TY - JOUR
T1 - Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion
AU - Cai, Yuqin
AU - Kropachev, Konstantin
AU - Xu, Rong
AU - Tang, Yijin
AU - Kolbanovskii, Marina
AU - Kolbanovskii, Alexander
AU - Amin, Shantu
AU - Patel, Dinshaw J.
AU - Broyde, Suse
AU - Geacintov, Nicholas E.
N1 - Funding Information:
The experimental portion of this work was supported by NIH grant CA-099194 to N.E.G. and the computational aspects were supported by NIH grant CA-28038 to S.B. Partial support for computational infrastructure and systems management was provided by NIH grant CA75449 to S.B. Support for this work to was provided by NIH grant CA-046533 to D.J.P. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health.
PY - 2010/6
Y1 - 2010/6
N2 - 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.
AB - 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.
KW - Benzo[a]pyrenyl-guanine lesionNucleotide excision repairSequence-dependenceDNA bendingFlexibility
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U2 - 10.1016/j.jmb.2010.04.004
DO - 10.1016/j.jmb.2010.04.004
M3 - Article
C2 - 20399214
AN - SCOPUS:77954759002
SN - 0022-2836
VL - 399
SP - 397
EP - 409
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 3
ER -