MLH1 mutations differentially affect meiotic functions in Saccharomyces cerevisiae. (2003)
Hoffmann, E.R., Shcherbakova, P.V., Kunkel, T.A., Borts, R.H.
Kunkel, T A, Patel, S S, Johnson, K A
We have examined the effect of thioredoxin, an accessory protein that confers high processivity to bacteriophage T7 DNA polymerase, on the fidelity of DNA synthesis. In the presence of thioredoxin,...
Thomas, D C, Veaute, X, Kunkel, T A, Fuchs, R P
We have analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of bidirectional replication of double-stranded DNA in a human cell...
We have examined the efficiency and fidelity of simian virus 40-origin-dependent replication of UV-irradiated double-stranded DNA in extracts of human cells. Using as a mutational target the...
Boyer, J C, Bebenek, K, Kunkel, T A
Sequence variation in the type 1 human immunodeficiency virus (HIV-1) results, in part, from inaccurate replication by reverse transcriptase. Although this enzyme is error-prone during synthesis in...
Exonucleolytic proofreading of leading and lagging strand DNA replication errors.
Roberts, J D, Thomas, D C, Kunkel, T A
We have asked whether exonucleolytic proofreading occurs during simian virus 40 origin-dependent, bidirectional DNA replication in extracts of human HeLa cells. In addition, we have compared the...
Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity.
Morrison, A, Bell, J B, Kunkel, T A, Sugino, A
We have identified an amino-proximal sequence motif, Phe-Asp-Ile-Glu-Thr, in Saccharomyces cerevisiae DNA polymerase II that is almost identical to a sequence comprising part of the 3'----5'...
Frameshift errors initiated by nucleotide misincorporation.
Studies presented here on the fidelity of DNA synthesis in vitro support the hypothesis that a classical base-substitution intermediate (i.e., a misincorporated nucleotide) can yield a frameshift...
Functional analysis of human MutSalpha and MutSbeta complexes in yeast.
Clark, A B, Cook, M E, Tran, H T, Gordenin, D A, Resnick, M A, Kunkel, T A
Mismatch repair (MMR) is initiated when a heterodimer of hMSH2*hMSH6 or hMSH2*hMSH3 binds to mismatches. Here we perform functional analyses of these human protein complexes in yeast. We use a...
Deletion errors generated during replication of CAG repeats.
Triplet repeat sequence instability is associated with hereditary neurological diseases and with certain types of cancer. Here we study one form of this instability, deletion of triplet repeats...
Thomas, D C, Svoboda, D L, Vos, J M, Kunkel, T A
Psoralens are mutagenic compounds of vegetable origin that are used as photosensitizing agents in the treatment of various skin diseases, blood cell cancer, and autoimmune disorders. To study the...
Fidelity of a human cell DNA replication complex.
We have measured the fidelity of bidirectional, semiconservative DNA synthesis by a human DNA replication complex in vitro. Replication was performed by extracts of HeLa cells in the presence of...
Ebright, R H, Kolb, A, Buc, H, Kunkel, T A, Krakow, J S, Beckwith, J
It has been proposed that Glu-181 of the catabolite gene activator protein (CAP) makes direct contact with certain base pairs of the specific DNA site. We have purified wild-type CAP and two...
Exonucleolytic proofreading by calf thymus DNA polymerase delta.
Kunkel, T A, Sabatino, R D, Bambara, R A
The fidelity of DNA synthesis by calf thymus DNA polymerase delta (pol delta) in vitro has been determined using an M13lacZ alpha nonsense codon reversion assay. Pol delta is highly accurate,...
Minnick, D T, Pavlov, Y I, Kunkel, T A
A product of oxidative metabolism, 8-oxodeoxyguanosine triphosphate (8-O-dGTP), readily pairs with adenine during DNA replication, ultimately causing A.T-->C.G transversions. This study utilized...
The accuracy of DNA synthesis catalyzed by the Thermus aquaticus DNA polymerase and the 3'-->5' exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I varies as a function of...
