polymerase, as indicated by the arrows, except that residues 323–325 have been replaced with residues ALA. Amino acid residue substitutions analogous to those introduced during the second round of mutagenesis of CS5 appear directly above the residues they replace, which are indicated in bold: DEE (3′-5′ exonuclease domain, SEQ ID NO:153; entire protein, SEQ ID NO:154), DDE (3′-5′ exonuclease domain, SEQ ID NO:155; entire protein, SEQ ID NO:156), DKE (3′-5′ exonuclease domain, SEQ ID NO:157; entire protein, SEQ ID NO:158), DNE (3′-5′ exonuclease domain, SEQ ID NO:159; entire protein, SEQ ID NO:160), DQE (3′-5′ exonuclease domain, SEQ ID NO:161; entire protein, SEQ ID NO:162), DHE (3′-5′ exonuclease domain, SEQ ID NO:163; entire protein, SEQ ID NO:164), DLD (3′-5′ exonuclease domain, SEQ ID NO:165; entire protein, SEQ ID NO:166), ELD (3′-5′ exonuclease domain, SEQ ID NO:167; entire protein, SEQ ID NO:168), ELE (3′-5′ exonuclease domain, SEQ ID NO:169; entire protein, SEQ ID NO:170). FIG. 7B presents the nucleic acid sequence that encodes CS8 (SEQ ID NO:171).
FIG. 8 presents a sequence alignment of an amino acid sequence from the region of the 3′-5′ exonuclease domain of the Eco DNA polymerase with other family A DNA polymerases: Tth (SEQ ID NO:172), Tca (SEQ ID NO:173), Z05 (SEQ ID NO:174), Taq (SEQ ID NO:175), Tfl (SEQ ID NO:176), Tfi (SEQ ID NO:177), Sps17 (SEQ ID NO:178), Dra (SEQ ID NO:179), HSP-B-7 (SEQ ID NO:180), Bst (SEQ ID NO:181), Bca (SEQ ID NO:182), E. coli (SEQ ID NO:183), Tma (SEQ ID NO:184), Tne (SEQ ID NO:185), Taf (SEQ ID NO:186), HSP-A (SEQ ID NO:187). The Exo I, Exo II (SEQ ID NO:188), Exo IIa (SEQ ID NO:189) and Exo III (SEQ ID NO:190) motifs are indicated in bold in the Tma sequence.
FIGS. 9A and 9B present growth curves of a reverse transcriptase/PCR amplification of a 1.7 kb HIV template using mutant DNA polymerases of the invention.
FIG. 10 presents photographs of electrophoresis analyses of the amplification products of the reverse transcriptase PCR amplifications of FIG. 9.
FIGS. 11A–11I present a sequence alignment of the Eco Pol II family B DNA polymerase with a number of other family B DNA polymerases (SEQ ID NOs: 191–202).



DETAILED DESCRIPTION OF THE INVENTION
To facilitate understanding of the invention, a number of terms are defined below.
The terms “cell”, “cell line”, and “cell culture” can be used interchangeably and all such designations include progeny. Thus, the words “transformants” or “transformed cells” include the primary transformed cell and cultures derived from that cell without regard to the number of transfers. All progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same functionality as screened for in the originally transformed cell are included in the definition of transformants. The cells can be prokaryotic or eukaryotic.
The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for procaryotes, for example, include a promoter, optionally an operator sequence, a ribosome binding site, positive retroregulatory elements (see U.S. Pat. No. 4,666,848, incorporated herein by reference), and possibly other sequences. Eucaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
The term “expression clone” refers to DNA sequences containing a desired coding sequence and control sequences in operable linkage, so that hosts transformed with these sequences are capable of producing the encoded proteins. The term “expression system” refers to a host transformed with an expression clone. To effect transformation, the expression clone may be included on a vector; however, the relevant DNA may also be integrated into the host chromosome.
The term “gene” refers to a DNA sequence that comprises control and coding sequences necessary for the production of a protein, polypeptide or precursor.
The term “operably linked” refers to the positioning of the coding sequence such that control sequences will function to drive expression of the protein encoded by the coding sequence. Thus, a coding sequence “operably linked” to control sequences refers to a configuration wherein the coding sequences can be expressed under the direction of a control sequence.
The term “oligonucleotide” as used herein is defined as a molecule comprised of two or more deoxyribonucleotides or ribonucleotides. The exact size will depend on many factors, which in turn depends on the ultimate function or use of the oligonucleotide. Oligonucleotides can be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences and direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth. Enzymol. 68:90–99; the phosphodiester method of Brown et al., 1979, Meth. Enzymol. 68:109–151; the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Lett. 22:1859–1862; and the solid support method of U.S. Pat. No. 4,458,066, each incorporated herein by reference. A review of synthesis methods is provided in Goodchild, 1990, Bioconjugate Chemistry 1(3):165–187, incorporated herein by reference.
The term “primer” as used herein refers to an oligonucleotide which is capable of acting as a point of initiation of synthesis when placed under conditions in which primer extension is initiated. The synthesis of a primer extension product that is complementary to a nucleic acid strand is initiated in the presence of the requisite four different nucleoside triphosphates and a thermostable or thermoactive DNA polymerase in an appropriate buffer at a suitable temperature. A “buffer” includes cofactors (such as divalent metal ions) and salt (to provide the appropriate ionic strength), adjusted to the desired pH.
A primer that hybridizes to the non-coding strand of a gene sequence (equivalently, is a subsequence of the coding strand) is referred to herein as an “upstream” or “forward” primer. A primer that hybridizes to the coding strand of a gene sequence is referred to herein as an “downstream” or “reverse” primer.
The terms “restriction endonucleases” and “restriction enzymes” refer to enzymes, typically bacterial in origin, which cut double-stranded DNA at or near a specific nucleotide sequence.
Families of amino acid residues having similar side chains are defined herein. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., asparagine, glutamine, serine, threonine, tyrosine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, cysteine, glycine), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
The term “thermostable polymerase” refers to an enzyme that is stable to heat, is heat resistant and retains sufficient activity to effect subsequent primer extension reactions after being subjected to the elevated temperatures for the time necessary to denature double-stranded nucleic acids. Heating conditions necessary for nucleic acid denaturation are well known in the art and are exemplified in U.S. Pat. Nos. 4,965,188 and 4,889,818, which are incorporated herein by reference. As used herein, a thermostable polymerase is suitable for use in a temperature cycling reaction such as PCR.
The term “thermoactive polymerase” refers to an enzyme that is active at the elevated temperatures necessary to ensure specific priming and primer extension (e.g., 55–80° C.).
The term “proofreading activity” refers to a 3′-5′ exonuclease activity possessed by a molecule that also possesses a 5′-3′ DNA polymerizing activity.
For a DNA polymerase activity, “enzymatic activity” refers to the catalysis of the combination of the nucleotides in the proper manner to form primer extension products that are complementary to a template nucleic acid strand. DNA polymerase activities are expressed as units/pmol as measured using the polymerase assay taught below in Example 3. One unit of polymerase activity is defined as the amount of enzyme activity required to incorporate a total of 10 nmoles dNMP into TCA-precipitable DNA product in 30 minutes using the polymerase assay conditions provided below in Example 3.
For a 3′-5′ exonuclease activity, “enzymatic activity” refers to the serial removal of the 3′-most nucleotide residues of a nucleic acid strand, polynucleotide or oligomer by catalysis of the hydrolysis of the phosphodiester bond. One unit of 3′-5′ exonuclease activity catalyzes the conversion of 50 pmol of single-stranded NJS40 oligonucleotide to shorter length oligonucleotides in 15 minutes under the Standard Assay conditions taught in Example 3, below.
For a 5′-3′ exonuclease activity, “enzymatic activity” refers to the serial removal of the 5′ most nucleotide residues of a nucleic acid strand, polynucleotide or oligonucleotide by catalysis of the hydrolysis of the phosphodiester bond. One unit of 5′-3′ exonuclease activity is defined and an assay for measuring 5′-3′ exonuclease activity is provided in U.S. Pat. No. 5,795,762.
As used herein, a “point mutation” in an amino acid sequence refers to either a single amino acid substitution, a single amino acid insertion or single amino acid deletion. A point mutation preferably is introduced into an amino acid sequence by a suitable codon change in the encoding DNA. Individual amino acids in a sequence are represented herein as AN, wherein A is the standard one letter symbol for the amino acid in the sequence, and N is the position in the sequence. Mutations within an amino acid sequence are represented herein as A1 NA2, wherein A1 is the standard one letter symbol for the amino acid in the unmutated protein sequence, A2 is the standard one letter symbol for the amino acid in the mutated protein sequence, and N is the position in the amino acid sequence. For example, a G46D mutation represents a change from glycine to an aspartate residue at amino acid position 46. When referring to mutations in a domain derived from a protein, the amino acid positions are numbered based on the full-length sequence of the protein from which the region encompassing the mutation is derived. Thus, in the present invention, mutations in the region of the protein which are derived from a Thermus species DNA polymerase are numbered according to the full-length Thermus species DNA polymerase sequence, whereas mutations in the region derived from Tma DNA polymerase are numbered according to the full-length Tma DNA polymerase sequence. Representations of nucleotides and point mutations in DNA sequences are analogous. However, when referring to a chimeric protein or a nucleic acid encoding a chimeric protein, amino acid residues or nucleic acids are numbered contiguously.
The terms “peptide,” “polypeptide,” and “protein” are used interchangeably. The terms “nucleic acid” and “polynucleotide” are used interchangeably. Amino acid sequences are written from amino terminus to carboxy terminus, unless otherwise indicated. Single-stranded nucleic acid sequences are written 5′ to 3′, unless otherwise indicated. The top strand of a double-stranded nucleic acid sequence is written 5′ to 3′, and the bottom strand is written 3′ to 5′, unless otherwise indicated.
As used herein, a “chimeric” protein refers to a protein whose amino acid sequence represents a fusion product of subsequences of the amino acid sequences from at least two distinct proteins. A chimeric protein preferably is not produced by direct manipulation of amino acid sequences, but, rather, is expressed from a “chimeric” gene that encodes the chimeric amino acid sequence. In one embodiment of the present invention, a chimeric protein is provided that consists of an amino-terminal (N-terminal) region derived from a Thermus species DNA polymerase and a carboxy-terminal (C-terminal) region derived from Tma DNA polymerase. The N-terminal region refers to a region extending from the N-terminus (amino acid position 1) to an internal amino acid. Similarly, the C-terminal region refers to a region extending from an internal amino acid to the C-terminus.
Unless otherwise specified, amino acid sequence identity is determined using the BLAST algorithm, described in Altschul et al., J. Mol. Biol. 215, 403–410, (1990) and Karlin et al., PNAS USA 90:5873–5787 (1993). A particularly useful BLAST program is the WU-BLAST-2 program that is described by Altschul et al., Methods in Enzymology, 266:460–480 (1996). WU-BLAST-2 uses several search parameters, most of which are set to the default values. The adjustable parameters are set with the following values: overlap span=1, overlap fraction=0.125, word threshold (T)=11. The HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched; however, the values may be adjusted to increase sensitivity. A percent amino acid sequence identity value is determined by the number of matching identical residues divided by the total number of residues of the “longer” sequence in the aligned region. The “longer” sequence is the one having the most actual residues in the aligned region (gaps introduced by WU-Blast-2 to maximize the alignment score are ignored). Percent amino acid sequence homology is determined based on the number of homologous amino acid residues in relation to the total number of amino acid residues.
Percent (%) nucleic acid sequence identity is defined as the percentage of nucleotide residues in a candidate sequence that are identical with the nucleotide residues of the sequence. Unless otherwise specified, percent nucleic acid sequence identity is calculated using the BLASTN module of WU-BLAST-2 set to the default parameters, with overlap span and overlap fraction set to 1 and 0.125, respectively. The alignment may include the introduction of gaps in the sequences to be aligned. Percent nucleic acid sequence homology is determined based on the number of homologous nucleosides in relation to the total number of nucleosides. For both nucleic acid and amino acid sequences, “% homology” and “% sequence homology” are used interchangeably with “% similarity” and “% sequence similarity.”
As used herein, an activity is “attenuated” if it is less than 100% but still measureable using the Standard Assay described in Example 3, below. An activity is “inactivated” or “essentially inactivated” if reduced to less than 0.1% of the activity of the fully functional enzyme.
The Thermostable and Thermoactive DNA Polymerases of the Invention
The present invention provides novel compositions that are thermostable or thermoactive DNA polymerases with an attenuated 3′-5′ exonuclease activity. The thermostable or thermoactive DNA polymerases of the invention are, for example, more suitable and desirable than previous thermostable or thermoactive DNA polymerases for use in PCR-based amplification methods, such as PCR-based amplification of a DNA fragment for cloning. Improved PCR amplification methods of the invention include the use of these thermostable or thermoactive DNA polymerases. Methods of making the thermostable or thermoactive DNA polymerases with attenuated proofreading activity, DNA sequences encoding them and vectors for expressing them also are provided.
1. Thermostable or Thermoactive DNA Polymerases with Attenuated 3′-5′ Exonuclease Activity
In one aspect, the present invention provides a thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity. In one embodiment, the polymerase is from a thermophilic eubacterium. In another embodiment, the thermophilic eubacterium is a species in the genus Thermotoga . In another embodiment, the thermophilic eubacterium is Thermotoga maritima (Tma). In another embodiment, the thermophilic eubacterium is Thermotoga neapolitana. In another embodiment, the thermophilic eubacterium is a species in the genus Thermosipho. In another embodiment, the thermophilic eubacterium is Thermosipho africanus. In another embodiment, the thermophilic eubacterium is a species in the genus Aquifex. In another embodiment, the thermophilic eubacterium is Aquifex pyrophilus. In another embodiment, the thermophilic eubacterium is Aquifex aeolieus. 
In another aspect, the polymerase is from a thermophilic archae. In one embodiment, the thermophilic archae is a species of the genus Thermococcus. In another embodiment, the thermophilic archae is Thermococcus barossi. In another embodiment, the thermophilic archae is Thermococcus litoralis. In another embodiment, the thermophilic archae is Thermococcus gorgonarius In another more embodiment, the thermophilic archae is a species of the genus Pyrococcus. In another embodiment, the thermophilic archae is Pyrococcus furiosus. In another embodiment, the thermophilic archae is Pyrococcus sp. GB-D. In another embodiment, the thermophilic archae is Pyrococcus woesei. In another embodiment, the thermophilic archae is Pyrococcus abyssi. In another embodiment, the thermophilic archae is a species of the genus Pyrodictium. In another embodiment, the thermophilic archae is Pyrodictium abyssi. In another embodiment, the thermophilic archae is Pyrodictium occultum. 
In another aspect, the invention provides a thermostable or thermoactive DNA polymerase comprising one or more point mutations (single amino acid substitution, insertion or deletion mutations) that reduce its 3′-5′ exonuclease activity. In one embodiment, the 3′-5′ exonuclease activity of the mutant thermostable or thermoactive DNA polymerase is between about 0.1% and about 65% that of the wild-type DNA polymerase as measured using the Standard Assay of Example 3. In another embodiment, the 3′-5′ exonuclease activity of the mutant thermostable or thermoactive DNA polymerase is between about 1.0% and about 30% that of the wild-type DNA polymerase. In another embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 3.0% and about 20% that of the wild-type DNA polymerase. In another embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 3.0% and about 10% that of the wild-type DNA polymerase. In another embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 3.0% and about 5.0% that of the wild-type DNA polymerase.
In another aspect, the 3′-5′ exonuclease activity of the mutant polymerase is 50% or less, but greater than 0%, that of the wild-type DNA polymerase, measured using the double-stranded DNA substrate and First Variant Assay of Example 4. In one embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 4% and about 35% that of the wild-type DNA polymerase. In another embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 4% and about 17% that of the wild-type DNA polymerase.
In another aspect, the 3′-5′ exonuclease activity of the mutant polymerase is between about 0.1% and about 70% that of the wild-type DNA polymerase, measured using the mismatch-containing double-stranded DNA substrate and Second Variant Assay of Example 4. In one embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 10% and about 50% that of the wild-type DNA polymerase. In another embodiment, the 3′-5′ exonuclease activity of the mutant polymerase is between about 10% and about 30% that of the wild-type DNA polymerase.
In another aspect, the instant invention provides a thermostable or thermoactive DNA polymerase having a 3′-5′ exonuclease activity of about 6.5 U/pmol or less, but greater than 0 U/pmol, measured using the Standard Assay of Example 3. In one embodiment, the thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.4 and about 3.0 units/pmol. In another embodiment, the thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.4 and about 1.6 units/pmol.
In another aspect, the instant invention provides a thermostable or thermoactive DNA polymerase having a 3′-5′ exonuclease activity of about 5.5 U/pmol or less, but greater than 0 U/pmol, measured using the double-stranded DNA substrate and First Variant Assay of Example 4. In one embodiment, the thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.5 and about 3.6 units/pmol. In another embodiment, the thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 0.5 and about 1.9 units/pmol.
In another aspect, the instant invention provides a thermostable or thermoactive DNA polymerase having a 3′-5′ exonuclease activity of between about 0.01 and 12.0 U/pmol, measured using the mismatch-containing double-stranded DNA substrate and Second Variant Assay of Example 4. In one embodiment, the thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 1.0 and about 7.0 units/pmol. In another embodiment, the thermostable or thermoactive DNA polymerase has a 3′-5′ exonuclease activity of between about 1.5 and about 5.0 units/pmol.
In another aspect, the instant invention provides a thermostable or thermoactive DNA polymerase having a ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity of between about 1 and 100, wherein the polymerase activity and the 3′-5′ exonuclease activity are measured as described in Example 3. In one embodiment, the ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity is between about 3.0 and about 50. In another embodiment, the ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity is between about 6.0 and about 25.0.
In another aspect, the instant invention provides a thermostable or thermoactive DNA polymerase having a ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity of between about 1 and 100, wherein the polymerase activity is measured as described in Example 3 and the 3′-5′ exonuclease activity is measured using the double-stranded DNA substrate and First Variant Assay of Example 4. In one embodiment, the ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity is between about 2.0 and about 50. In one embodiment, the ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity is between about 5.0 and about 25.0.
In another aspect, the instant invention provides a thermostable or thermoactive DNA polymerase having a ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity of between about 0.75 and 10, wherein the polymerase activity is measured as described in Example 3 and the 3′-5′ exonuclease activity is measured using the mismatch-containing double-stranded DNA substrate and Second Variant Assay of Example 4. In one embodiment, the ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity is between about 1.2 and about 5.0. In another embodiment, the ratio of 5′-3′ template-dependent DNA polymerase activity to 3′-5′ exonuclease activity is between about 2.0 and about 4.5.
In another aspect of the invention, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from the Tma DNA polymerase. In one embodiment of the invention, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity is derived from a Thermus/Thermotoga chimeric DNA polymerase that includes a Tma 3′-5′ exonuclease domain. Tma DNA polymerase is a thermostable and thermoactive enzyme with 3′-5′ exonuclease activity. See U.S. Pat. No.s 5,624,833 and 5,374,553. Amino acid residues about 292 to about 484 of the Tma DNA polymerase depicted in FIG. 1 comprise the 3′-5′ exonuclease domain. In another embodiment, the thermostable or thermoactive DNA polymerase of the present invention comprises one or more mutations in the 3′-5′ exonuclease domain of Tma DNA polymerase. In another embodiment, the mutant Tma DNA polymerase comprises a mutation in L329. In another embodiment, the mutation is L329A. In another embodiment, the mutant Tma DNA polymerase comprises a mutation in D389. In another embodiment, the mutation is D389E. In another embodiment, the mutant Tma DNA polymerase comprises a mutation in Q384. In another embodiment, the mutation is Q384A. In another embodiment, the mutant Tma DNA polymerase comprises a mutation in N385. In another embodiment, the mutation is N385A. In another embodiment, the mutant Tma DNA polymerase comprises mutations at Q384 and N385. In another embodiment, the mutations are Q384A N385A.
