Fidelity of DNA synthesis catalyzed by human DNA polymerase α and HIV-1 reverse transcriptase: Effect of reaction pH

Kristin Eckert, Thomas A. Kunkel

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

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 reaction pH (Eckert,K.A. and Kunkel,T.A. (1990) Nucleic Acids Res. 18, 3739-3744; Eckert.K.A. and Kunkel T.A. (1993) J. Biol. Chem. 268,13462-13471). In the current study, we demonstrate that the fidelity of human DNA polymerase a increases 10-fold when the pH of the in vitro synthesis reaction is lowered from pH 8.6 to pH6.1 (37°C), as determined using a base substitution reversion assay to score polymerase errors within the lacZα gene of bacteriophage M13mp2. Similarly, the base substitution fidelity of DNA-dependent DNA synthesis by the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) was improved ninefold at pH 6.5 relative to pH 8.0 (37°C). A detailed comparison of HIV-1 RT error specificity at neutral and low pH in a lacZα forward mutation assay revealed that low pH suppresses both mispairing-mediated and misalignment-mediated mutations; however, the characteristic HIV-1 RT pattern of mutational hotspots at homopolymeric sequences is retained at the lower pH. Consistent with the presumption that these mutations result, in part, from increased termination of DNA synthesis within the hotspot sequences relative to other homopolymeric sequences, the HIV-1 RT termination pattern during processive DNA synthesis is not altered by low pH. The HIV-1 RT results are in agreement with our previous hypothesis that the observed increase in polymerase fidelity at low pH results from a decreased efficiency of continuing DNA synthesis from premutational DNA intermediates.

Original languageEnglish (US)
Pages (from-to)5212-5220
Number of pages9
JournalNucleic acids research
Volume21
Issue number22
DOIs
StatePublished - Nov 11 1993

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DNA-Directed DNA Polymerase
DNA
HIV-1
DNA Polymerase I
Mutation
Human immunodeficiency virus 1 reverse transcriptase
Taq Polymerase
Exonucleases
Lac Operon
Bacteriophages
Nucleic Acids
Escherichia coli

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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abstract = "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 reaction pH (Eckert,K.A. and Kunkel,T.A. (1990) Nucleic Acids Res. 18, 3739-3744; Eckert.K.A. and Kunkel T.A. (1993) J. Biol. Chem. 268,13462-13471). In the current study, we demonstrate that the fidelity of human DNA polymerase a increases 10-fold when the pH of the in vitro synthesis reaction is lowered from pH 8.6 to pH6.1 (37°C), as determined using a base substitution reversion assay to score polymerase errors within the lacZα gene of bacteriophage M13mp2. Similarly, the base substitution fidelity of DNA-dependent DNA synthesis by the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) was improved ninefold at pH 6.5 relative to pH 8.0 (37°C). A detailed comparison of HIV-1 RT error specificity at neutral and low pH in a lacZα forward mutation assay revealed that low pH suppresses both mispairing-mediated and misalignment-mediated mutations; however, the characteristic HIV-1 RT pattern of mutational hotspots at homopolymeric sequences is retained at the lower pH. Consistent with the presumption that these mutations result, in part, from increased termination of DNA synthesis within the hotspot sequences relative to other homopolymeric sequences, the HIV-1 RT termination pattern during processive DNA synthesis is not altered by low pH. The HIV-1 RT results are in agreement with our previous hypothesis that the observed increase in polymerase fidelity at low pH results from a decreased efficiency of continuing DNA synthesis from premutational DNA intermediates.",
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Fidelity of DNA synthesis catalyzed by human DNA polymerase α and HIV-1 reverse transcriptase : Effect of reaction pH. / Eckert, Kristin; Kunkel, Thomas A.

In: Nucleic acids research, Vol. 21, No. 22, 11.11.1993, p. 5212-5220.

Research output: Contribution to journalArticle

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AB - 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 reaction pH (Eckert,K.A. and Kunkel,T.A. (1990) Nucleic Acids Res. 18, 3739-3744; Eckert.K.A. and Kunkel T.A. (1993) J. Biol. Chem. 268,13462-13471). In the current study, we demonstrate that the fidelity of human DNA polymerase a increases 10-fold when the pH of the in vitro synthesis reaction is lowered from pH 8.6 to pH6.1 (37°C), as determined using a base substitution reversion assay to score polymerase errors within the lacZα gene of bacteriophage M13mp2. Similarly, the base substitution fidelity of DNA-dependent DNA synthesis by the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) was improved ninefold at pH 6.5 relative to pH 8.0 (37°C). A detailed comparison of HIV-1 RT error specificity at neutral and low pH in a lacZα forward mutation assay revealed that low pH suppresses both mispairing-mediated and misalignment-mediated mutations; however, the characteristic HIV-1 RT pattern of mutational hotspots at homopolymeric sequences is retained at the lower pH. Consistent with the presumption that these mutations result, in part, from increased termination of DNA synthesis within the hotspot sequences relative to other homopolymeric sequences, the HIV-1 RT termination pattern during processive DNA synthesis is not altered by low pH. The HIV-1 RT results are in agreement with our previous hypothesis that the observed increase in polymerase fidelity at low pH results from a decreased efficiency of continuing DNA synthesis from premutational DNA intermediates.

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