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.
- Benzo[a]pyrenyl-guanine lesionNucleotide excision repairSequence-dependenceDNA bendingFlexibility
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology