Effect of pH on the misincorporation rate of DNA polymerase η

Naomi Nishimoto, Motoshi Suzuki, Shunji Izuta

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The many known eukaryotic DNA polymerases are classified into four families; A, B, X, and Y. Among them, DNA polymerase η, a Y family polymerase, is a low fidelity enzyme that contributes to translesional synthesis and somatic hypermutation. Although a high mutation frequency is observed in immunoglobulin genes, translesional synthesis occurs with a high accuracy. We determined whether the misincorporation rate of DNA polymerase η varies with ambient conditions. It has been reported that DNA polymerase η is unable to exclude water molecules from the active site. This finding suggests that some ions affect hydrogen bond formation at the active site. We focused on the effect of pH and evaluated the misincorporation rate of deoxyguanosine triphosphate (dGTP) opposite template T by DNA polymerase η at various pH levels with a synthetic template-primer. The misincorporation rate of dGTP by DNA polymerase η drastically increased at pH 8.0-9.0 compared with that at pH 6.5-7.5. Kinetic analysis revealed that the Km value for dGTP on the misincorporation opposite template T was markedly affected by pH. However, this drastic change was not seen with the low fidelity DNA polymerase α.

Original languageEnglish
Pages (from-to)953-958
Number of pages6
JournalBiological and Pharmaceutical Bulletin
Volume39
Issue number6
DOIs
Publication statusPublished - 01-06-2016

Fingerprint

DNA-Directed DNA Polymerase
Catalytic Domain
Immunoglobulin Genes
Mutation Rate
Protons
Water
Enzymes
deoxyguanosine triphosphate

All Science Journal Classification (ASJC) codes

  • Pharmacology
  • Pharmaceutical Science

Cite this

Nishimoto, Naomi ; Suzuki, Motoshi ; Izuta, Shunji. / Effect of pH on the misincorporation rate of DNA polymerase η. In: Biological and Pharmaceutical Bulletin. 2016 ; Vol. 39, No. 6. pp. 953-958.
@article{cef5cebc85c54e33a632b21d0ad27b59,
title = "Effect of pH on the misincorporation rate of DNA polymerase η",
abstract = "The many known eukaryotic DNA polymerases are classified into four families; A, B, X, and Y. Among them, DNA polymerase η, a Y family polymerase, is a low fidelity enzyme that contributes to translesional synthesis and somatic hypermutation. Although a high mutation frequency is observed in immunoglobulin genes, translesional synthesis occurs with a high accuracy. We determined whether the misincorporation rate of DNA polymerase η varies with ambient conditions. It has been reported that DNA polymerase η is unable to exclude water molecules from the active site. This finding suggests that some ions affect hydrogen bond formation at the active site. We focused on the effect of pH and evaluated the misincorporation rate of deoxyguanosine triphosphate (dGTP) opposite template T by DNA polymerase η at various pH levels with a synthetic template-primer. The misincorporation rate of dGTP by DNA polymerase η drastically increased at pH 8.0-9.0 compared with that at pH 6.5-7.5. Kinetic analysis revealed that the Km value for dGTP on the misincorporation opposite template T was markedly affected by pH. However, this drastic change was not seen with the low fidelity DNA polymerase α.",
author = "Naomi Nishimoto and Motoshi Suzuki and Shunji Izuta",
year = "2016",
month = "6",
day = "1",
doi = "10.1248/bpb.b15-00900",
language = "English",
volume = "39",
pages = "953--958",
journal = "Biological and Pharmaceutical Bulletin",
issn = "0918-6158",
publisher = "Pharmaceutical Society of Japan",
number = "6",

}

Effect of pH on the misincorporation rate of DNA polymerase η. / Nishimoto, Naomi; Suzuki, Motoshi; Izuta, Shunji.

In: Biological and Pharmaceutical Bulletin, Vol. 39, No. 6, 01.06.2016, p. 953-958.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Effect of pH on the misincorporation rate of DNA polymerase η

AU - Nishimoto, Naomi

AU - Suzuki, Motoshi

AU - Izuta, Shunji

PY - 2016/6/1

Y1 - 2016/6/1

N2 - The many known eukaryotic DNA polymerases are classified into four families; A, B, X, and Y. Among them, DNA polymerase η, a Y family polymerase, is a low fidelity enzyme that contributes to translesional synthesis and somatic hypermutation. Although a high mutation frequency is observed in immunoglobulin genes, translesional synthesis occurs with a high accuracy. We determined whether the misincorporation rate of DNA polymerase η varies with ambient conditions. It has been reported that DNA polymerase η is unable to exclude water molecules from the active site. This finding suggests that some ions affect hydrogen bond formation at the active site. We focused on the effect of pH and evaluated the misincorporation rate of deoxyguanosine triphosphate (dGTP) opposite template T by DNA polymerase η at various pH levels with a synthetic template-primer. The misincorporation rate of dGTP by DNA polymerase η drastically increased at pH 8.0-9.0 compared with that at pH 6.5-7.5. Kinetic analysis revealed that the Km value for dGTP on the misincorporation opposite template T was markedly affected by pH. However, this drastic change was not seen with the low fidelity DNA polymerase α.

AB - The many known eukaryotic DNA polymerases are classified into four families; A, B, X, and Y. Among them, DNA polymerase η, a Y family polymerase, is a low fidelity enzyme that contributes to translesional synthesis and somatic hypermutation. Although a high mutation frequency is observed in immunoglobulin genes, translesional synthesis occurs with a high accuracy. We determined whether the misincorporation rate of DNA polymerase η varies with ambient conditions. It has been reported that DNA polymerase η is unable to exclude water molecules from the active site. This finding suggests that some ions affect hydrogen bond formation at the active site. We focused on the effect of pH and evaluated the misincorporation rate of deoxyguanosine triphosphate (dGTP) opposite template T by DNA polymerase η at various pH levels with a synthetic template-primer. The misincorporation rate of dGTP by DNA polymerase η drastically increased at pH 8.0-9.0 compared with that at pH 6.5-7.5. Kinetic analysis revealed that the Km value for dGTP on the misincorporation opposite template T was markedly affected by pH. However, this drastic change was not seen with the low fidelity DNA polymerase α.

UR - http://www.scopus.com/inward/record.url?scp=84971349939&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84971349939&partnerID=8YFLogxK

U2 - 10.1248/bpb.b15-00900

DO - 10.1248/bpb.b15-00900

M3 - Article

C2 - 27251497

AN - SCOPUS:84971349939

VL - 39

SP - 953

EP - 958

JO - Biological and Pharmaceutical Bulletin

JF - Biological and Pharmaceutical Bulletin

SN - 0918-6158

IS - 6

ER -