Rearrangements of DNA mediated by terminal transferase.
Kunkel, T A, Gopinathan, K P, Dube, D K, Snow, E T, Loeb, L A
To assess the involvement of terminal transferase in generating immunoglobulin diversity, the mutagenic potential of this enzyme has been measured. The frequency of single base substitutions during...
Ebright, R H, Gunasekera, A, Zhang, X P, Kunkel, T A, Krakow, J S
Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977,...
High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase.
We demonstrate that despite lacking a 3'----5' proofreading exonuclease, the Thermus aquaticus (Taq) DNA polymerase can catalyze highly accurate DNA synthesis in vitro. Under defined reaction...
Mosbaugh, D W, Kunkel, T A, Stalker, D M, Tcheng, J E, Meyer, R R
Unlike other beta-class eukaryotic DNA polymerases, the enzyme purified from the Novikoff hepatoma is inhibited by both sulfhydryl blocking agents N-ethylmaleimide (NEM) and p-hydroxymercuribenzoate...
Mutational specificity of depurination.
The mutagenic consequences of damage to DNA produced by low pH and high temperature have been determined in a forward mutational system capable of detecting all classes of mutagenic events. When...
Deoxynucleoside [1-thio]triphosphates prevent proofreading during in vitro DNA synthesis.
Kunkel, T A, Eckstein, F, Mildvan, A S, Koplitz, R M, Loeb, L A
The contribution of proofreading to the fidelity of catalysis by DNA polymerases has been determined with deoxyribonucleoside [1-thio]triphosphate substrates. These analogues, which contain a sulfur...
Kunkel, T A, Hamatake, R K, Motto-Fox, J, Fitzgerald, M P, Sugino, A
We have determined the fidelity of DNA synthesis by DNA polymerase I (yPol I) from Saccharomyces cerevisiae. To determine whether subunits other than the polymerase catalytic subunit influence...
Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro.
Roberts, J D, Preston, B D, Johnston, L A, Soni, A, Loeb, L A, Kunkel, T A
We determined the fidelity of avian myeloblastosis virus and Moloney murine leukemia virus reverse transcriptases (RTs) during DNA synthesis in vitro using the M13mp2 lacZ alpha gene as a mutational...
Infidelity of DNA synthesis associated with bypass of apurinic sites.
Schaaper, R M, Kunkel, T A, Loeb, L A
The mutagenic potential of apurinic sites in vivo has been studied by transfection of depurinated phi X174 DNA containing amber mutations into SOS-induced Escherichia coli spheroplasts. Mutagenicity...
Rapid and efficient site-specific mutagenesis without phenotypic selection.
Several single-base substitution mutations have been introduced into the lacZ alpha gene in cloning vector M13mp2, at 40-60% efficiency, in a rapid procedure requiring only transfection of the...
Single-strand binding protein enhances fidelity of DNA synthesis in vitro.
Kunkel, T A, Meyer, R R, Loeb, L A
The effect of Escherichia coli single-strand binding protein on the accuracy of in vitro DNA synthesis has been determined by using two independent methods. By using the synthetic polynucleotide...
Functional overlap in mismatch repair by human MSH3 and MSH6.
Umar, A, Risinger, J I, Glaab, W E, Tindall, K R, Barrett, J C, Kunkel, T A
Three human genes, hMSH2, hMSH3, and hMSH6, are homologues of the bacterial MutS gene whose products bind DNA mismatches to initiate strand-specific repair of DNA replication errors. Several studies...
Pavlov, Y I, Shcherbakova, P V, Kunkel, T A
Several amino acids in the active site of family A DNA polymerases contribute to accurate DNA synthesis. For two of these residues, family B DNA polymerases have conserved tyrosine residues in...
Metal-induced infidelity of DNA synthesis.
Zakour, R A, Kunkel, T A, Loeb, L A
In this paper, we consider the effects of metal ions on the accuracy of catalysis by DNA polymerases. Certain activating and nonactivating metal ions have been shown to diminish the fidelity of DNA...
