Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts

Hierarchies of Recognition Signals

Yuqin Cai, Dinshaw J. Patel, Nicholas E. Geacintov, Suse Broyde

Research output: Contribution to journalArticle

Abstract

The structural origin underlying differential nucleotide excision repair (NER) susceptibilities of bulky DNA lesions remains a challenging problem. We investigated the 10S (+)-trans-anti-[BP]-N2-2′-deoxyguanosine (G*) adduct in double-stranded DNA. This adduct arises from the reaction, in vitro and in vivo, of a major genotoxic metabolite of benzo[a]pyrene (BP), (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, with the exocyclic amino group of guanine. Removal of this lesion by the NER apparatus in cell-free extracts has been found to depend on the base sequence context in which the lesion is embedded, providing an excellent opportunity for elucidating the properties of the damaged DNA duplexes that favor NER. While the BP ring system is in the B-DNA minor groove, 5′ directed along the modified strand, there are orientational distinctions that are sequence dependent and are governed by flanking amino groups [Nucleic Acids Res. 35 (2007), 1555-1568]. To elucidate sequence-governed NER susceptibility, we conducted molecular dynamics simulations for the 5′-...CG*GC..., 5′-...CGG*C..., and 5′-...TCG*CT... adduct-containing duplexes. We also investigated the 5′-...CG*IC... and 5′-...CIG*C... sequences, which contain "I" (2′-deoxyinosine), with hydrogen replacing the amino group in 2′-deoxyguanosine, to further characterize the structural and dynamic roles of the flanking amino groups in the damaged duplexes. Our results pinpoint explicit roles for the amino groups in tandem GG sequences on the efficiency of NER and suggest a hierarchy of destabilizing structural features that differentially facilitate NER of the BP lesion in the sequence contexts investigated. Furthermore, combinations of several locally destabilizing features in the hierarchy, consistent with a multipartite model, may provide a relatively strong recognition signal.

Original languageEnglish (US)
Pages (from-to)30-44
Number of pages15
JournalJournal of Molecular Biology
Volume385
Issue number1
DOIs
StatePublished - Jan 9 2009

Fingerprint

DNA Adducts
DNA Repair
Deoxyguanosine
DNA
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
B-Form DNA
Benzo(a)pyrene
Guanine
Molecular Dynamics Simulation
Cell Extracts
Nucleic Acids
Hydrogen

Keywords

  • benzo[a]pyrenyl-guanine lesion
  • GG mutation hotspot
  • guanine amino group
  • nucleotide excision repair susceptibility
  • sequence-dependent conformational variability

ASJC Scopus subject areas

  • Molecular Biology

Cite this

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title = "Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals",
abstract = "The structural origin underlying differential nucleotide excision repair (NER) susceptibilities of bulky DNA lesions remains a challenging problem. We investigated the 10S (+)-trans-anti-[BP]-N2-2′-deoxyguanosine (G*) adduct in double-stranded DNA. This adduct arises from the reaction, in vitro and in vivo, of a major genotoxic metabolite of benzo[a]pyrene (BP), (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, with the exocyclic amino group of guanine. Removal of this lesion by the NER apparatus in cell-free extracts has been found to depend on the base sequence context in which the lesion is embedded, providing an excellent opportunity for elucidating the properties of the damaged DNA duplexes that favor NER. While the BP ring system is in the B-DNA minor groove, 5′ directed along the modified strand, there are orientational distinctions that are sequence dependent and are governed by flanking amino groups [Nucleic Acids Res. 35 (2007), 1555-1568]. To elucidate sequence-governed NER susceptibility, we conducted molecular dynamics simulations for the 5′-...CG*GC..., 5′-...CGG*C..., and 5′-...TCG*CT... adduct-containing duplexes. We also investigated the 5′-...CG*IC... and 5′-...CIG*C... sequences, which contain {"}I{"} (2′-deoxyinosine), with hydrogen replacing the amino group in 2′-deoxyguanosine, to further characterize the structural and dynamic roles of the flanking amino groups in the damaged duplexes. Our results pinpoint explicit roles for the amino groups in tandem GG sequences on the efficiency of NER and suggest a hierarchy of destabilizing structural features that differentially facilitate NER of the BP lesion in the sequence contexts investigated. Furthermore, combinations of several locally destabilizing features in the hierarchy, consistent with a multipartite model, may provide a relatively strong recognition signal.",
keywords = "benzo[a]pyrenyl-guanine lesion, GG mutation hotspot, guanine amino group, nucleotide excision repair susceptibility, sequence-dependent conformational variability",
author = "Yuqin Cai and Patel, {Dinshaw J.} and Geacintov, {Nicholas E.} and Suse Broyde",
year = "2009",
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T1 - Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts

T2 - Hierarchies of Recognition Signals

AU - Cai, Yuqin

AU - Patel, Dinshaw J.

