Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase

A 5′-slippage mechanism

Pingna Xu, Lida Oum, Nicholas E. Geacintov, Suse Broyde

Research output: Contribution to journalArticle

Abstract

The Y-family DNA polymerase Dpo4, from the archaeon bacterium Sulfolobus solfataricus, is a member of the DinB family, which also contains human Pol κ. It has a spacious active site that can accommodate two templating bases simultaneously, with one of them skipped by the incoming dNTP. Assays of single dNTP insertion opposite a benzo[a]pyrene-derived N2-dG adduct, 10S(+)-trans-anti-[BP]-N2-dG ([BP]G*), reveal that an incoming dATP is significantly preferred over the other three dNTPs in the TG1 *G2 sequence context. Molecular modeling and dynamics simulations were carried out to interpret this experimental observation on a molecular level. Modeling studies suggest that the significant preference for dATP insertion observed experimentally can result from two possible dATP incorporation modes. The dATP can be inserted opposite the T on the 5′ side of the adduct G1*, using an unusual 5′-slippage pattern, in which the unadducted G2, rather than G 1*, is skipped, to produce a -1 deletion. In addition, the dATP can be misincorporated opposite the adduct. The 5′-slippage pattern may be generally facilitated in cases where the base 3′ to the lesion is the same as the adducted base.

Original languageEnglish (US)
Pages (from-to)2701-2709
Number of pages9
JournalBiochemistry
Volume47
Issue number9
DOIs
StatePublished - Mar 4 2008

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Sulfolobus solfataricus
Molecular modeling
Benzo(a)pyrene
Archaea
DNA-Directed DNA Polymerase
Molecular Dynamics Simulation
Molecular dynamics
Assays
Catalytic Domain
Bacteria
Nucleotides
Computer simulation
DNA polymerase A
benzo(a)pyrene N2-dG adduct

ASJC Scopus subject areas

  • Biochemistry

Cite this

Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase : A 5′-slippage mechanism. / Xu, Pingna; Oum, Lida; Geacintov, Nicholas E.; Broyde, Suse.

In: Biochemistry, Vol. 47, No. 9, 04.03.2008, p. 2701-2709.

Research output: Contribution to journalArticle

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