Other mutations at these or other amino acid positions that result in attenuated 3′-5′ exonuclease activity can be identified by creating and testing the mutants using standard techniques and the exonuclease activity assays taught herein. One method of making a mutant Tma DNA polymerase with reduced 3′-5′ exonuclease activity is to either delete one or more amino acid residues or mutate them to an amino acid having a different chemical property. For example, an amino acid residue having an acidic side chain such as aspartate may be changed to a residue having a basic, uncharged polar, nonpolar, beta-branched or aromatic side chain. Substitution mutations that preserve the charge property of the amino acid also may attenuate the 3′-5′ exonuclease activity, e.g., changing an aspartate residue to a glutamate residue.
Another method of generating mutant thermostable or thermoactive DNA polymerases is to make changes to the polymerase near a residue known or suspected to affect the polymerase's 3′-5′ exonuclease activity. For example, one or more amino acid residues can be inserted, deleted or substituted adjacent to a critical residue in the 3′-5′ exonuclease domain of the polymerase. Alternatively, one or more residues can be inserted, deleted or substituted that are not adjacent to a critical residue in the primary sequence of the protein but that are adjacent to the critical residue in the tertiary structure of the polymerase. This method is particularly favored where mutation of the critical residue itself causes a greater than desired reduction in the 3′-5′ exonuclease activity of the polymerase, or causes other problems, such as misfolding of the polymerase.
As an alternative to the site-directed mutagenesis techniques described above, more random mutagenesis techniques can be used to generate the mutant thermostable or thermoactive DNA polymerases of the invention. For example, insertion, deletion and/or substitution mutations can be introduced into the Tma DNA polymerase at any position, without regard for the critical residues discussed above, or even for the domain structure of the protein. In one embodiment, mutations are introduced randomly throughout the Tma DNA polymerase 3′-5′ exonuclease domain. In another embodiment, mutations are introduced randomly throughout the entire DNA polymerase molecule. Each mutagenized polymerase then can be assayed for 3′-5′ exonuclease activity, as described in the examples, and mutant polymerases having the desired level of 3′-5′ exonuclease activity then can be selected for use.
Mutant thermostable or thermoactive DNA polymerases according to the invention also can be made by introducing more than one mutation into Tma DNA polymerase. For example, two or more mutations, each of which on its own does not sufficiently reduce the 3′-5′ exonuclease activity of the mutant polymerase, can be combined in one polymerase molecule to reduce the 3′-5′ exonuclease activity to within the desired range. Alternatively, one or more mutations that preferentially reduce the 3′-5′ exonuclease activity of Tma DNA polymerase on an ssDNA substrate can be combined in one polymerase molecule with one or more mutations that preferentially reduce the 3′-5′ exonuclease activity of Tma DNA polymerase on a dsDNA substrate.
Mutant thermostable or thermoactive DNA polymerases according to the invention also can be made by deleting, inserting, substituting or rearranging a plurality of adjacent residues, provided that the mutant DNA polymerase has an attenuated 3′-5′ exonuclease activity.
Not every mutation of every amino acid of Tma DNA polymerase will result in a mutant thermostable or thermoactive DNA polymerase with the desired level of 3′-5′ exonuclease activity. Some mutations will not reduce the 3′-5′ exonuclease activity sufficiently, others will reduce it too much. For example, U.S. Pat. Nos. 6,015,668; 5,939,301 and 5,948,614 describe mutations of a metal-binding aspartate to an alanine residue in the 3′-5′ exonuclease domain of the Tma and Tne DNA polymerases. These mutations reduce the 3′-5′ exonuclease activities of these enzymes to below detectable levels, and so are not encompassed by the present invention. Similarly, U.S. Pat. No. 5,882,904 describes an analogous aspartate-to-alanine mutation in Thermococcus barossi, and U.S. Pat. No. 5,489,523 teaches the double-mutant D141A E143A of the Pyrococcus wosei DNA polymerases. Both of these mutant polymerases have virtually no detectable 3′-5′ exonuclease activity. Thus, one of skill in the art will appreciate that it is necessary to assay each mutant thermostable or thermoactive DNA polymerase to determine its 3′-5′ exonuclease activity. Methods of assaying 3′-5′ exonuclease activity are provided below. Other methods are well-known in the art. See, e.g., Freemont et al., 1986, Proteins 1:66; Derbyshire et al., 1991, EMBO J. 16:17 and Derbyshire et al., 1995, Methods in Enzymology 262:363–85.
In another aspect, the present invention provides a mutant Tma DNA polymerase having an attenuated 3′-5′ exonuclease activity and comprising one or more mutations affecting one or more properties of Tma DNA polymerase. Examples of these properties include, but are not limited to, the ability of Tma DNA polymerase to discriminate between dNTPs and dNTP analogs or derivatives, see, e.g., U.S. Pat. No.s 5,939,292 and 5,614,365, 5′-3′ exonuclease activity, see, e.g., U.S. Pat. No.s 6,228,628; 5,466,591 and 5,420,029, thermostability, cold stability, see, e.g., U.S. Pat. No. 6,214,557, ease or expense of manufacture, processivity, rate of polymerization, etc.
Mutations in the amino acid sequence are achieved by incorporating appropriate mutations in the encoding gene sequence. Such mutations in the DNA sequence are carried out using techniques well known in the art, as described further, below.
In another aspect, the present invention provides a thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity that has been chemically modified. See, e.g., U.S. Pat. No. 6,183,998. In one embodiment, the chemical modification is a post-translational modification. In another embodiment, the modified amino acid residue is one that is identified herein as being important or critical for 3′-5′ exonuclease activity. The post-translational modification can be made in vitro or in vivo. Examples of post-translational modifications include, but are not limited to, processing by a protease and phosphorylation, glycosylation and acylation of amino acid residues. See, e.g., Molecular Biology of the Cell, 1994, (Alberts et al., ed.s), 3d ed., Garland Publishing, New York.
Each of the types of mutations and modifications discussed above with reference to Tma DNA polymerase can be introduced into other thermostable or thermoactive DNA polymerases to generate mutant thermostable or thermoactive DNA polymerases of the present invention. Based on amino acid sequence alignments, DNA polymerases have been classified into groups, designated families A, B, and C, according to the homology with E. coli DNA polymerases I, II, and III. See, e.g., Ito et al., Nucl. Acids Res. 19:4045–47, incorporated herein by reference in its entirety. The Thermotoga and Thermus species DNA polymerases are members of the family A DNA polymerases, which also includes E. coli DNA polymerase I. Amino acids that are conserved among family A DNA polymerases have been identified. An alignment of an amino acid sequence from the region of the 3′-5′ exonuclease domain of the Tma DNA polymerase with the amino acid sequences of other family A DNA polymerases is shown in FIG. 8 (SEQ ID NO:172–187). Because of the conservation of amino acids between family A DNA polymerases, the identification of amino acids that affect 3′-5′ exonuclease activity in one DNA polymerase, such as E. coli DNA polymerase I or Tma DNA polymerase, coupled with the teachings provided herein, allows identification of amino acids affecting 3′-5′ exonuclease activity in other family A DNA polymerases based on a sequence alignment. Conserved sequence motifs Exo I, Exo II, Exo IIa and Exo III are indicated in FIG. 8. Thus, in one embodiment, the present invention provides a mutant thermostable or thermoactive family A DNA polymerase with an attenuated 3′-5′ exonuclease activity. In another embodiment, the thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity has a mutation in Exo I, Exo II, Exo IIa or Exo III. In another embodiment, the mutation is in Exo I, Exo II or Exo III.
A large number of thermophilic species have been identified that have DNA polymerases with a 3′-5′ exonuclease activity that can be attenuated according to the present invention. Representative eubacterial species include Thermotoga maritima, Thermotoga neapolitina, see, e.g., U.S. Pat. No.s 6,077,664; 6,015,668; 6,001,645 and 5,912,155, Thermosipho africanus, see, e.g., 5,968,799; Hot Spring family A.
Corresponding amino acids and regions within these DNA polymerases can be identified by aligning their amino acid sequences. Correspondence refers both to amino acids that are identical (conserved) among the sequences and to amino acids that are not identical, but that are aligned to maximize overall sequence similarity.
Using such alignments, one of skill in the art can determine which residues in a family A thermostable or thermoactive DNA polymerase correspond to the 3′-5′ exonuclease domain or the critical residues discussed above of the Tma DNA polymerase. Thus, in one embodiment, the invention provides a mutant thermostable or thermoactive DNA polymerase comprising a mutation in a residue corresponding to the L329 residue of Tma. In another embodiment, the residue corresponding to the L329 residue of Tma is mutated to alanine. In another embodiment, the invention provides a mutant thermostable or thermoactive DNA polymerase comprising a mutation in a residue corresponding to the D389 residue of Tma. In another embodiment, the residue corresponding to the D389 residue of Tma is mutated to glutamate. In another embodiment, the invention provides a mutant thermostable or thermoactive DNA polymerase comprising a mutation in a residue corresponding to the Q384 residue of Tma. In another embodiment, the residue corresponding to the Q384 residue of Tma is mutated to alanine. In another embodiment, the invention provides a mutant thermostable or thermoactive DNA polymerase comprising a mutation in a residue corresponding to the N385 residue of Tma. In another embodiment, the residue corresponding to the N385 residue of Tma is mutated to alanine. In another embodiment, the invention provides a mutant thermostable or thermoactive DNA polymerase comprising mutations in residues corresponding to the Q384 and N385 residues of Tma. In another embodiment, each of the residues corresponding to the Q384 and N385 residues of Tma is mutated to alanine.
Additional species of thermophilic eubacteria have been identified and are available from depositories such the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, Va. 20110-2209) and the Deutsche Sammlung von Mikroorganismen (DSM, Macheroder Weg 1b, D-38124 Braunschweig, Germany). As discussed below, DNA polymerases and the genes encoding them can be recovered from the deposited strains and sequenced in a routine manner. A routine sequence alignment of the amino acid sequence of a thermophilic eubacterium's family A DNA polymerase with the amino acid sequence of the Tma DNA polymerase using, for example, the GAP program (Accelrys, Madison, Wis.), enables the use of the thermophilic eubacterium's DNA polymerase sequence in a mutant DNA polymerase of the present invention.
In another aspect of the present invention, a commercially available thermostable or thermoactive DNA polymerase with 3′-5′ exonuclease activity is used to generate a mutant thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity. Examples of commercially available thermostable or thermoactive DNA polymerases that possess substantial 3′-5′ exonuclease activity include VENTR® and DEEP VENTR® DNA polymerases (New England Biolabs, Beverly Mass.) and Pfu DNA polymerase (Stratagene, San Diego, Calif.).
In another aspect, the mutant thermostable or thermoactive DNA polymerase of the invention is derived from a DNA polymerase that is naturally found in a mesophilic organism and that has been mutated or engineered into a thermostable or thermoactive enzyme. See, e.g., Sanchez-Ruiz et al., 2001, Trends Biotechnol. 19:132–35; Fontana, 1991, Curr Opin Biotechnol. 2:551–60.; Nosoh et al., 1990, Trends Biotechnol. 8:16–20; Pace, 1990, Trends Biotechnol. 8:93–98 and Peters, 1998, Science 281:368–69. In one embodiment, the polymerase is a family A DNA polymerase. In another embodiment, the mesophilic organism is a mesophilic eubacterium. In another embodiment, the mesophilic eubacterium is E. coli. See Villbrandt et al., 2000, Protein Eng. 9:645–54.
2. Chimeric Proteins of the Invention
In another aspect, the invention provides a chimeric thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity, said polymerase comprising an amino terminal portion and a carboxy terminal portion, with the amino terminal portion derived from the amino terminal portion of a first DNA polymerase and the carboxy terminal portion derived from a second DNA polymerase. In one embodiment, said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity comprises an amino terminal portion derived from the amino terminal portion of a first thermostable or thermoactive DNA polymerase and a carboxy terminal portion derived from a second thermostable or thermoactive DNA polymerase, said second polymerase preferably being one that exhibits 3′-5′ exonuclease activity. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, said amino terminal and/or carboxy terminal portion is derived from a DNA polymerase from a Thermus species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, said amino terminal and/or carboxy terminal portion is derived from a DNA polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal and/or carboxy terminal portion is derived from a DNA polymerase from a Thermus species and the other terminal portion is derived from a DNA polymerase from a Thermotoga species; for example, in one embodiment, the amino terminal portion is derived from a DNA polymerase from a Thermus species and the carboxy terminal portion is derived from a DNA polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal portion is derived from a Thermus species and comprises a 5′-3′ exonuclease domain and the carboxy terminal portion is derived from a Thermotoga species and comprises a 3′-5′ exonuclease domain and a polymerase domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal portion is derived from a Thermus species and comprises a 5′-3′ exonuclease domain and has greater than about 80% sequence identity with a corresponding amino terminal portion the DNA polymerase from the Thermus species and said carboxy terminal portion has greater than about 80% sequence identity with a corresponding carboxy terminal portion of the DNA polymerase from the Thermotoga species. In another embodiment, said Thermus species is Thermus sp. Z05 and said Thermotoga species is Thermotoga maritima. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 4 modified by one or more of the mutations indicated in the figure. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 5 modified by one or more of the mutations indicated in the figure. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity comprises an amino terminal portion, a middle portion, and a carboxy terminal portion. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminal portion comprises a 5′-3′ exonuclease domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the middle portion comprises a 3′-5′ exonuclease domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the carboxy terminal portion comprises a polymerase domain. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the carboxy terminal portion and the amino terminal portion are derived from a polymerase from a Thermus species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the amino terminus and/or the carboxy terminus have greater than 80% sequence identity with a corresponding amino and/or carboxy terminus portion of a polymerase from a Thermus species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the middle portion is derived from a polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the middle portion has greater than 80%, but less than 100%, sequence identity to the corresponding polymerase from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, an amino portion and a carboxy portion are derived from a polymerase from a Thermus species and a middle portion is derived from a Thermotoga species. In another embodiment, in said chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity, the Thermus species is Thermus sp. Z05 and the Thermotoga species is Thermotoga maritima. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 6 modified by one or more of the mutations indicated in the figure. In another embodiment, the chimeric thermostable or thermoactive DNA polymerase comprises the amino acid sequence of FIG. 7 modified by one or more of the mutations indicated in the figure.
In another aspect, the chimeric DNA polymerase with an attenuated 3′-5′ exonuclease activity comprises sequences from two or more thermostable or thermoactive DNA polymerases. In one embodiment, the chimeric polymerase comprises at its N-terminal end a 5′-3′ exonuclease domain derived from a DNA polymerase from a first species and at its C-terminal end a DNA polymerase domain and a 3′-5′ exonuclease domain from a DNA polymerase from a second species. In another embodiment, the first species and the second species are bacterial species. In another embodiment, the first species and the second species are thermophilic species. In another embodiment, the first species is a Thermus species. In another embodiment, the Thermus species is Thermus aquaticus (Taq). In another embodiment, the Thermus species is Thermus flavus (Tfl). In another embodiment, the Thermus species is Thermus thermophilus (Tth). In another embodiment, the Thermus species is Thermus species Z05 (TZ05). In another embodiment, the Thermus species is Thermus species 17 (Tsps17). In another embodiment, the Thermus species is Thermus caldofilus (Tca). In another embodiment, the second species is a Thermotoga species. In another embodiment, the Thermotoga species is Thermotoga maritima (Tma). In another embodiment, the first species is TZ05 and the second species is Tma.
In another aspect of the present invention, the chimeric thermostable or thermoactive DNA polymerase with attenuated 3′-5′ exonuclease activity comprises sequences from a thermostable or thermoactive DNA polymerase and from another protein, wherein the sequences from the other protein confer a beneficial property to the chimeric protein. In one embodiment, the beneficial property affects the expression, purification, stability, half-life, susceptibility to proteases, post-translational modification, enzymatic activity or thermostability of the chimeric protein.
DNA polymerases from species of the genus Thermus and Tma DNA polymerase are similar in overall structure. In these DNA polymerases, the 5′-nuclease and DNA polymerase activities of the enzymes are present in discrete regions of the protein (the activity domains). The approximate activity domains of a representative Thermus species DNA polymerase, Taq DNA polymerase, and Tma DNA polymerase are shown in Table 1. See also U.S. Pat. No. 5,420,029. The difference in length between the region that encodes 3′-5′ exonuclease activity in Tma DNA polymerase and the corresponding region in Taq DNA polymerase contributes or corresponds to the lack of 3′-5′ exonuclease activity in Taq DNA polymerase.