Kunkel, T A, Patel, S S, Johnson, K A
We have examined the effect of thioredoxin, an accessory protein that confers high processivity to bacteriophage T7 DNA polymerase, on the fidelity of DNA synthesis. In the presence of thioredoxin,...
Thomas, D C, Veaute, X, Kunkel, T A, Fuchs, R P
We have analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of bidirectional replication of double-stranded DNA in a human cell...
We have examined the efficiency and fidelity of simian virus 40-origin-dependent replication of UV-irradiated double-stranded DNA in extracts of human cells. Using as a mutational target the...
Boyer, J C, Bebenek, K, Kunkel, T A
Sequence variation in the type 1 human immunodeficiency virus (HIV-1) results, in part, from inaccurate replication by reverse transcriptase. Although this enzyme is error-prone during synthesis in...
Exonucleolytic proofreading of leading and lagging strand DNA replication errors.
Roberts, J D, Thomas, D C, Kunkel, T A
We have asked whether exonucleolytic proofreading occurs during simian virus 40 origin-dependent, bidirectional DNA replication in extracts of human HeLa cells. In addition, we have compared the...
Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity.
Morrison, A, Bell, J B, Kunkel, T A, Sugino, A
We have identified an amino-proximal sequence motif, Phe-Asp-Ile-Glu-Thr, in Saccharomyces cerevisiae DNA polymerase II that is almost identical to a sequence comprising part of the 3'----5'...
Frameshift errors initiated by nucleotide misincorporation.
Studies presented here on the fidelity of DNA synthesis in vitro support the hypothesis that a classical base-substitution intermediate (i.e., a misincorporated nucleotide) can yield a frameshift...
Functional analysis of human MutSalpha and MutSbeta complexes in yeast.
Clark, A B, Cook, M E, Tran, H T, Gordenin, D A, Resnick, M A, Kunkel, T A
Mismatch repair (MMR) is initiated when a heterodimer of hMSH2*hMSH6 or hMSH2*hMSH3 binds to mismatches. Here we perform functional analyses of these human protein complexes in yeast. We use a...
Deletion errors generated during replication of CAG repeats.
Triplet repeat sequence instability is associated with hereditary neurological diseases and with certain types of cancer. Here we study one form of this instability, deletion of triplet repeats...
Thomas, D C, Svoboda, D L, Vos, J M, Kunkel, T A
Psoralens are mutagenic compounds of vegetable origin that are used as photosensitizing agents in the treatment of various skin diseases, blood cell cancer, and autoimmune disorders. To study the...
Fidelity of a human cell DNA replication complex.
We have measured the fidelity of bidirectional, semiconservative DNA synthesis by a human DNA replication complex in vitro. Replication was performed by extracts of HeLa cells in the presence of...
Ebright, R H, Kolb, A, Buc, H, Kunkel, T A, Krakow, J S, Beckwith, J
It has been proposed that Glu-181 of the catabolite gene activator protein (CAP) makes direct contact with certain base pairs of the specific DNA site. We have purified wild-type CAP and two...
Exonucleolytic proofreading by calf thymus DNA polymerase delta.
Kunkel, T A, Sabatino, R D, Bambara, R A
The fidelity of DNA synthesis by calf thymus DNA polymerase delta (pol delta) in vitro has been determined using an M13lacZ alpha nonsense codon reversion assay. Pol delta is highly accurate,...
Minnick, D T, Pavlov, Y I, Kunkel, T A
A product of oxidative metabolism, 8-oxodeoxyguanosine triphosphate (8-O-dGTP), readily pairs with adenine during DNA replication, ultimately causing A.T-->C.G transversions. This study utilized...
The accuracy of DNA synthesis catalyzed by the Thermus aquaticus DNA polymerase and the 3'-->5' exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I varies as a function of...
Rearrangements of DNA mediated by terminal transferase.
