Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-l

Rinku Jain, Jayati Roy Choudhury, Angeliki Buku, Robert E. Johnson, Louise Prakash, Satya Prakash, Aneel K. Aggarwal

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-l (Poll) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Poll is ∼100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Poll bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold" and is largely disordered. Together, our kinetic and structural studies show how Poll maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.

Original languageEnglish (US)
Article number43904
JournalScientific Reports
Volume7
DOIs
StatePublished - Mar 8 2017

Fingerprint

DNA-Directed DNA Polymerase
Nucleotides
Base Pairing
DNA
Methylation
Genome
2'-deoxycytidine 5'-triphosphate
thymidine 5'-triphosphate
2'-deoxyadenosine

ASJC Scopus subject areas

  • General

Cite this

Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-l. / Jain, Rinku; Choudhury, Jayati Roy; Buku, Angeliki; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.

In: Scientific Reports, Vol. 7, 43904, 08.03.2017.

Research output: Contribution to journalArticle

Jain, Rinku ; Choudhury, Jayati Roy ; Buku, Angeliki ; Johnson, Robert E. ; Prakash, Louise ; Prakash, Satya ; Aggarwal, Aneel K. / Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-l. In: Scientific Reports. 2017 ; Vol. 7.
@article{8ac0d2469d964b338b4662ba4b7f9976,
title = "Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-l",
abstract = "N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-l (Poll) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Poll is ∼100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Poll bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a {"}foothold{"} and is largely disordered. Together, our kinetic and structural studies show how Poll maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.",
author = "Rinku Jain and Choudhury, {Jayati Roy} and Angeliki Buku and Johnson, {Robert E.} and Louise Prakash and Satya Prakash and Aggarwal, {Aneel K.}",
year = "2017",
month = "3",
day = "8",
doi = "10.1038/srep43904",
language = "English (US)",
volume = "7",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-l

AU - Jain, Rinku

AU - Choudhury, Jayati Roy

AU - Buku, Angeliki

AU - Johnson, Robert E.

AU - Prakash, Louise

AU - Prakash, Satya

AU - Aggarwal, Aneel K.

PY - 2017/3/8

Y1 - 2017/3/8

N2 - N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-l (Poll) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Poll is ∼100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Poll bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold" and is largely disordered. Together, our kinetic and structural studies show how Poll maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.

AB - N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-l (Poll) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Poll is ∼100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Poll bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold" and is largely disordered. Together, our kinetic and structural studies show how Poll maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.

UR - http://www.scopus.com/inward/record.url?scp=85019583258&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019583258&partnerID=8YFLogxK

U2 - 10.1038/srep43904

DO - 10.1038/srep43904

M3 - Article

VL - 7

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 43904

ER -