TABLE 1







Activity Domains (approximate amino acid positions)











5′-3′ exo
3′-5′ exo
Polymerase
















Taq DNA polymerase
1-289
—
423-832



Tma DNA polymerase
1-291
292-484
485-893










Significant amino acid sequence similarity exists between Thermus species DNA polymerases and Tma DNA polymerase. For example, an amino acid sequence comparison of a representative Thermus species DNA polymerase, Taq DNA polymerase, and Tma DNA polymerase using the GAP computer program (Accelrys, Madison, Wis.) with the default parameter values, indicates that the amino acid sequences are approximately 44% identical and 66% similar over their entire amino acid sequences.
Because of the overall structural and sequence similarity of Tma and Thermus species DNA polymerases, a Tma/Thermus chimeric enzyme can be constructed that preserves the overall structure and activity domains present in Tma DNA polymerase. In one embodiment, the chimeric enzyme comprises the C-terminal region of Tma DNA polymerase and the N-terminal region of a Thermus species DNA polymerase. In another embodiment, the chimeric enzyme of the present invention corresponds to a mutated Tma DNA polymerase, wherein the 5′-3′ exonuclease domain has been replaced by the corresponding domain from a Thermus species DNA polymerase. The “corresponding domain” is defined herein by an amino acid sequence alignment, as provided in U.S. Pat. No. 6,228,628.
In another aspect of the invention, the first amino acid of the region from Tma DNA polymerase begins with the amino acid following the amino acid that corresponds to the last amino acid of the Thermus species DNA polymerase sequence and contains the rest (through amino acid 893) of the Tma DNA polymerase sequence. The amino acid sequence of an entire Tma DNA polymerase is provided in FIG. 1A (SEQ ID NO:85). Preferably, the amino acid sequence from the Thermus species DNA polymerase is joined to an amino acid sequence from Tma DNA polymerase at a point where the two amino acid sequences are identical or similar. For example, one embodiment consists of amino acids 1–190 from Taq DNA polymerase and amino acids 191–893 of Tma DNA polymerase. Amino acid 190 of Tma DNA polymerase corresponds to amino acid 190 of Taq DNA polymerase, and the Tma DNA polymerase portion of the chimeric enzyme begins with the next amino acid, amino acid 191.
In regions where the two DNA polymerases are identical, identification of the last amino acid from the Thermus species DNA polymerase is arbitrary within the region. For example, because amino acids 191 and 192 are identical in Taq DNA polymerase and Tma DNA polymerase (and conserved among Thermus species DNA polymerases), a chimeric protein that contains amino acids 1–190 of Taq DNA polymerase is indistinguishable from chimeric proteins containing amino acids 1–191 or 1–192 of Taq DNA polymerase. The embodiment of the invention described in the examples is referred to as containing amino acids 1–190 of Taq DNA polymerase in view of the original derivation of the enzyme.
In one aspect of the present invention the chimeric DNA polymerase is encoded by a chimeric gene in which the region encoding the Tma DNA polymerase sequence through at least the alternative ribosomal binding site present at about codons 133–137 in the full-length Tma DNA polymerase gene, and preferably through the methionine 140 start codon, is replaced by a gene sequence encoding the corresponding region from a Thermus species DNA polymerase. The presence in the full-length Tma DNA polymerase gene of this alternative ribosomal binding site and start codon results in the preferential expression of a truncated Tma DNA polymerase starting with amino acid 140. As described below, replacement of this region of the Tma DNA polymerase gene is useful for the efficient expression of the full-length chimeric protein. Thus, in one embodiment of the chimeric DNA polymerase of the invention, the N-terminal region from a Thermus species DNA polymerase replaces a region of Tma DNA polymerase that encompasses at least through amino acid 137, and preferably through amino acid 140.
The region of each Thermus species DNA polymerase that corresponds to amino acids 1–137 of Tma DNA polymerase is obtained from an amino acid sequence alignment as provided in U.S. Pat. No. 6,228,628. For example, the region of Taq DNA polymerase that corresponds to amino acids 1–137 of Tma DNA polymerase is amino acids 1–142, and the amino acid of Taq DNA polymerase that corresponds M140 of Tma DNA polymerase is L145. Thus, embodiments in which the N-terminal region is from Taq DNA polymerase comprise at least amino acids 1–142 and preferably, amino acids 1–145 of Taq DNA polymerase. Similarly, for embodiments in which the N-terminal region is from another Thermus species DNA polymerase, the region of the Thermus species DNA polymerase that corresponds to amino acids 1–137 and 140 of Tma DNA polymerase is obtained from the sequence alignment provided in U.S. Pat. No. 6,228,628.
One of skill in the art will recognize that minor mutations, additions, or deletions can be introduced into a DNA polymerase that do not alter the functional properties of the enzyme, and that such a mutated enzyme is equivalent, for all intents and purposes, to the unmutated enzyme. For example, it is known that a deletion in Taq DNA polymerase of several N-terminal amino acids does not alter the functional properties of the enzyme. Similarly, it is known that substitution mutations at many of the amino acid positions appear to have essentially no effect. For the purposes of the present invention, DNA polymerases that contain minor mutations that do not alter the functional properties of the enzyme are considered to be equivalent to the unmutated DNA polymerase.
3. Mixtures of Thermostable or Thermoactive DNA Polymerases
In another aspect, the present invention provides a mixture comprising a plurality of thermostable or thermoactive DNA polymerases, wherein at least one of the polymerases has an attenuated 3′-5′ exonuclease activity, as described above. In one embodiment, at least one of the polymerases has an essentially inactivated 3′-5′ exonuclease activity.
In one aspect, the mixture has a 3′-5′ exonuclease activity of between about 6.5 or less, but greater than 0, units/pmol, measured using the Standard Assay described in Example 3, below. In one embodiment, the mixture has a 3′-5′ exonuclease activity of between about 0.4 and 3.0 units/pmol. In another embodiment, the mixture has a 3′-5′ exonuclease activity of between about 0.4 and 1.6 units/pmol.
In another aspect, the mixture has a ratio of template dependent 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity of between about 1 and 100, wherein the polymerase activity is measured using the polymerase assay described below in Example 3 and the 3′-5′ exonuclease activity is measured using the Standard Assay described in Example 3, below. In one embodiment, the mixture has a ratio of template dependent 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity of between about 3.0 and 50. In another embodiment, the mixture has a ratio of template dependent 5′-3′ DNA polymerase activity to 3′-5′ exonuclease activity of between about 6.0 and 25.0.
4. Advantages of the DNA Polymerase of the Invention
The mutant thermostable or thermoactive DNA polymerase of the invention represents a significant improvement over thermostable or thermoactive DNA polymerases described in the literature. In particular, the DNA polymerase of the invention provides the following combination of properties:
(1) reduced degradation of primers as compared to wild-type thermostable or thermoactive DNA polymerase;
(2) more efficient use of dNTPs, reduction of unproductive “idling” reaction, as compared to wild-type thermostable or thermoactive DNA polymerases;
(3) increased fidelity of replication as compared to mutant thermostable or thermoactive DNA polymerases without a 3′-5′ exonuclease activity;
(4) reduced handling and expense compared to mixtures of thermostable or thermoactive DNA polymerases;
(5) the DNA polymerase can be easily and efficiently expressed to a high level in a recombinant expression system, thereby facilitating commercial production of the enzyme; and
(6) DNA polymerases of the invention readily incorporate nucleoside triphosphate analogs, in contrast to thermostable archae proofreading DNA polymerases.
The combination of properties possessed by the DNA polymerase of the invention is particularly useful in PCR, and provides significantly improved results.
(1) Reduced Degradation of Primers
In in vitro applications using a thermostable or thermoactive DNA polymerase with a robust ssDNA 3′-5′ exonuclease activity, the polymerase degrades primers. This affects the reaction in two ways. First, it lowers the concentration of primers in the reaction. Second, it creates partially degraded primers of varying lengths. As the specificity of a primer for its target is directly specified by the primer's sequence and length, the shortened primers may have less specificity for their particular target sequences. This can cause simultaneously a decrease in the replication of the desired sequence and an increase in the replication of spurious or unintended sequences. Upon heating to cause DNA strand separation and duplex denaturation, the presence of the ssDNA 3′-5′ exonuclease activity also may cause a reduction in length of the ends of the synthesized strands, which in subsequent rounds of polymerization act as templates. Because primers bind to these ends, a reduction in their length reduces the strength of their binding to the primers. This too can cause a decrease in the amount of the desired PCR product and an increase in the amount of spurious PCR products. These effects are particularly troublesome for PCR, wherein a decrease in the ratio of amplified target sequence to amplified spurious sequences may reduce the specificity of the reaction and thus decrease the sensitivity of target detection.
The thermostable or thermoactive DNA polymerases of the instant invention overcome this problem by having an attenuated level of 3′-5′ exonuclease activity.
(2) Reduced Idling Reaction
The dsDNA exonuclease activity of thermostable or thermoactive DNA polymerases can cause the polymerase to “idle” when it reaches the end of a linear template. That is, it goes through repeated cycles of polymerizing to the end of the template, then hydrolyzing residues at the just completed end of the synthesized strand. This cycle of polymerization and hydrolysis reduces the concentration of dNTPs and increases the concentration of pyrophosphate in the reaction mix, reducng the reaction efficiency of later cycles. Product yield can be reduced as a result.
The mutant thermostable or thermoactive DNA polymerases of the present invention overcome this problem by having a reduced dsDNA 3′-5′ exonuclease activity. In one embodiment, the mutant polymerases of the invention have a 3′-5′ exonuclease activity that is about 0.1% to about 65% of the activity of the wild-type enzyme, as measured using the single-stranded DNA substrate and Standard Assay of Example 3. In another embodiment, the mutant polymerases of the invention have a 3′-5′ exonuclease activity that is about 1% to about 30% of the activity of the wild-type enzyme. In another embodiment, the mutant polymerases of the invention have a 3′-5′ exonuclease activity that is about 3% to about 20% of the activity of the wild-type enzyme. In another embodiment, the mutant polymerases of the invention have a 3′-5′ exonuclease activity that is about 3% to about 10% of the activity of the wild-type enzyme. In another embodiment, the mutant polymerases of the invention have a 3′-5′ exonuclease activity that is about 3% to about 5% of the activity of the wild-type enzyme.
(3) High Level of Fidelity
Previous attempts to overcome the deleterious effects of the 3′-5′ exonuclease activity of thermostable or thermoactive DNA polymerases have employed mutant polymerases with no or essentially no 3′-5′ exonuclease activity, or polymerases that naturally lack this activity. This approach can create its own problems. Polymerases without 3′-5′ exonuclease activity have a higher error rate than polymerases with this activity. For certain applications of PCR, for example, where the amplified sequence is to be cloned, it is important that the error rate be kept low. Further, the presence of a 3′-5′ exonuclease activity increases amplification and/or reverse transcriptase efficiency for longer targets because nucleotide misincorporation can be corrected. Thus, thermostable or thermoactive DNA polymerases completely lacking a proofreading activity are less suitable for these applications.
The instant invention overcomes this problem by providing isolated thermostable or thermoactive DNA polymerases that have attenuated 3′-5′ exonuclease activity. It has now been determined that an attenuated level of 3′-5′ activity is sufficient to enhance PCR efficiency of longer templates through efficient removal of mis-inserted dNTPs and thus facilitate longer PCR and RT-PCR.
(4) Reduced Handling
Another approach that has been used to overcome the problems associated with robust 3′-5′ exonuclease activity is to mix a polymerase with a wild-type level of proofreading activity with a polymerase that has essentially no proofreading activity. One can achieve the desired ratio of proofreading activity to polymerase activity by manipulating the ratio of these two polymerases in the mixture. While this approach has been used successfully, it has its own drawbacks. The 3′-5′ exonuclease and polymerase activities of both enzymes must be accurately measured for each preparation of each enzyme, then the amount of each enzyme needed calculated. Then, for each reaction, the correct amount of each enzyme must be added. This approach also requires that both enzymes have comparable storage stability. Thus, reactions using mixtures of enzymes require more manipulations, which increases costs and reduces efficiency.
The thermostable or thermoactive DNA polymerases of the instant invention overcome these problems by providing, in one embodiment, a single polymerase that has the desired ratio of proofreading activity to polymerase activity. Only one enzyme needs to be added to each reaction. Unexpectedly, it also was discovered that less total enzyme is required when the polymerases of the invention are used instead of a mixture of enzymes.
(5) Efficiency of Expression
As described above, in one aspect the present invention provides a chimeric enzyme that corresponds to a mutated Tma DNA polymerase, wherein the 5′-nuclease domain has been replaced by the corresponding domain from a Thermus species DNA polymerase. The enzyme is expressed from a chimeric gene that corresponds to a mutated Tma DNA polymerase gene, wherein the region of the gene that encodes the 5′-nuclease domain has been replaced by the corresponding region of the Thermus species DNA polymerase gene. A significant advantage of the chimeric gene is that it enables the expression of a full-length DNA polymerase in a recombinant expression system much more efficiently than is possible from the Tma DNA polymerase gene.
The expression of a full-length DNA polymerase from a recombinant expression system containing the full-length natural Tma DNA polymerase gene sequence is problematical because of the preferential expression of a truncated form of the protein. See U.S. Pat. No. 5,420,029. The truncated protein, referred to as Met140 Tma, consists of amino acids 140–893 of the full-length protein and appears to result from translation beginning at the methionine at position 140. The presence of a putative ribosomal binding site at codons 133–137 further suggests that the truncated protein results from translation beginning at the internal methionine. The preferential expression of the Met140 Tma truncated protein represents a significant difficulty in expressing and purifying a full-length Tma DNA polymerase.
In one embodiment of the present invention, the chimeric DNA polymerase gene contains a Thermus species DNA polymerase gene sequence in a region corresponding at least through the alternative ribosomal binding site present at about codons 133–137 in the full-length Tma DNA polymerase gene, and preferably through the internal start codon, codon 140. Thus, the Tma DNA polymerase gene sequence up through the region containing the ribosomal binding site and, preferably, the start codon responsible for the translation of Met140 Tma, is replaced by the corresponding region of a Thermus species DNA polymerase gene. The corresponding region of a Thermus species DNA polymerase gene does not provide for the undesirable internal initiation of a truncated protein. As a result, a recombinant expression system containing the chimeric DNA polymerase gene expresses a full-length chimeric DNA polymerase exclusively.
(6) Incorporation of Nucleoside Triphosphate Analogs
In another aspect, the thermostable or thermoactive proofreading DNA polymerases of this invention tolerate and readily incorporate nucleoside triphosphate analogs such as dUTP and dITP, in contrast to thermostable archae proofreading DNA polymerases (e.g., VENTTM, DEEPVENTTM, Pfu, Pwo, Poc, Pab, Tgo, etc.). That is, these polymerases are not inhibited by the presence of dUTP or dITP or by the presence of dUMP or dIMP in a template strand. In contrast, the aforementioned archae thermostable proofreading DNA polymerases or mixtures of DNA polymerases containing a proofreading archae DNA polymerase are inhibited by the presence of dUTP or dITP or by the presence of dUPM or dIMP in a template strand. Accordingly, the many benefits of using dUTP with or in place of dTTP or of using dITP with or in place of dGTP may be realized with enzymes of this invention, but not with archae thermostable DNA polymerases. See, e.g., PCR Applications: Protocols for Functional Genomics, 1999, Innis et al. (ed.s), Acaderic Press, San Diego, pages 4, 5, 142 and 143. Thus, while the previously described archae DNA polymerases or mixtures containing an archae DNA polymerase cannot carry out primer extension or PCR amplifications with dUTP or dITP, in one embodiment the thermostable and thermoactive DNA polymerases of the present invention are compatible with the use of these analogs.
5. Preparation of the DNA Polymerase of the Invention
The gene encoding Tma DNA polymerase is described in U.S. Pat. Nos. 5,420,029 and 5,466,591. The nucleotide sequence of the Tma DNA polymerase gene, as well as the full amino acid sequence of the encoded protein, are described therein. Example 5 of the '029 patent describes the construction of a variety of plasmids containing the full-length Tma DNA polymerase gene starting with plasmids pTma01 (ATCC No. 68471, deposited Nov. 7, 1990, and redeposited as ATCC No. 98764 on May 22, 1998) and pTma04 (ATCC No. 68472, deposited Nov. 7, 1990, and redeposited as ATCC No. 98765 on May 22, 1998), such as plasmids pTma12-1 and pTma13. Any of these expression vectors is suitable as a source of the Tma DNA polymerase gene.
Other thermostable or thermoactive DNA polymerases with 3′-5′ exonuclease activity that can be mutated to make the polymerases of the invention include, but are not limited to, those described in U.S. Pat. No.s 6,077,664; 6,015,668; 6,001,645 and 5,912,155 (Thermotoga neapolitina), U.S. Pat. No.s 6,066,483; 5,874,282; 5,834,253; 5,747,298; 6,013,451 and 5,830,714, U.S. Pat. No.s 5,882,904 and 5,602,011 (Thermococcus barossi), U.S. Pat. No.s 5,322,785 and 5,210,036 (Thermococcus litoralis), U.S. Pat. No.s 5,948,663 and 5,866,395; Dabrowski et al., 1998, Protein Expr Purif 14:131–38 (Pyrococcus furiosus), see, e.g., U.S. Pat. No. 5,834,285 (Pyrococcus sp. GB-D) and Dabrowski (1998) (Pyrococcus woesei).
In one aspect, the DNA polymerase of the invention is a chimeric enzyme that comprises a portion derived from a Thermus species DNA polymerase and a portion derived from Tma DNA polymerase. In one embodiment, the DNA polymerase of the invention is a chimeric enzyme that consists of a portion derived from a Thermus species DNA polymerase and a portion derived from Tma DNA polymerase. The chimeric enzyme is prepared from a chimeric gene, i.e., a DNA that encodes the chimeric enzyme and consists of a portion derived from the Thermus species DNA polymerase gene and a portion derived from the Tma DNA polymerase gene. The chimeric gene is produced from the Thermus species DNA polymerase gene and the Tma DNA polymerase gene using standard gene manipulation techniques well known in the field of molecular biology, as described in detail below.
Genes encoding DNA polymerases from a number of Thermus species, including the nucleotide sequence of the DNA polymerase gene and the amino acid sequence of the encoded protein, have been described. A number of these genes are obtainable from publicly available plasmids. The genes from additional Thermus species are obtainable from the host organisms using methods described in U.S. Pat. Nos. 5,079,352; 5,618,711; 5,455,170; 5,405,774; and 5,466,591; each incorporated by reference.
The gene encoding Taq DNA polymerase is described in U.S. Pat. Nos. 5,079,352 and 5,466,591. The nucleotide sequence of the Taq DNA polymerase gene, as well as the full amino acid sequence of the encoded protein, are described therein. Examples V–VII of the '352 patent describes the construction of a variety of expression plasmids containing the full-length Taq DNA polymerase gene starting with plasmids pFC83 (ATCC No. 67422, deposited on May 29, 1987, and redeposited as ATCC No. 98763 on May 22, 1998) and pFC85 (ATCC No. 67421, deposited May 29, 1987, and redeposited as ATCC No. 98762 on May 22, 1998), such as plasmids pLSG1, pLSG2, pSYC1578, pLSG5, and pLSG6. Any of these expression vectors is suitable as a source of the Taq DNA polymerase gene.
The gene encoding Tth DNA polymerase, methods for obtaining the gene, and expression plasmids containing the gene are described in U.S. Pat. No. 5,618,711 and 5,466,591.
The gene encoding TZ05 DNA polymerase, methods for obtaining the gene, and expression plasmids containing the gene are described in U.S. Pat. No. 5,455,170 and 5,466,591.
The gene encoding Tsps17 DNA polymerase, methods for obtaining the gene, and expression plasmids containing the gene are described in U.S. Pat. No. 5,405,774 and 5,466,591.
The Tfl DNA polymerase gene is described in Akhmetzjanov et al., 1992, Nucleic Acids Research 20:5839, incorporated herein by reference in its entirety.
The Tfi DNA polymerase gene can be recovered from ATCC 43280 using the methods described in the referenced patents. See also 1984, FEMS Microbiol. Lett. 22:149–53.
The Tca DNA polymerase gene is described in Kwon, 1997, Mol. Cells 7: 264–71; and the nucleotide sequence is available under EMBL/GenBank Accession No. U62584.
Additional Thermus species DNA polymerase genes can be recovered using techniques described in the above cited patents from the following ATCC deposits: ATCC 43814 and 43815, see Alfredsson, 1986, Appl. Environ. Microbiol. 52:1313–16; ATCC 27978, see Ramaley, 1970, J. Bacteriol. 114:556–62; 1973; ibid. 103:527–528; ATCC 31674, see U.S. Pat. Nos. 4,442,214 and 4,480,036; ATCC 35948 (T. ruber, see Loginova, 1984, Int. J. Syst. Bacteriol. 34:498–99. All references are incorporated herein by reference.
Additional Thermus species can be recovered using techniques described in the above cited patents from the following Deutsche Sammlung von Mikroorganismen (DSM) deposits: DSM:1279 (NUM: 2244), see Loginova et al., 1975, Izv. Akad. Nauk SSSR Ser. Biol.: 304–07; DSM:579; DSM:625 (NUM: 2248), see Degryse et al., 1978, Arch. Microbiol. 189:196; DSM:1279 (NUM: 3844), see Loginova et al., 1984, Int. J. Syst. Bacteriol.:498–99; and DSM:625(NUM: 1002), see Brock et al., 1969, J. Bacteriol.: 289–97. All references are incorporated herein by reference in their entireties.
Additional Thermus species which have been described include T. oshimai, see Williams et al., 1996, Int. J. Syst. Bacteriol. 46:403–08; T. silvanus and T. chliarophilus, see Tenreiro et al. 1995, Int. J. Syst. Bacteriol. 45:633–39; T. scotoductus, see Tenreiro et al., 1995, Res. Microbiol. 146:315–24; and T. ruber, see Shadrina et al., 1982, Mikrobiologiia 51:611–15; all incorporated herein by reference in their entireties.
Following the guidance provided herein, and using only well known techniques, one skilled in the art will be able to prepare from the DNA polymerase genes any number of expression vectors containing a chimeric gene suitable for expressing a chimeric DNA polymerase of the invention in any of a variety of host systems.
In one aspect, the chimeric enzyme of the invention comprises amino acids 1–291 from Z05 DNA polymerase and amino acids 292–893 from Tma DNA polymerase suitably mutated to reduce associated 3′-5′ exonuclease activity. In one embodiment, the chimeric enzyme of the invention consists of amino acids 1–291 from Z05 DNA polymerase and amino acids 292–893 from Tma DNA polymerase suitably mutated to reduce associated 3′-5′ exonuclease activity. These embodiments can be constructed directly from the Z05 DNA polymerase and Tma DNA polymerase genes, either obtained from the deposited plasmids described above or recovered from the host organisms.
Because of the redundancy in the genetic code, typically a large number of DNA sequences encode any given amino acid sequence and are, in this sense, equivalent. As described below, it may be desirable to select one or another equivalent DNA sequences for use in a expression vector, based on the preferred codon usage of the host cell into which the expression vector will be inserted. The present invention is intended to encompass all DNA sequences that encode the chimeric enzyme. Thus, chimeric genes of the present invention are not limited to containing only sequences from a wild-type Thermus species and Tma DNA polymerase genes, but can contain any of the DNA sequences that encode a chimeric DNA polymerase of the present invention.