Kunkel, T A, Gopinathan, K P, Dube, D K, Snow, E T, Loeb, L A
To assess the involvement of terminal transferase in generating immunoglobulin diversity, the mutagenic potential of this enzyme has been measured. The frequency of single base substitutions during...
Ebright, R H, Gunasekera, A, Zhang, X P, Kunkel, T A, Krakow, J S
Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977,...
High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase.
We demonstrate that despite lacking a 3'----5' proofreading exonuclease, the Thermus aquaticus (Taq) DNA polymerase can catalyze highly accurate DNA synthesis in vitro. Under defined reaction...
Mosbaugh, D W, Kunkel, T A, Stalker, D M, Tcheng, J E, Meyer, R R
Unlike other beta-class eukaryotic DNA polymerases, the enzyme purified from the Novikoff hepatoma is inhibited by both sulfhydryl blocking agents N-ethylmaleimide (NEM) and p-hydroxymercuribenzoate...
Mutational specificity of depurination.
The mutagenic consequences of damage to DNA produced by low pH and high temperature have been determined in a forward mutational system capable of detecting all classes of mutagenic events. When...
Deoxynucleoside [1-thio]triphosphates prevent proofreading during in vitro DNA synthesis.
Kunkel, T A, Eckstein, F, Mildvan, A S, Koplitz, R M, Loeb, L A
The contribution of proofreading to the fidelity of catalysis by DNA polymerases has been determined with deoxyribonucleoside [1-thio]triphosphate substrates. These analogues, which contain a sulfur...
Kunkel, T A, Hamatake, R K, Motto-Fox, J, Fitzgerald, M P, Sugino, A
We have determined the fidelity of DNA synthesis by DNA polymerase I (yPol I) from Saccharomyces cerevisiae. To determine whether subunits other than the polymerase catalytic subunit influence...
Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro.
Roberts, J D, Preston, B D, Johnston, L A, Soni, A, Loeb, L A, Kunkel, T A
We determined the fidelity of avian myeloblastosis virus and Moloney murine leukemia virus reverse transcriptases (RTs) during DNA synthesis in vitro using the M13mp2 lacZ alpha gene as a mutational...
Infidelity of DNA synthesis associated with bypass of apurinic sites.
Schaaper, R M, Kunkel, T A, Loeb, L A
The mutagenic potential of apurinic sites in vivo has been studied by transfection of depurinated phi X174 DNA containing amber mutations into SOS-induced Escherichia coli spheroplasts. Mutagenicity...
Rapid and efficient site-specific mutagenesis without phenotypic selection.
Several single-base substitution mutations have been introduced into the lacZ alpha gene in cloning vector M13mp2, at 40-60% efficiency, in a rapid procedure requiring only transfection of the...
Single-strand binding protein enhances fidelity of DNA synthesis in vitro.
Kunkel, T A, Meyer, R R, Loeb, L A
The effect of Escherichia coli single-strand binding protein on the accuracy of in vitro DNA synthesis has been determined by using two independent methods. By using the synthetic polynucleotide...
Functional overlap in mismatch repair by human MSH3 and MSH6.
Umar, A, Risinger, J I, Glaab, W E, Tindall, K R, Barrett, J C, Kunkel, T A
Three human genes, hMSH2, hMSH3, and hMSH6, are homologues of the bacterial MutS gene whose products bind DNA mismatches to initiate strand-specific repair of DNA replication errors. Several studies...
Pavlov, Y I, Shcherbakova, P V, Kunkel, T A
Several amino acids in the active site of family A DNA polymerases contribute to accurate DNA synthesis. For two of these residues, family B DNA polymerases have conserved tyrosine residues in...
Metal-induced infidelity of DNA synthesis.
Zakour, R A, Kunkel, T A, Loeb, L A
In this paper, we consider the effects of metal ions on the accuracy of catalysis by DNA polymerases. Certain activating and nonactivating metal ions have been shown to diminish the fidelity of DNA...