AU - Geacintov, Nicholas E.

AU - Broyde, Suse

PY - 2009/1/9

Y1 - 2009/1/9

N2 - The structural origin underlying differential nucleotide excision repair (NER) susceptibilities of bulky DNA lesions remains a challenging problem. We investigated the 10S (+)-trans-anti-[BP]-N2-2′-deoxyguanosine (G*) adduct in double-stranded DNA. This adduct arises from the reaction, in vitro and in vivo, of a major genotoxic metabolite of benzo[a]pyrene (BP), (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, with the exocyclic amino group of guanine. Removal of this lesion by the NER apparatus in cell-free extracts has been found to depend on the base sequence context in which the lesion is embedded, providing an excellent opportunity for elucidating the properties of the damaged DNA duplexes that favor NER. While the BP ring system is in the B-DNA minor groove, 5′ directed along the modified strand, there are orientational distinctions that are sequence dependent and are governed by flanking amino groups [Nucleic Acids Res. 35 (2007), 1555-1568]. To elucidate sequence-governed NER susceptibility, we conducted molecular dynamics simulations for the 5′-...CG*GC..., 5′-...CGG*C..., and 5′-...TCG*CT... adduct-containing duplexes. We also investigated the 5′-...CG*IC... and 5′-...CIG*C... sequences, which contain "I" (2′-deoxyinosine), with hydrogen replacing the amino group in 2′-deoxyguanosine, to further characterize the structural and dynamic roles of the flanking amino groups in the damaged duplexes. Our results pinpoint explicit roles for the amino groups in tandem GG sequences on the efficiency of NER and suggest a hierarchy of destabilizing structural features that differentially facilitate NER of the BP lesion in the sequence contexts investigated. Furthermore, combinations of several locally destabilizing features in the hierarchy, consistent with a multipartite model, may provide a relatively strong recognition signal.

AB - The structural origin underlying differential nucleotide excision repair (NER) susceptibilities of bulky DNA lesions remains a challenging problem. We investigated the 10S (+)-trans-anti-[BP]-N2-2′-deoxyguanosine (G*) adduct in double-stranded DNA. This adduct arises from the reaction, in vitro and in vivo, of a major genotoxic metabolite of benzo[a]pyrene (BP), (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, with the exocyclic amino group of guanine. Removal of this lesion by the NER apparatus in cell-free extracts has been found to depend on the base sequence context in which the lesion is embedded, providing an excellent opportunity for elucidating the properties of the damaged DNA duplexes that favor NER. While the BP ring system is in the B-DNA minor groove, 5′ directed along the modified strand, there are orientational distinctions that are sequence dependent and are governed by flanking amino groups [Nucleic Acids Res. 35 (2007), 1555-1568]. To elucidate sequence-governed NER susceptibility, we conducted molecular dynamics simulations for the 5′-...CG*GC..., 5′-...CGG*C..., and 5′-...TCG*CT... adduct-containing duplexes. We also investigated the 5′-...CG*IC... and 5′-...CIG*C... sequences, which contain "I" (2′-deoxyinosine), with hydrogen replacing the amino group in 2′-deoxyguanosine, to further characterize the structural and dynamic roles of the flanking amino groups in the damaged duplexes. Our results pinpoint explicit roles for the amino groups in tandem GG sequences on the efficiency of NER and suggest a hierarchy of destabilizing structural features that differentially facilitate NER of the BP lesion in the sequence contexts investigated. Furthermore, combinations of several locally destabilizing features in the hierarchy, consistent with a multipartite model, may provide a relatively strong recognition signal.

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KW - nucleotide excision repair susceptibility

KW - sequence-dependent conformational variability

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