Production of the enzyme of the invention is carried out using a recombinant expression clone. The construction of the recombinant expression clone, the transformation of a host cell with the expression clone, and the culture of the transformed host cell under conditions which promote expression, can be carried out in a variety of ways using techniques of molecular biology well understood in the art. Methods for each of these steps are described in general below and specifically in the examples.
An operable expression clone is constructed by placing the coding sequence in operable linkage with a suitable control sequences in an expression vector. The vector can be designed to replicate autonomously in the host cell or to integrate into the chromosomal DNA of the host cell. The resulting clone is used to transform a suitable host, and the transformed host is cultured under conditions suitable for expression of the coding sequence. The expressed protein is isolated from the medium or from the cells, although recovery and purification of the protein may not be necessary in some instances.
Construction of suitable clones containing the coding sequence and a suitable control sequence employs standard ligation and restriction techniques that are well understood in the art. In general, isolated plasmids, DNA sequences, or synthesized oligonucleotides are cleaved, modified, and religated in the form desired. Suitable restriction sites can, if not normally available, be added to the ends of the coding sequence so as to facilitate construction of an expression clone.
Site-specific DNA cleavage is performed by treating with a suitable restriction enzyme (or enzymes) under conditions that are generally understood in the art and specified by the manufacturers of commercially available restriction enzymes. See, e.g., product catalogs from Amersham (Arlington Heights, Ill.), Roche Molecular Biochemicals (Indianapolis, Ind.), and New England Biolabs (Beverly, Mass.). In general, about 1 μg of plasmid or other DNA is cleaved by one unit of enzyme in about 20 μl of buffer solution; in the examples below, an excess of restriction enzyme is generally used to ensure complete digestion of the DNA. Incubation times of about one to two hours at a temperature which is optimal for the particular enzyme are typical. After each incubation, protein is removed by extraction with phenol and chloroform; this extraction can be followed by ether extraction and recovery of the DNA from aqueous fractions by precipitation with ethanol. If desired, size separation of the cleaved fragments may be performed by polyacrylamide gel or agarose gel electrophoresis using standard techniques. See, e.g., Maxam et al., 1980, Methods in Enzymology 65:499–560.
Restriction enzyme-cleaved DNA fragments with single-strand “overhanging” termini can be made blunt-ended (double-strand ends) by treating with the large fragment of E. coli DNA polymerase I (Klenow) in the presence of the four deoxynucleoside triphosphates (dNTPs) using incubation times of about 15 to 25 minutes at 20° C. to 25° C. in 50 mM Tris, pH 7.6, 50 mM NaCl, 10 mM MgCl2, 10 mM DTT, and 5 to 10 μM dNTPs. The Klenow fragment fills in at 5′ protruding ends, but chews back protruding 3′ single strands, even though the four dNTPs are present. If desired, selective repair can be performed by supplying one or more selected dNTPs, within the limitations dictated by the nature of the protruding ends. After treatment with Klenow, the mixture is extracted with phenol/chloroform and ethanol precipitated. Similar results can be achieved using S1 nuclease, because treatment under appropriate conditions with S1 nuclease results in hydrolysis of any single-stranded portion of a nucleic acid.
Ligations are performed in 15–30 μl volumes under the following standard conditions and temperatures: 20 mM Tris-Cl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 33 μg/ml BSA, 10–50 mM NaCl, and either 40 μM ATP and 0.01–0.02 (Weiss) units T4 DNA ligase at 0° C. (for ligation of fragments with complementary single-stranded ends) or 1 mM ATP and 0.3–0.6 units T4 DNA ligase at 14° C. (for “blunt end” ligation). Intermolecular ligations of fragments with complementary ends are usually performed at 33–100 μg/ml total DNA concentrations (5–100 nM total ends concentration). Intermolecular blunt end ligations (usually employing a 20–30 fold molar excess of linkers, optionally) are performed at 1 μM total ends concentration.
In vector construction, the vector fragment is commonly treated with bacterial or calf intestinal alkaline phosphatase (BAP or CIAP) to remove the 5′ phosphate and prevent religation and reconstruction of the vector. BAP and CIAP digestion conditions are well known in the art, and published protocols usually accompany the commercially available BAP and CIAP enzymes. To recover the nucleic acid fragments, the preparation is extracted with phenol-chloroform and ethanol precipitated to remove the phosphatase and purify the DNA. Alternatively, religation of unwanted vector fragments can be prevented by restriction enzyme digestion before or after ligation, if appropriate restriction sites are available.
Correct ligations for plasmid construction can be confirmed using any suitable method known in the art. In the construction set forth below, correct ligations for plasmid construction are confirmed by first transforming a suitable host, such as E. coli strain DG101 (ATCC 47043) or E. coli strain DG116 (ATCC 53606), with the ligation mixture. Successful transformants are selected by ampicillin, tetracycline or other antibiotic resistance or sensitivity or by using other markers, depending on the mode of plasmid construction, as is understood in the art. Plasmids from the transformants are then prepared according to the method of Clewell et al., 1969, Proc. Natl. Acad. Sci. USA 62:1159, optionally following chloramphenicol amplification. See Clewell, 1972, J. Bacteriol. 110:667. Alternatively, plasmid DNA can be prepared using the “Base-Acid” extraction method at page II of the Bethesda Research Laboratories publication Focus 5 (2), and very pure plasmid DNA can be obtained by replacing steps 12 through 17 of the protocol with CsCl/ethidium bromide ultracentrifugation of the DNA. As another alternative, a commercially available plasmid DNA isolation kit, e.g., HISPEEDTM, QIAFILTERTM and QIAGEN® plasmid DNA isolation kits (Qiagen, Valencia Calif.) can be employed following the protocols supplied by the vendor. The isolated DNA is analyzed by restriction enzyme digestion and/or sequenced by the dideoxy method of Sanger et al., 1977, Proc. Natl. Acad. Sci. USA 74:5463, as further described by Messing et al., 1981, Nuc Acids Res. 9:309, or by the method of Maxam et al., 1980, Methods in Enzymology 65:499.
The control sequences, expression vectors, and transformation methods are dependent on the type of host cell used to express the gene. Generally, procaryotic, yeast, insect, or mammalian cells are used as hosts. Procaryotic hosts are in general the most efficient and convenient for the production of recombinant proteins and are therefore preferred for the expression of the protein.
The procaryote most frequently used to express recombinant proteins is E. coli. However, microbial strains other than E. coli can also be used, such as bacilli, for example Bacillus subtilis, various species of Pseudomonas and Salmonella, and other bacterial strains, for recombinant expression of the protein. In such procaryotic systems, plasmid vectors that contain replication sites and control sequences derived from the host or a species compatible with the host are typically used.
For expression of constructions under control of most bacterial promoters, E. coli K12 strain MM294, obtained from the E. coli Genetic Stock Center under GCSC #6135, can be used as the host. For expression vectors with the PLNRBS or PLT7RBS control sequence, E. coli K12 strain MC1000 lambda lysogen, N7N53cI857 SusP80, ATCC 39531, may be used. E. coli DG116, which was deposited with the ATCC (ATCC 53606) on Apr. 7, 1987, and E. coli KB2, which was deposited with the ATCC (ATCC 53075) on Mar. 29, 1985, are also useful host cells. For M13 phage recombinants, E. coli strains susceptible to phage infection, such as E. coli K12 strain DG98 (ATCC 39768), are employed. The DG98 strain was deposited with the ATCC on Jul. 13, 1984.
For example, E. coli is typically transformed using derivatives of pBR322, described by Bolivar et al., 1977, Gene 2:95. Plasmid pBR322 contains genes for ampicillin and tetracycline resistance. These drug resistance markers can be either retained or destroyed in constructing the desired vector and so help to detect the presence of a desired recombinant. Commonly used procaryotic control sequences, i.e., a promoter for transcription initiation, optionally with an operator, along with a ribosome binding site sequence, include the β-lactamase (penicillinase) and lactose (lac) promoter systems, see Chang et al., 1977, Nature 198:1056, the tryptophan (trp) promoter system, see Goeddel et al., 1980, Nuc. Acids Res. 8:4057, and the lambda-derived PL promoter, see Shimatake et al., 1981, Nature 292:128, and gene N ribosome binding site (NRBS). A portable control system cassette is set forth in U.S. Pat. No. 4,711,845, issued Dec. 8, 1987. This cassette comprises a PL promoter operably linked to the NRBS in turn positioned upstream of a third DNA sequence having at least one restriction site that permits cleavage within six base pairs 3′ of the NRBS sequence. Also useful is the phosphatase A (phoA) system described by Chang et al., in European Patent Publication No. 196,864, published Oct. 8, 1986. However, any available promoter system compatible with procaryotes can be used to construct a expression vector of the invention.
In addition to bacteria, eucaryotic microbes, such as yeast, can also be used as recombinant host cells. Laboratory strains of Saccharomyces cerevisiae, Baker's yeast, are most often used, although a number of other strains are commonly available. While vectors employing the two micron origin of replication are common, see Broach, 1983, Meth. Enz. 101:307, other plasmid vectors suitable for yeast expression are known. See, e.g., Stinchcomb et al., 1979, Nature 282:39; Tschempe et al., 1980, Gene 10: 157; and Clarke et al., 1983, Meth. Enz. 101:300. Control sequences for yeast vectors include promoters for the synthesis of glycolytic enzymes. See Hess et al., 1968, J. Adv. Enzyme Reg. 7:149; Holland et al., 1978, Biotechnology 17:4900; and Holland et al., 1981, J. Biol. Chem. 256:1385. Additional promoters known in the art include the promoter for 3-phosphoglycerate kinase, see Hitzeman et al., 1980, J. Biol. Chem. 255:2073, and those for other glycolytic enzymes, such as glyceraldehyde 3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase. Other promoters that have the additional advantage of transcription controlled by growth conditions are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, and enzymes responsible for maltose and galactose utilization (Holland, supra).
Terminator sequences may also be used to enhance expression when placed at the 3′ end of the coding sequence. Such terminators are found in the 3′ untranslated region following the coding sequences in yeast-derived genes. Any vector containing a yeast-compatible promoter, origin of replication, and other control sequences is suitable for use in constructing yeast expression vectors.
The coding sequence can also be expressed in eucaryotic host cell cultures derived from multicellular organisms. See, e.g., Cell & Tissue Culture: Laboratory Procedures, Wiley, Doyle et al., editors (1993). Useful host cell lines include COS-7, COS-A2, CV-1, murine cells such as murine myelomas N51 and VERO, HeLa cells, and Chinese hamster ovary (CHO) cells. Expression vectors for such cells ordinarily include promoters and control sequences compatible with mammalian cells such as, for example, the commonly used early and late promoters from Simian Virus 40 (SV 40), see Fiers et al., 1978, Nature 273:113, or other viral promoters such as those derived from polyoma, adenovirus 2, bovine papilloma virus (BPV), or avian sarcoma viruses, or immunoglobulin promoters and heat shock promoters. A system for expressing DNA in mammalian systems using a BPV vector system is disclosed in U.S. Pat. No. 4,419,446. A modification of this system is described in U.S. Pat. No. 4,601,978. General aspects of mammalian cell host system transformations have been described by Axel, U.S. Pat. No. 4,399,216. “Enhancer” regions are also important in optimizing expression; these are, generally, sequences found upstream of the promoter region. Origins of replication may be obtained, if needed, from viral sources. However, integration into the chromosome is a common mechanism for DNA replication in eucaryotes.
Plant cells can also be used as hosts, and control sequences compatible with plant cells, such as the nopaline synthase promoter and polyadenylation signal sequences, see Depicker et al., 1982, J. Mol. Appl. Gen. 1:561, are available. Expression systems employing insect cells utilizing the control systems provided by baculovirus vectors have also been described. See Miller et al., in Genetic Engineering (1986), Setlow et al., eds., Plenum Publishing, Vol. 8, pp. 277–97. Insect cell-based expression can be accomplished in Spodoptera frugipeida. These systems are also successful in producing recombinant enzymes.
Depending on the host cell used, transformation is done using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described by Cohen, 1972, Proc. Natl. Acad. Sci. USA 69:2110 is used for procaryotes or other cells that contain substantial cell wall barriers. Infection with Agrobacterium tumefaciens, see Shaw et al., 1983, Gene 23:315, is used for certain plant cells. For mammalian cells, the calcium phosphate precipitation method of Grahamet al., 1978, Virology 52:546 is preferred. Transformations into yeast are carried out according to the method of Van Solingen et al., 1977, J. Bact. 130:946, and Hsiao et al., 1979, Proc. Natl. Acad. Sci. USA 76:3829.
It may be desirable to modify the sequence of the DNA encoding the enzyme of the invention to provide, for example, a sequence more compatible with the codon usage of the host cell without modifying the amino acid sequence of the encoded protein. Such modifications to the initial 5–6 codons may improve expression efficiency. DNA sequences which have been modified to improve expression efficiency, but which encode the same amino acid sequence, are considered to be equivalent and encompassed by the present invention.
A variety of site-specific primer-directed mutagenesis methods are available and well-known in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, 1989, second edition, chapter 15.51, “Oligonucleotide-mediated mutagenesis,” which is incorporated herein by reference. The polymerase chain reaction (PCR) can be used to perform site-specific mutagenesis. In another technique now standard in the art, a synthetic oligonucleotide encoding the desired mutation is used as a primer to direct synthesis of a complementary nucleic acid sequence contained in a single-stranded vector, such as pBSM13+ derivatives, that serves as a template for construction of the extension product of the mutagenizing primer. The mutagenized DNA is transformed into a host bacterium, and cultures of the transformed bacteria are plated and identified. The identification of modified vectors may involve transfer of the DNA of selected transformants to a nitrocellulose filter or other membrane and the “lifts” hybridized with kinased synthetic mutagenic primer at a temperature that permits hybridization of an exact match to the modified sequence but prevents hybridization with the original unmutagenized strand. Transformants that contain DNA that hybridizes with the probe are then cultured (the sequence of the DNA is generally confirmed by sequence analysis) and serve as a reservoir of the modified DNA.
Once the protein has been expressed in a recombinant host cell, purification of the protein may be desired. A variety of purification procedures can be used to purify the recombinant thermostable or thermoactive DNA polymerase of the invention. Examples include the methods for purifying Taq DNA polymerase described in U.S. Pat. Nos. 4,889,818; 5,352,600; and 5,079,352; the methods for purifying the DNA polymerase from Thermus thermophilis (Tth) described in U.S. Pat. Nos. 5,618,711 and 5,310,652; the methods for purifying Tma DNA polymerase described in U.S. Pat. Nos. 5,374,553 and 5,420,029. Methods for purifying these DNA polymerases are also described in U.S. Pat. No. 5,466,591. All of the above patents are incorporated herein by reference.
In one aspect of the invention, the expression of the DNA polymerase is carried out in E. coli, which is a mesophilic bacterial host cell. Because most E. coli host proteins are heat-sensitive, the recombinant thermostable or thermoactive DNA polymerase can be substantially enriched by heat inactivating the crude lysate. This step is done in the presence of a sufficient amount of salt (typically 0.2–0.4 M ammonium sulfate) to reduce ionic interactions of the DNA polymerase with other cell lysate proteins. In one embodiment, the activity of the purified DNA polymerase is assayed using the method described below in Example 3.
For long-term stability, the purified DNA polymerase enzyme must be stored in a buffer that contains one or more non-ionic polymeric detergents. Such detergents are generally those that have a molecular weight in the range of approximately 100 to 250,00 preferably about 4,000 to 200,000 daltons and stabilize the enzyme at a pH of from about 3.5 to about 9.5, preferably from about 4 to 8.5. Examples of such detergents include those specified on pages 295–298 of McCutcheon's Emulsifiers & Detergents, North American edition (1983), published by the McCutcheon Division of MC Publishing Co., 175 Rock Road, Glen Rock, N.J. (USA), the entire disclosure of which is incorporated herein by reference. In one embodiment the detergents are selected from the group comprising ethoxylated fatty alcohol ethers and lauryl ethers, ethoxylated alkyl phenols, octylphenoxy polyethoxy ethanol compounds, modified oxyethylated and/or oxypropylated straight-chain alcohols, polyethylene glycol monooleate compounds, polysorbate compounds, and phenolic fatty alcohol ethers. In another embodiment the detergents are selected from the group comprising Tween 20TM, a polyoxyethylated (20) sorbitan monolaurate from ICI Americas Inc. (Wilmington, Del.), and IconolTM NP-40, an ethoxylated alkyl phenol (nonyl) from BASF Wyandotte Corp. (Parsippany, N.J.).
6. Uses of the Thermostable or Thermoactive DNA Polymerases of the Invention
The thermostable or thermoactive enzyme of this invention may be used for any purpose in which a thermostable or thermoactive DNA polymerase with an attenuated 3′-5′ exonuclease activity is necessary or desired. In one embodiment, the enzyme is used for PCR. Examples of applications using the PCR include, for example, direct cloning from genomic DNA or cDNA, in vitro mutagenesis and engineering of DNA, genetic fingerprinting of forensic samples, assays for the presence of infectious agents, prenatal diagnosis of genetic diseases, analysis of allelic sequence variations, analysis of RNA transcript structure, genomic footprinting, and direct nucleotide sequencing of genomic DNA and cDNA. See, e.g., Current Protocols in Molecular Biology, 2001, Ausubel et al. (ed.s), John Wiley & Sons, Chapter 15 and PCR Strategies, 1995, Innis et al. (ed.s), Academic Press, Inc., incorporated herein by reference in their entireties.
7. Kits
The thermostable or thermoactive DNA polymerases of the invention are suited for the preparation of a kit. Kits comprising the mutant DNA polymerases of the invention may be used for detectably labeling DNA molecules, DNA sequencing, or amplifying DNA molecules by well known techniques, depending on the content of the kit. Such kits may comprise a carrying means being compartmentalized to receive in close confinement one or more container means such as vials, test tubes and the like. Each of such container means comprises components or a mixture of components needed to perform DNA sequencing, DNA labeling, or DNA amplification.
A kit for sequencing DNA may comprise a number of container means. A first container means may, for example, contain a substantially purified sample of a thermostable or thermoactive DNA polymerase of the invention. A second container means may contain one or a number of types of nucleotides needed to synthesize a DNA molecule complementary to DNA template. A third container means may contain one or a number different types of dideoxynucleotide triphosphates. In addition to the above container means, additional container means may be included in the kit which contain one or a number of DNA primers.
A kit used for amplifying DNA will comprise, for example, a first container means containing a substantially pure mutant DNA polymerase of the present invention and one or a number of additional container means that contain a single type of nucleotide or mixtures of nucleotides. Various primers may or may not be included in a kit for amplifying DNA.
When desired, the kit of the present invention also may include container means that contain detectably labeled nucleotides which may be used during the synthesis or sequencing of a DNA molecule. One of a number of labels may be used to detect such nucleotides. Illustrative labels include, but are not limited to, radioactive isotopes, fluorescent labels, chemiluminescent labels, bioluminescent labels and enzyme labels, or any other label for directly or indirectly labeling a nucleotide or nucleic acid.
In the following non-limiting examples, all percentages are by weight if for solids and by volume if for liquids, unless otherwise noted.
EXAMPLE 1
Mutagenesis of pCS6 and pCS5
This example describes the site directed mutagenesis of the 3′-5′ exonuclease domain of a thermostable and thermoactive DNA polymerase.
In a first round of mutagenesis, a site-directed mutagenesis approach was used to alter residues in a thermostable DNA polymerase that are either homologous residues known to be important for coordinating divalent metal cations in the active site of the proofreading domain of the Klenow fragment or located between the homologous residues. See Derbyshire et al., 1995, Methods in Enzymology 262:363–85, incorporated herein by reference in its entirety. Plasmid pCS6, encoding the mutant chimeric thermostable DNA polymerase CS6, was used. See FIG. 5. CS6 is a mutant form of the chimeric thermostable DNA polymerase CS5. See FIG. 4. The N-terminal portion of CS5 is the N-terminal 291 residues of the DNA polymerase from Thermus species Z05, encoding its 5′-3′ exonuclease activity. See U.S. Pat. No. 6,228,628. The remainder of CS5 is the C-terminal 602 residues from the Tma DNA polymerase, comprising its 3′-5′ exonuclease activities and its DNA polymerase activities. CS6 is identical to CS5 except that it has the mutations D323A and E325A (the numbering of residues from the wild-type Tma enzyme are used throughout unless otherwise specified) in the 3′-5′ exonuclease domain. As shown herein, these mutations cause CS6 to have no detectable 3′-5′ exonuclease activity.
The acidic residues at positions 323 and 325 and the leucine residue at position 324 were targeted. Each mutation (except the D323E mutation, as explained below) was made using the same basic method. Pairs of degenerate oligonucleotides were synthesized, as shown in Table 2. One degenerate oligonucleotide of each pair was an 11-mer, the other a 17-mer. Apart from the degenerate nucleotides, the 11 mer of each pair of oligonucleotides was perfectly complementary to an 11 nucleotide subsequence of the 17mer of the pair. For the D323E mutation, a non-degenerate pair of complementary oligonucleotides was designed, as shown in Table 2. The degenerate oligonucleotides of each pair were mixed under annealing conditions such that oligonucleotides that were perfectly complementary to one another, including at their degenerate positions, annealed to form an 1-mer dsDNA strand flanked on one end by a 3′-TA overhang and on the other end by a 5′-CTAG overhang, as shown in Table 2. These ends are compatible with ends generated by the restriction enzymes SgfI and SpeI, respectively. Thus, each annealing reaction produced a mixture of perfectly complementary and annealed oligonucleotide pairs as shown in Table 2.
Five μg pCS6 were then digested in a 25 μl reaction comprising 15 units of the restriction enzyme Spe I, 50 mM Tris.HCl, 10 mM Mg Cl2, 100 mM NaCl, pH 7.5 at 37° C. for 2.5 hr. The enzyme was inactivated by heating at 75° C. for 10 minutes, then cooled to room temperature. 15 units of the restriction enzyme SgfI were then added and the incubation continued for 2 hr at 37° C. The reaction was then stored overnight at 25° C. These steps linearized pCS6 and removed the codons encoding the two acidic residues at 323 and 325 (which are mutated in pCS6) and the leucine at position 324. It also left ends that were compatible with the ends of the annealed degenerate primer pairs.
In separate reactions, 0.5 pmol of each of the annealed oligonucleotide pair mixtures was mixed with 0.1 pmol of the linearized pCS6 and 0.5 units of T4 DNA ligase (Amersham Pharmacia Biotech AB, Uppsala Sweden), in the supplied buffer and incubated overnight at 4° C.
One μl (20 ng) of each ligation mix was then used to transform E. coli strain DG116 using a GENE PULSERTM electroporater (Bio-Rad Laboratories, Hercules Calif.) essentially according to the manufacturer's instructions. The electroporated cells were diluted with 1 ml SOC medium, then incubated for 1 hr at 30° C. with agitation. 50 or 100 μl aliquots of the resuspended cells were plated on LB plates with 100 μg/ml added ampicillin, to select for transformed cells, and incubated overnight.
For each transformation, five colonies were picked for PCR amplification and restriction analysis to determine which, if any, of the mutated pCS6 plasmids they contained. Each colony was suspended in a 50 μl master mix containing PCR buffer II (PE-Applied BioSystems, Redwood City, Calif.), 40 μM dNTP mix and 20 pmol each of the primers CS4 and CS 1A.










