Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion

Yuqin Cai, Konstantin Kropachev, Rong Xu, Yijin Tang, Marina Kolbanovskii, Alexander Kolbanovskii, Shantu Amin, Dinshaw J. Patel, Suse Broyde, Nicholas E. Geacintov

Research output: Contribution to journalArticlepeer-review


The effects of non-nearest base sequences, beyond the nucleotides flanking a DNA lesion on either side, on nucleotide excision repair (NER) in extracts from human cells were investigated. We constructed two duplexes containing the same minor groove-aligned 10S (+)-trans-anti-B[a]P-N2-dG (G) DNA adduct, derived from the environmental carcinogen benzo[a]pyrene (B[a]P): 5'-C-C-A-T-C-G-C-T-A-C-C-3' (CGC-I), and 5'-C-A-C3-A4-C5-G-C-A-C-A-C-3' (CGC-II). We used polyacrylamide gel electrophoresis to compare the extent of DNA bending, and molecular dynamics simulations to analyze the structural characteristics of these two DNA duplexes. The NER efficiencies are 1.6(±0.2)-fold greater in the case of the CGC-II than the CGC-I sequence context in 135-mer duplexes. Gel electrophoresis and self-ligation circularization experiments revealed that the CGC-II duplex is more bent than the CGC-I duplex, while molecular dynamics simulations showed that the unique -C3-A4-C5- segment in the CGC-II duplex plays a key role. The presence of a minor groove-positioned guanine amino group, the Watson-Crick partner to C3, acts as a wedge; facilitated by a highly deformable local -C3-A4- base step, this amino group allows the B[a]P ring system to produce a more enlarged minor groove in CGC-II than in CGC-I, as well as a local untwisting and enlarged and flexible Roll only in the CGC-II sequence. These structural properties fit well with our earlier findings that in the case of the family of minor groove 10S (+)-trans-anti-B[a]P-N2-dG lesions, flexible bends and enlarged minor groove widths constitute NER recognition signals, and extend our understanding of sequence context effects on NER to the neighbors that are distant to the lesion.

Original languageEnglish (US)
Pages (from-to)397-409
Number of pages13
JournalJournal of Molecular Biology
Issue number3
StatePublished - Jun 2010


  • Benzo[a]pyrenyl-guanine lesionNucleotide excision repairSequence-dependenceDNA bendingFlexibility

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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