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Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion.
- Source :
-
Journal of molecular biology [J Mol Biol] 2010 Jun 11; Vol. 399 (3), pp. 397-409. Date of Electronic Publication: 2010 Apr 22. - Publication Year :
- 2010
-
Abstract
- 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-N(2)-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' (CG*C-I), and 5'-C-A-C3-A4-C5-G*-C-A-C-A-C-3' (CG*C-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 CG*C-II than the CG*C-I sequence context in 135-mer duplexes. Gel electrophoresis and self-ligation circularization experiments revealed that the CG*C-II duplex is more bent than the CG*C-I duplex, while molecular dynamics simulations showed that the unique -C3-A4-C5- segment in the CG*C-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 CG*C-II than in CG*C-I, as well as a local untwisting and enlarged and flexible Roll only in the CG*C-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-N(2)-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.<br /> (Copyright 2010 Elsevier Ltd. All rights reserved.)
- Subjects :
- Base Sequence
Benzo(a)pyrene chemistry
Benzopyrenes chemistry
Carcinogens, Environmental chemistry
Cell Extracts
DNA Adducts chemistry
Deoxyguanosine chemistry
Deoxyguanosine metabolism
Electrophoresis, Polyacrylamide Gel
HeLa Cells
Humans
Molecular Dynamics Simulation
Nucleic Acid Conformation
Oligonucleotides chemistry
Benzo(a)pyrene metabolism
Benzopyrenes metabolism
Carcinogens, Environmental metabolism
DNA Adducts metabolism
DNA Repair
Deoxyguanosine analogs & derivatives
Subjects
Details
- Language :
- English
- ISSN :
- 1089-8638
- Volume :
- 399
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Journal of molecular biology
- Publication Type :
- Academic Journal
- Accession number :
- 20399214
- Full Text :
- https://doi.org/10.1016/j.jmb.2010.04.004