CS1A:
GTATGTAGTACGCTTCCTTTGGTTTGAA
(SEQ ID NO:35)



 


CS4:
TGGCTTTGGGAGAAGTACGGCCT
(SEQ ID NO:36)






Amplified DNA from each colony was digested with a diagnostic array of restriction enzymes, as shown in Table 3, in order to determine whether it had correctly incorporated a synthetic oligonucleotide and, if so, which mutant sequence it had incorporated. Clones that had the correct pattern of restriction sites were then sequenced in the region of the insert to ensure that each plasmid selected for further use incorporated only the desired mutations.








TABLE 2







Oligonucleotides Used In Round I











Degenerate Oligo Pairs





(degenerate positions in bold

Hybridized Mutagenic Oligo


lower-case letters)
Mutation
Pairs





CS6 5′ CGACGAa/tGAGA
L324 −> E
5′ CGACGAAGAGA



(SEQ ID NO:37)

(SEQ ID NO:39)


 


CS7 3′ TAGCTGCTt/aCTCTGATC

3′ TAGCTGCTTCTCTGATC


(SEQ ID NO:38)

(SEQ ID NO:40)


 



L324 −> D
5′ CGACGATGAGA




(SEQ ID NO:41)


 




3′ TAGCTGCTACTCTGATC




(SEQ ID NO:42)


 


C58 5′ TGATa/cAGGAAA
L324 −> K
5′ TGATAAGGAAA


(SEQ ID NO:43)

(SEQ ID NO:45)


 


CS9 3′ TAACTAt/gTCCTTTGATC

3′ TAACTATTCCTTTGATC


(SEQ ID NO:44)

(SEQ ID NO:46)


 



L324 −> Q
5′ TGATCAGGAAA




(SEQ ID NO:47)


 




3′ TAACTAGTCCTTTGATC




(SEQ ID NO:48)


 


CS10 5′ CGATa/cATGAAA
L324 −> N
5′ CGATAATGAAA


(SEQ ID NO:49)

(SEQ ID NO:51)


 


CS11 3′ TAGCTAt/gTACTTTGATC

3′ TAGCTATTACTTTGATC


(SEQ ID NO:50)

(SEQ ID NO:52)


 



L324 −> H
5′ CGATCATGAAA




(SEQ ID NO:53)


 




3′ TAGCTAGTACTTTGATC




(SEQ ID NO:54)


 


CS12 5′ TGAc/gCTGGATA
E325 −> D
5′ TGACCTGGATA


(SEQ ID NO:55)

(SEQ ID NO:57)


 


CS13 3′ TAACTg/cGACCTAAGATC

3′ TAACTGGACCTATGATC


(SEQ ID NO:56)

(SEQ ID NO:58)


 



D323 −> E; E325 −> D
5′ TGAGCTGGATA




(SEQ ID NO:59)


 




3′ TAACTCGACCTATGATC




(SEQ ID NO:60)


 


CS14 5′ TGAGCTTGAGA
D323 −> E
5′ TGAGCTTGAGA


(SEQ ID NO:61)

(SEQ ID NO:63)


 


CS15 3′ TAACTCGAACTCTGATC

3′ TAACTCGAACTCTGATC


(SEQ ID NO:62)

(SEQ ID NO:64)
















TABLE 3







Restriction Enzyme Sites in Tma L324 E/D/K/N/Q/H


and 323/325 Mutants














L324









Mutant



BclI
BclI

BspH


(D323 E325)
BsmAI
ClaI*
TaqI*
@A321
@D323
EarI
I





E
+
−
+
+
−
+
−


D
+
−
+
+
−
−
−


K
−
−
−
−
−
−
−


N
−
+
+
+
−
−
−


Q
−
−
−-
−
+
−
−


H
−
+
+
+
+
−
+


X323L324
BstNI
AluI
SmlI


X325


D-L-D
+
−
−
−
−
−
−


E-L-D
−
+
−
−
−
−
−


E-L-E
−
+
+
−
−
−
−


Parents
BsmAI
ClaI
SmlI
BclI
BclI I
EarI
BspH



BstNI
TaqI

@A321
@D323

I


CS5(D-L-E)
−
+
−
−
−
−
−


CS6(A-L-A)
−
−
−
+
−
−
−






also Sg/I+





*No in Dam+ E. coli; yes in PCR products and Dam− E. coli.






In a second round of mutagenesis, a PCR-based site-directed mutagenesis procedure was used to target residues known or suspected to contribute to the binding of substrate for the 3′-5′ exoncuclease activity. Primer pairs were designed for each mutagenesis, as shown in Table 4. Each primer pair allowed for the amplification of a portion of the polymerase encoding gene of pCS5. Only one primer pair was used for the L329A mutation. For this mutation, one primer of the pair introduced a mutation into the amplicon, and both primers contained restriction sites near their ends that allowed them to be subcloned into pCS5 that had been digested with the same enzymes, thus generating an expression plasmid encoding a Z05-Tma hybrid DNA polymerase with the L329A mutation. Two primer pairs were used to create each of the remaining mutations in the second round of mutagenesis. For each mutation, one primer in each pair contained the desired mutation but was otherwise complementary to pCS5. The other primer of each pair was perfectly complementary to a portion of pCS5. PCR using pCS5 as the template was carried out separately for each primer pair. These reactions produced amplicons that overlapped by approximately 35 nucleotides. The overlapping portion of the amplicons contained the desired mutation. Another PCR amplification was then done wherein the two partially overlapping amplicons were mixed and the flanking sequence primers from each pair (i.e., the respective amplification primers from each pair that did not comprise the mutant sequence) were used. This reaction resulted in one large amplicon that consisted of the two partially overlapping amplicons produced by the earlier PCRs. The flanking sequence primers were designed to be complementary to portions of the polymerase-encoding gene that had restriction sites useful for cloning. The amplicon and pCS5 were then digested with those restriction enzymes, mixed, and ligated, to produce an expression plasmid that contained the desired mutation. The ligation products were used to transform E. coli as described above. The success of the mutageneses was verified using the restriction sites listed in Table 5, as described above.








TABLE 4







Primers Used In Round II








Mutation














Forward Primer (changed





codon(s) in bold lower case)
Reverse Primer


L329A
CS20
CS36



GAAACTAGTTCCgctGATCCTTTCGA
GAAAAGAGAAGGACATGAGCTCTTGGTAA



(SEQ ID NO:65)
(SEQ ID NO:66)


 



Mutagenic Primers
Flanking Sequence Primers


Y464A
CS21 (forward overlap primer)
CS37



AGAAAAAGCtGCGAAtgcaTCCTGTGAAGA
TTTCCAGATCTGCCTCGTGCAGTTTTAA



TGCAGA (SEQ ID NO:67)
(SEQ ID NO:68)


 



CS22 (reverse overlap primer)
CS35



CTGCATCTTCACAGGAtgcaTTCGCaGCTT
ACCAAGAGCTCATGTCCTTCTCTTTTCCG



TTTCTA (SEQ ID NO:69)
(SEQ ID NO:70)


 


Q384A
CS23 (forward overlap primer)
CS36



CGTTGGTgccAATTTGAAATTCGATTACAA
GAAAAGAGAAGGACATGAGCTCTTGGTAA



(SEQ ID NO:71)
(SEQ ID NO:66)


 



CS24 (reverse overlap primer)
AW964



TGTAATCGAATTTCAAATTggcACCAACGA
GGAAACTAGTTCCCTCGATCC



(SEQ ID NO:72)
(SEQ ID NO:73)


 


N385A
CS25 (forward overlap primer)
CS36



CCTTGGTCAGgccTTGAAATTCGATTACAA
GAAAAGAGAAGGACATGAGCTCTTGGTAA



(SEQ ID NO:74)
(SEQ ID NO:66)


 



CS26 (reverse overlap primer)
AW964



TGTAATCGAATTTCAAggcCTGACCAACGA
GGAAACTAGTTCCCTCGATCC



(SEQ ID NO:75)
(SEQ ID NO:73)


 


Q384A
CS27 (forward overlapy primer)
CS36



CGTTGGTgccgcTcTGAAATTCGATTACAA
GAAAAGAGAAGGACATGAGCTCTTGGTAA


N385A
(SEQ ID NO:76)
(SEQ ID NO:66)


 



CS28 (reverse overlap primer)
AW964



TGTAATCGAATTTCAgAgcggcACCAACGA
GGAAACTAGTTCCCTCCATCC



(SEQ ID NO:77)
(SEQ ID NO:73)


 


D389E
CS29 (forward overlap primer)
CS36



TGAAATTCCAgTACAAGGTGTTGATGGTGA
GAAAAGAGAAGGACATCAGCTCTTGGTAA



A (SEQ ID NO:78)
(SEQ ID NO:66)


 



CS30 (reverse overlap primer)
AW964



CAACACCTTGTAcTCGAATTTCAAA
GGAAACTAGTTCCCTCGATCC



(SEQ ID NO:79)
(SEQ ID NO:73)
















TABLE 5







Round II Primers and their Restriction Sites










Cloning Restriction
Screening


Primer
Sites
Restriction Sites













CS20
(SEQ ID NO: 65)
SpeI
MspA1I


CS36
(SEQ ID NO: 66)
SacI


Cs21
(SEQ ID NO: 67)

BsmI, NsiI


CS37
(SEQ ID NO: 68)
Bg1II


CS35
(SEQ ID NO: 70)
SacI


CS22
(SEQ ID NO: 69)

BsmI, NsiI


CS23
(SEQ ID NO: 71)

BanI


CS24
(SEQ ID NO: 72)

BanI


AW964
(SEQ ID NO: 73)
SpeI


CS25
(SEQ TD NO: 74)

StuI


CS26
(SEQ ID NO: 75)

StuI


CS27
(SEQ ID NO: 76)

BanI, BsrBI


CS28
(SEQ ID NO: 77)

BanI, BsrBI


CS29
(SEQ ID NO: 78)

TatI, RsaI


CS30
(SEQ ID NO: 79)

TatI, RsaI









EXAMPLE 2
Production and Purification of Mutant Thermostable DNA Polymerases
The plasmids resulting from the ligation described above contain the polymerase gene under control of the λ PL promoter. Host cells (DG116, ATCC #53606) containing a cI857 (thermolabile) λ repressor were transformed with the plasmids. DG116 cells transformed with the plasmids containing the wild type or mutagenized polymerase gene were used to inoculate 10 ml standard flask media (SFM; comprising glucose, vitamin B1, casamino acids, and minimal medium) with ampicilin (100 μg/ml) and grown overnight at 30 C, 250 rpm. 5 ml of the overnight culture was used to inoculate 450 ml SFM+ampicillin and shaken at 30 C, 250 rpm until the culture reached an OD600 of 0.6–0.8. The culture was then transferred to 37 C and grown overnight at 250 rpm to achieve a temperature-induced expression of the polymerase. See, e.g., U.S. Pat. No.s 5,079,352, 5,420,029 and 5,618,711. The overnight growth was pelleted at 3,000×g for 15 min.
The pellets were resuspended in 30 ml lysis buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1 mM DTT, 1 mM Pefabloc, 1 μg/ml Leupeptin, 0.2 mM TLCK) and cells were lysed by french press at 16,000 psi. The lysed cell suspension was brought to 0.2M (NH4)2SO4 and heated at 75□C. for 15 min. to inactivate and denature E. coli host proteins. The heated extracts were chilled at 0□C. for 15 min., adjusted to 0.6% polyethyleneamine to precipitate host DNA, and centrifuged at 16,000×g for 30 min. The clarified extracts were loaded onto a 2 ml Phenyl-Sepharose column pre-equilibrated with 50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1 mM DTT, 0.2M (NH4)2SO4. The column was washed with 6 ml of equilibration buffer, followed by a 2 ml wash with 50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1 mM DTT, and a final wash with 2 ml 50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1 mM DTT, 20% ethylene glycol. The protein was eluted in 50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1 mM DTT, 2.5M urea. The eluate was adjusted to 100 mM KCl and loaded onto a 2 ml Heparin-Sepharose column pre-equilibrated with 25 mM Tris-HCl, pH 7.5, 1 mM EDTA, 1 mM DTT, 100 mM KCl. The column was washed with 6 ml equilibration buffer and eluted with 6 ml 25 mM Tris-HCl, pH 7.5, 1 mM EDTA, 1 mM DTT, 400 mM KCl. The final eluate was adjusted to 20 mM Tris-HCl, pH 8.0, 0.1 mM EDTA, 100 mM KCl, 1 mM DTT, 0.2% TWEEN 20, 50% v/v glycerol by dialysis and dilution and stored at −20° C.
EXAMPLE 3
Standard Assay for 3′-5′ Exonuclease Activity
The following example provides the Standard Assay for determining the 3′-5′ exonuclease activity of thermostable or thermoactive DNA polymerase and the definition of a unit of 3′-5′ exonuclease activity.
To compare the 3′-5′ exonuclease activities of the mutant derivatives of CS5, degradation of the carboxyfluorescein (FAM)-labeled single-stranded oligonucleotide substrate NJS40 was measured:

NJS40: FAM-GCGCTAGGGCGCTGGCAAGTGTAGCGGTCAC  (SEQ ID NO:80)

The Standard Assay (40 μl) contained 4 pmol (100 nM) FAM-labeled single-stranded NJS40 oligonucleotide in 50 mM Tricine, pH 8.3, 25 mM KOAc, 5% w/v DMSO, 0.5 mM Mn(OAc)2 and 5% (v/v) contributions from enzyme storage buffer (in reaction: 1 mM Tris, pH 8.0, 5 mM KCl, 0.005 mM EDTA, 0.025% TWEEN-20, 0.05 mM DTT, 2.5% glycerol). Reactions were initiated by addition of NJS40 and the Mn(OAc)2 and were incubated at 63° C. for 15 minutes. Reactions were quenched by addition of 40 μl 50 mM EDTA. The enzyme concentration and reaction times were adjusted to achieve linearity. The reaction is linear over a range of approximately 1–20% conversion of starting oligonucleotide to shorter product, corresponding to 0.5–10 milliUnits of enzyme; enzyme concentration was always less than substrate concentration. The quenched reaction solutions were diluted in formamide to 0.1 nM oligonucleotide and analyzed by capillary electrophoresis (ABI 3100, Applied Biosystems, Foster City Calif.). The peak height of the starting size and degraded oligonucleotides was determined using GENESCANTM Software (Applied Bioystems, Foster City, Calif.). The pmol of oligonucleotide converted to shorter oligonucleotide products is equal to

{1−(relative amount of Pn remaining after 15 min)}×(pmol of Pn at start of reaction)

where Pn is the substrate oligonucleotide (NJS40) of initial length n. The relative amount of Pn remaining after 15 minutes was determined by measuring the height of the peak corresponding to the starting size oligonucleotide and dividing it by the sum of all peak heights. This assay thus measures the rate of release of the 3′-terminal nucleotide from the oligonucleotide NJS40. One unit of 3′-5′ exonuclease activity catalyzes the conversion of 50 pmol of single-stranded NJS40 oligonucleotide to shorter length oligonucleotides in 15 minutes under the Standard Assay conditions.

The mutant polymerases made as described above were characterized using the Standard Assay. The results of these assays are presented in Table 6 under the columns labeled “ssDNA.”
The polymerase activity of each mutant enzyme was measured using the assay taught in U.S. Pat. No. 4,889,818. Briefly, an amount of enzyme stock in storage buffer (20 mM Tris, 100 mM KCl, 0.1 mM EDTA, 0.5% Tween-20, 1 mM DTT, 50% glycerol) was diluted in enzyme diluent (25 mM Tris-HCl, pH 8.0, 50 mM KCl, 1 mM β-mercaptoethanol, 0.5% Tween-20, 0.5% NP40, 100 μg/ml gelatin) to yield between about 0.02 and 0.1 units of polymerase activity per assay. Five microliters of the diluted enzyme were added to 45 μl of reaction buffer (25 mM TAPS, pH 9.4, 50 mM KCl, 2 mM MgCl2, 1 mM α-mercaptoethanol, 200 μM d(GTA)TP, 100 μM α-33P-dCTP, 30 μg activated salmon sperm DNA (“activated” DNA is a native preparation of DNA after partial hydrolysis with DNase I until 5% of the DNA was transferred to the acid-soluble fraction)). The reaction was incubated for 10 minutes at 74° C., then quenched with 10 μl of 60 mM EDTA. 50 μl from each quenched reaction was added to tubes containing 1 ml of 2 mM EDTA pH 8.0 with 50 μg/ml carrier DNA (salmon sperm DNA that has been sheared by passage through a 21 gauge needle). 1 ml of 20% trichloroacetic acid (TCA) and 2% sodium pyrophosphate was added and the tubes were gently agitated using a vortex agitator. The tubes were incubated on ice for ten to 20 minutes to allow for complete precipitation of the DNA. The precipitated DNA was collected on a GF/C filter on a vacuum filtration manifold. The filters were washed three times each in 5% TCA, 1% sodium pyrophosphate, then with 20% TCA, and finally with 95% ethanol. Two blank filters were treated similarly in order to determine the instrument's background. Radioactivity incorporated into the precipitated DNA was quantified using OMNIFLUOR® (Packard BioScience B.V., Groningen, The Netherlands) and a LS6000ICTM scintillation counter (Beckman Coulter, Fullerton Calif.). One unit of polymerase activity is defined as the amount of enzyme activity required to incorporate a total of 10 nmoles dNMP into TCA-precipitable DNA product in 30 minutes using the assay conditions provided above.
EXAMPLE 4
Variant Assays for Measuring 3′-5′ Exonuclease Activity
Two variations of the Standard Assay also were used to characterize the 3′-5′ exonuclease activities of the mutant thermostable or thermoactive DNA polymerases described above. These variant assays were identical to the Standard Assay except that each used a different substrate. In each variant assay, as in the Standard Assay, the rate of release of the 3′-terminal nucleotide from the oligonucleotide NJS40 was measured. However, in the variant assays, NJS40 was hybridized to a complementary oligonucleotide. The first variant assay used a double-stranded DNA substrate that was perfectly matched:










NJS40:
3′ FAM-GCGCTAGGGCGCTGGCAAGTGTAGCGGTCAC
(SEQ ID NO:80)



 


NJS43:
5′ pAGCGATCCCGCGACCGTTCACATCGCCAGTGCGACGCGCATTGGTGGTGTGGGCGGCGCC
(SEQ ID NO:81)






Results for the mutants described above using the first variant assay are provided in Table 6 under the columns marked “dsDNA.”
The second variant assay used a double-stranded DNA substrate that contained a mismatch:










NJS40:
3′ FAM-GCGCTAGGGCGCTGGCAAGTGTAGCGGTCAC
(SEQ ID NO:80)



 


NJS44:
5′ pAGCGATCCCGCGACCGTTCACATCGCCAGTTCGACGCGCATTGGTGGTGTGGGCGGCGCC
(SEQ ID NO:82)






Results for the mutants described above using the second variant assay are provided in Table 6 under the columns marked “dsDNA with mismatch.”







TABLE 6







Polymerase and 3′-5′ Exonuclease Activities of Round I and Round II Mutants










5′-3′
3′-5′ Exonuclease












Polymerase
ssDNA
dsDNA
dsDNA with mismatch





















Specific

Specific



Specific



Specific





activity,
Rate#
Activity,

Polymerase/
Rate
Activity,

Polymerase/
Rate,
Activity,

Polymerase/


Enzyme
U/pmol
pM/s
U/pmol
%
3′Exo Ratio
pM/s
U/pmol
%
3′Exo Ratio
pM/s
U/pmol
%
3′Exo Ratio























CS5
8.6
136.1
9.9
100.0
0.9
154.7
11.3
100.0
0.8
228.1
16.6
100.0
0.5


Y464A
14.7
0.2
0.0
0.1
1008.0
0.2
0.0
0.1
1008.0
0.2
0.01
0.1
1008.0


D389E
13.0
22
1.6
16.2
8.1
25.5
1.9
16.5
7.0
66.8
4.9
29.3
2.7


L329A
6.4
14.5
1.1
10.7
6.1
12.1
0.9
7.8
7.3
44.1
3.2
19.3
2.0


Q384A—
7.7
5.1
0.4
3.7
20.9
6.3
0.5
4.1
16.9
24.8
1.8
10.9
4.3


N385A


Q384A
13.0
31.1
2.3
22.9
5.8
36.7
2.7
23.7
4.9
104.4
7.6
45.8
1.7


N385A
11.8
48.4
3.5
35.6
3.4
59.7
4.3
38.6
2.7
145.6
10.6
63.8
1.1


L324Q
8.2
37
2.7
27.2
3.0
49.8
3.6
32.2
2.3
94.8
6.9
41.6
1.2


L324H
10.3
46.3
3.4
34.0
3.1
54.3
3.9
35.1
2.6
99.6
7.2
43.7
1.4


L324E
7.1
65.6
4.8
48.2
1.5
56.8
4.1
36.7
1.7
102.4
7.4
44.9
1.0


L324D
8.6
83.4
6.1
61.3
1.4
61
4.4
39.4
1.9
130.6
9.5
57.3
0.9


L324K
8.0
46.9
3.4
34.5
2.4
69.4
5.0
44.9
1.6
127.1
9.2
55.7
0.9


L324N
8.3
55.1
4.0
40.5
2.1
72.7
5.3
47.0
1.6
152.4
11.1
66.8
0.8





#Rate is for 0.25 nM enzyme






EXAMPLE 5
Comparison of the 3′-5′ Exonuclease Activities of Mutant Thermostable or Thermoactive DNA Polymerases and Mutant E. coli DNA Polymerases
This example demonstrates that the 3′-5′ exonuclease activity of a mutant thermostable or thermoactive DNA polymerase cannot be predicted from the enzymatic properties of analogous Eco DNA Pol I mutant polymerases. Table 7 presents a comparison of the 3′-5′ exonuclease activities of the Round II polymerase mutants and of analogous E. coli Pol I mutants.







TABLE 7







Comparison of E. coli* Pol I Mutants with CS5 RoundII Mutants


Residual proofreading activity †


(% wild-type)













Double-
Single-

Double-
Single-


Mutation in
stranded
stranded
Mutation in
stranded
stranded


E. coli
DNA
DNA
CS5
DNA
DNA















Y497A
5.6%
2.9%
Y464A
0.1%
0.1%


L361A
4.0
37
L329A
7.8
10.7


D424E
4.0
8.3
D389E
16.5
16.2


Q419A
23
20
Q384A
23.7
22.9





*based on Derbyshire et al., 1995, Methods in Enzymology 262:363–85


† from Table 6






The results presented in Table 7 show that analogous mutations in the 3′-5′ exonuclease domains of the Eco and CS5 DNA polymerases frequently have different effects on the proofreading activity of the enzymes, relative to the activity of the corresponding wild-type enzyme's activity. Comparison of the Eco Q419A mutant with the CS5 Q384A mutant shows that analogous mutations in these two enzymes can affect their 3′-5′ exonuclease activities similarly. However, for some analogous mutants, significant differences in enzymatic activity are observed. In some mutant pairs this difference is simply quantitative. For example, the Eco Y497A mutant has substantially more residual enzymatic activity than the CS5 Y464A mutation on both ssDNA and dsDNA substrates. Other analogous mutants additionally show qualitative differences. For example, the Eco L361A and D424E mutants both have much greater activity against a ssDNA substrate than against a dsDNA substrate. However, the analogous CS5 mutants (L329A and D389E, respectively) have similar residual enzymatic activities against both ssDNA and dsDNA substrates.
EXAMPLE 6
Use of Mutant Thermostable DNA Polymerases with Attenuated 3′-5′ Exonuclease Activity for PCR
The mutant enzymes Y464A, D389E, L329A, Q484A/N385A, Q384A, N385A and L324Q were tested for Reverse Transcriptase/PCR activity using an HIV drug resistance assay. A mixture of 120 units of CS6 (having no detectable 3′-5′ exonuclease activity) and 5 units CS5 (having wild-type 3′-5′ exonuclease activity) was used as a control. The 1.7 kb HIVr assay conditions were used (50 mM Tricine pH 8.3, 45 mM KOAc pH 7.5, 0.9 mM Mn(OAc)2, 5% DMSO, 0.2 mM d(AGC)TP, 0.3 mM dUTP, 0.03 mM dTTP, 0.2×SYBR Green I, G46E CS5/CS6 enzyme blend (5/125 units) or 60 or 30 units of polymerase activity of each mutant enzyme, 1 unit UNG, and 0.4 M each (−1) 2′-amino modified primers (RN326 and RN328) and kinetic thermocycling, see Myers et al., 2000, Antiviral Therapy 5: Abstract 49) to specifically and sensitively amplify the protease gene and the first 400 codons of the reverse transcriptase gene of HIV.











RN326:
GAGGGGTATTGACAAACTCCCACTCAGGAATCXA
(X = 2′amino-dC)
(SEQ ID NO:83)



 


RN328:
GGGAATTTTCTTCAGAGCAGACCAGAGCCAAXA
(X = 2′amino-dC)
(SEQ ID NO:84)






A GENEAMPTM 5700 SDS thermocycler (PE Biosystems, Foster City, Calif.) was used with the following thermocycling protocol: 50° C. for 2 min, 60° C. for 60 min, and 95° C. 1 min, followed by 4 cycles of 95° C., 20 sec., 58° C. 15 sec., 65° C. 1 min 45 sec, followed by 36 cycles of 90° C. 20 sec., 58° C., 15 sec., 65° C. 1 min. 45 sec., followed by 65° C. 10 min. hold. The growth curves of the PCR amplifications are shown in FIG. 9. Amplifications using the same protocol with varying amounts of enzyme also were run and analyzed using gel electrophoresis. 5 μl from each 100 μl reaction was loaded onto a 1% agarose gel following PCR which was run essentially as described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, 1989, second edition. The gels were stained using a 1 μg/ml solution of ethidium bromide. The resulting gels are shown in FIG. 10. In FIG. 10, lanes 20, 40 and 48=Bst II digested lambda DNA (New England Biolabs, Beverly, Mass.) as a molecular weight marker; lanes 36–38 and 58–60=negative control (5 U CS5, 125 U CS6, no template); lanes 33–35 and 55–57=positive control (5 U CS5, 125 U CS6); lanes 1–3=60 U Y464A CS5; lanes 4–6=30 U Y464A CS5; lanes 7–9=60 U D389E CS5; lanes 10–12=30 U D389E CS5; lanes 13–15=60 U L329A CS5; lanes 16–18=30 U L329A CS5; lanes 21–23=60 U Q384A-N385A CS5; lanes 24–26=30 U Q384A-N385A CS5; lanes 27–29=60 U Q384A CS5; lanes 30–32=30 U Q384A CS5; lanes 41–43=60 U N385A CS5; lanes 44–46=30 U N385A CS5; lanes=49–51=60 U L324Q CS5; lanes 52–54=30 U L329Q CS5 (wherein all units refer to DNA polymerase activity).
Mutant enzymes were judged by their CT values (FIG. 9), and by their yield of specific and non-specific amplification products, detected using gel analysis of amplification products (FIG. 10). These results demonstrate that mutants with proofreading activities greater than 3% but less than 20% of wild typelevels (as measured using the Standard Assay described in Example 3, above) work well for reverse transcription PCR amplification of the 1.7 kb HIV RNA template. These mutants also had specific activities between 0.4 and 1.6 U/pmol, and a ratio of polymerase activity to 3′-5′ exonuclease activity of greater than 6.0 but less than 25.0 U pol/U exo, the enzymatic activities being measured as described in Example 3, and yielded PCR results comparable to those obtained with the blend of CS5 and CS6. Q384A CS5 and N385A CS5 also work well as judged by gel analysis of their amplification products, although not as well as judged by their CT values.
EXAMPLE 7
Identification of Target Residues for Site-Specific Mutagenesis to Attenuate the 3′-5′ Exonuclease Activity of Thermostable or Thermoactive Family A DNA Polymerases
This example provides a method for identifying residues in thermostable or thermoactive family A DNA polymerases that can be mutated and tested to identify mutants with attenuated 3′-5′ exonuclease activity.
The X-ray structure of E. coli Pol I complexed with DNA in the 3′-5′ exonuclease site (see Brautigan et al., 1998, J. Mol. Biol. 277:363–77) was analysed using the “3D>sequence contacts” feature of the XSAE program (see Higgins et al., 1992, Cabios 8, 189–91) to identify all residues of the selected protein (Pol I; 1kfs.pdb, chain A) that are within 5 A of the DNA substrate (1kfs.pdb, chain B). Using this method, the residues in Table 8 were identified in E. coli Pol I. Analogous residues can be identified in a thermostable or thermoactive family A DNA polymerase by inspection of a sequence alignment of the polymerases (as shown, for example, in FIG. 8). These candidate residues then can be mutated and tested for attenuated 3′-5′ exonuclease activity using, for example, the Standard Assay described in Example 3, above.







TABLE 8





Candidate Residues in E. coli Pol I


















D355
T356



E357
T358



S360
L361



Q419
N420



K422
Y423



M443
R455



H456
D457



M458
D459



F473
E474



Q483
F486



Y497
D501



E541
S658



Y659
H660










EXAMPLE 8
Identification of Mutants of Family B DNA Polymerase with Attenuated 3′-5′ Exonuclease Activity
As disclosed herein, one of skill in the art guided by the instant disclosure can readily make a mutant of a family A DNA polymerase that has an attenuated 3′-5′ exonuclease activity by, for example, making mutations in its 3′-5′ exonuclease domain that correspond to the mutations of the 3′-5′ exonuclease domain of Tma DNA polymerase described herein. Such a sequence-based approach to designing mutants of family B DNA polymerases with attenuated proofreading activity is of only limited utility because the only region of significant sequence similarity between the Tma DNA polymerase and family B DNA polymerase 3′-5′ exonuclease domains is the “DXE” metal binding motif. However, X-ray crystallographic studies have shown that the 3′-5′ exonuclease domains of family A and family B polymerases have similar three-dimensional stuctures. See Zhao et al., 1999, Structure Fold Des. 7:1189–99, Karam et al, 2000, Prog Nucleic Acid Res Mol Biol. 64:65–96, Hopfner et al., 1999, Proc Natl Acad Sci USA. 96:3600–5, Wang et al., 1997, Cell 89:1087–99. A structure-based method therefore was developed to identify residues that can be mutated to produce family B DNA polymerases with attenuated proofreading activity.
FIG. 11 presents an alignment of the E. coli Pol II DNA polymerase, a family B polymerase, with the sequences of a number of other family B DNA polymerases. Rather than simply identify those residues that are conserved between all or almost all of these proteins on the assumption that their conservation indicates that they are important for proofreading function, the three dimensional-structure of the 3′-5′ exonuclease domain of the family B DNA polymerase isolated from the bacteriophage RB69 (Shamoo et al., 1999, Cell 99:155–66; structure available from the Protein Data Bank (Berman et al., 2000, Nucleic Acids Res. 28:235–42; www.pdb.org/) under PDB ID No. 1CLQ) was examined and compared to the proofreading domain of Tma. All of the residues in each of these proteins predicted to contact the 3′ terminal nucleotides of a single-stranded DNA sequence bound to the proofreading domain were identified. This information and the sequence alignment in FIG. 11 were used to identify the analogous residues in other family B DNA polymerases, as shown in Table 9, below. These data indicate that mutations at these particular positions will result in DNA polymerase molecules with attenuated 3′-5′ exonuclease activity.











TABLE 9





Residue
Residue
Residue
Residue



in RB69
in Tgo
in PocI
in KODI
Proposed function







F123
Y146
Y191
Y146
Ring stacking with






base of P(n-1)


F221
F214
F253
F214
Binding to sugar of






P(n-1)


S287
T272
M309
T272
H-bonding to






phosphodiester






between P(n-1) and P(n-2)









The foregoing examples, both prophetic and actual, are offered by way of illustration only and are not intended to limit the scope of the claimed invention in any respect.
All references cited herein are incorporated by reference in their entireties.

## Claims

1. An isolated thermostable or thermoactive DNA polymerase comprising a 3′-5′ exonuclease domain and exhibiting an attenuated 3′-5′ exonuclease activity of about 6.5 or less, but greater than 0, U/pmol, wherein one unit (U) of 3′-5′ exonuclease activity catalyzes the conversion of 50 pmol of a labeled single-stranded oligonucleotide of SEQ ID NO:80 to shorter length oligonucleotides in 15 minutes at 63° C., the enzymatic activity being measured in a reaction mixture containing 4 pmol (100 nM) of the oligonucleotide of SEQ ID NO: 80 in 50 mM Tricine, pH 8.3, 25 mM KOAc, 5% w/v DMSO, 0.5 mM Mn(OAc)2 and the polymerase, and incubated at 63° C. for 15 minutes, wherein degradation of the oligonucleotide of SEQ ID NO: 80 is measured, wherein said 3′-5′ exonuclease domain comprises a sequence motif selected from the following sequence motifs:
(a) A sequence motif having the formula DX1EX2X3SX4, wherein
D is an aspartate residue,
X1 is any amino acid residue
E is a glutamate residue,
X2 is a threonine,
X3 is any amino acid residue,
S is a serine residue, and
X4 is a leucine or an alanine, or

(b) A sequence motif having the formula X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO:1), wherein
X5 is a glutamine or an alanine,
X6 is an asparagine or an alanine,
X7 is a cysteine or a leucine residue,
X8 is a lysine,
X9 is a phenylalanine or a tyrosine residue,
X10 is an aspartate or a glutamate,
X11 is any amino acid residue,
X12 is any amino acid residue,
X13 is an isoleucine or valine residue, and
X14 is a leucine or phenylalanine residue.

2. An isolated thermostable or thermoactive DNA polymerase comprising a 3′-5′ exonuclease domain and having a 5′-3′ polymerase activity and an attenuated 3′-5′ exonuclease activity wherein the ratio of said 5′-3′ polymerase activity in U/pmol to said 3′-5′ exonuclease activity in U/pmol is between about 100 and 1, wherein one unit (U) of 3′-5′ exonuclease activity catalyzes the conversion of 50 pmol of a labeled single-stranded oligonucleotide of SEQ ID NO:80 to shorter length oligonucleotides in 15 minutes at 63° C. wherein the 3′-5′ exonuclease activity is measured in a reaction mixture containing 4 pmol (100 nM) of the oligonucleotide of SEQ ID NO: 80 in 50 mM Tricine, pH 8.3, 25 mM KOAc, 5% w/v DMSO, 0.5 mM Mn(OAc)2 and the polymerase, and incubated at 63° C. for 15 minutes, wherein degradation of the oligonucleotide of SEQ ID NO: 80 is measured, and one unit of 5′-3′ polymerase activity is the amount of enzyme activity required to incorporate 10 nmoles of dNMP into TCA-precipitable DNA product in 30 minutes at 74° C. wherein the 5′-3′ polymerase activity is measured in a reaction mixture containing 25 mM TAPS, pH 9.4, 50 mM KCl, 2 mM MgCl2, 1 mM β-mercaptoethanol, 200 μM d(GTA)TP, 100 μM α-33P-dCTP, 30 μg activated salmon sperm DNA and the polymerase, and incubated at 74° C. for 10 minutes wherein the amount of TCA precipitable DNA is measured, set forth in Example 3 for 5′-3′ polymerase activity, and said 3′-5′ exonuclease domain comprises a sequence motif selected from the following sequence motifs:
(a) A sequence motif having the formula DX1EX2X3SX4, wherein
D is an aspartate residue,
X1 is any amino acid residue,
E is a glutamate residue,
X2 is a threonine,
X3 is any amino acid residue,
S is a serine residue, and
X4 is a leucine or an alanine, or

(b) A sequence motif having the formula X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO:1), wherein
X5 is a glutamine or an alanine,
X6 is an asparagine or an alanine,
X7 is a cysteine or a leucine residue,
X8 is a lysine,
X9 is a phenylalanine or a tyrosine residue,
X10 is an aspartate or a glutamate,
X11 is any amino acid residue,
X12 is any amino acid residue,
X13 is an isoleucine or valine residue, and
X14 is a leucine or phenylalanine residue.

3. An isolated modified thermostable or thermoactive DNA polymerase wherein said modified polymerase comprises a 3′-5′ exonuclease domain, has about 0.1 to 65% of a 3′-5′ exonuclease activity of the DNA polymerase before modification, wherein one unit (U) of 3′-5′ exonuclease activity catalyzes the conversion of 50 pmol of a labeled single-stranded oligonucleotide of SEQ ID NO:80 to shorter length oligonucleotides in 15 minutes at 63° C., the enzymatic activity being measured in a reaction mixture containing 4 pmol (100 nM) of the oligonucleotide of SEQ ID NO: 80 in 50 mM Tricine, pH 8.3, 25 mM KOAc, 5% w/v DMSO, 0.5 mM Mn(OAc)2 and polymerase, and incubated at 63° C. for 15 minutes, wherein degradation of the oligonucleotide of SEQ ID NO. 80 is measured, and said 3′-5′ exonuclease domain comprises a sequence motif selected from the following sequence motifs:
(a) A sequence motif having the formula DX1EX2X3SX4, wherein
D is an aspartate residue,
X1 is any amino acid residue
E is a glutamate residue,
X2 is a threonine,
X3 is any amino acid residue,
S is a serine residue, and
X4 is a leucine or an alanine, or

(b) A sequence motif having the formula X5X6X7X8X9X10X11X12X13X14 (SEQ ID NO:1), wherein
X5 is a glutamine or an alanine,
X6 is an asparagine or an alanine,
X7 is a cysteine or a leucine residue,
X8 is a lysine,
X9 is a phenylalanine or a tyrosine residue,
X10is an aspartate or a glutamate,
X11 is any amino acid residue,
X12 is any amino acid residue,
X13 is an isoleucine or valine residue, and
X14 is a leucine or phenylalanine residue.