title: Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion.
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.
authors.affiliation: Department of Biology, New York University, New York, NY 10003, USA.
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Cai
authors.forename: Konstantin
authors.initials: K
authors.lastname: Kropachev
authors.forename: Rong
authors.initials: R
authors.lastname: Xu
authors.forename: Yijin
authors.initials: Y
authors.lastname: Tang
authors.forename: Marina
authors.initials: M
authors.lastname: Kolbanovskii
authors.forename: Alexander
authors.initials: A
authors.lastname: Kolbanovskii
authors.forename: Shantu
authors.initials: S
authors.lastname: Amin
authors.forename: Dinshaw J
authors.initials: DJ
authors.lastname: Patel
authors.forename: Suse
authors.initials: S
authors.lastname: Broyde
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
mesh_terms: D001483:Base Sequence; D001564:Benzo(a)pyrene / Q000737:chemistry / Q000378:metabolism*; D001580:Benzopyrenes / Q000737:chemistry / Q000378:metabolism*; D002274:Carcinogens, Environmental / Q000737:chemistry / Q000378:metabolism*; D002457:Cell Extracts; D018736:DNA Adducts / Q000737:chemistry / Q000378:metabolism*; D004260:DNA Repair; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D006367:HeLa Cells; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry
chemical_list: D001580:Benzopyrenes; D002274:Carcinogens, Environmental; D002457:Cell Extracts; D018736:DNA Adducts; D009841:Oligonucleotides; C478198:benzo(a)pyrene N2-dG adduct; D001564:Benzo(a)pyrene; D003849:Deoxyguanosine
references.citation: Biochemistry. 1993 Apr 20;32(15):4121-7
references.pmid: 8471619
references.citation: J Mol Biol. 1982 Oct 25;161(2):343-52
references.pmid: 7154084
references.citation: J Mol Biol. 2009 Mar 13;386(5):1193-203
references.pmid: 19162041
references.citation: Chem Res Toxicol. 2002 Feb;15(2):118-26
references.pmid: 11849037
references.citation: Nat Rev Cancer. 2005 Feb;5(2):113-25
references.pmid: 15660110
references.citation: Nature. 2007 Oct 4;449(7162):570-5
references.pmid: 17882165
references.citation: Int J Cancer. 2009 Mar 1;124(5):999-1007
references.pmid: 19065660
references.citation: Nature. 1983 Jun 9-15;303(5917):468-72
references.pmid: 6304528
references.citation: DNA Repair (Amst). 2004 May 4;3(5):455-64
references.pmid: 15162792
references.citation: Science. 1987 Apr 24;236(4800):416-22
references.pmid: 2951850
references.citation: J Biol Chem. 1996 Oct 11;271(41):25089-98
references.pmid: 8810263
references.citation: J Biol Chem. 1994 Mar 11;269(10):7824-33
references.pmid: 8126009
references.citation: Biopolymers. 2002 Nov 5;65(3):202-10
references.pmid: 12228925
references.citation: Biopolymers. 1982 Nov;21(11):2315-6
references.pmid: 7171739
references.citation: J Mol Biol. 2007 Nov 23;374(2):292-305
references.pmid: 17942115
references.citation: J Biol Chem. 1982 Dec 25;257(24):14686-707
references.pmid: 7174662
references.citation: J Mol Biol. 1983 Nov 15;170(4):957-81
references.pmid: 6315955
references.citation: Nature. 1986 Apr 10-16;320(6062):501-6
references.pmid: 3960133
references.citation: Nature. 1984 Apr 5-11;308(5959):509-13
references.pmid: 6323997
references.citation: Proc Natl Acad Sci U S A. 1986 Feb;83(4):862-6
references.pmid: 3456570
references.citation: Cancer Res. 1982 Dec;42(12):4875-917
references.pmid: 6814745
references.citation: Mol Cell Biol. 1997 Dec;17(12):7069-76
references.pmid: 9372938
references.citation: DNA Repair (Amst). 2006 Jun 10;5(6):654-66
references.pmid: 16574501
references.citation: Biochemistry. 2007 Jun 12;46(23):7006-15
references.pmid: 17506530
references.citation: Methods Mol Biol. 1999;113:373-92
references.pmid: 10443435
references.citation: J Am Chem Soc. 2008 Jan 30;130(4):1304-8
references.pmid: 18163624
references.citation: Biophys Chem. 1995 Nov;56(3):281-96
references.pmid: 7578905
references.citation: J Biomol Struct Dyn. 1989 Feb;6(4):669-99
references.pmid: 2619934
references.citation: Biochemistry. 1998 Jan 13;37(2):769-78
references.pmid: 9425101
references.citation: Biochemistry. 1993 Apr 27;32(16):4145-55
references.pmid: 8476845
references.citation: Biochemistry. 1985 Dec 3;24(25):7033-7
references.pmid: 4084556
references.citation: J Mol Biol. 2009 Jan 9;385(1):30-44
references.pmid: 18948114
references.citation: Chem Rev. 2006 Feb;106(2):253-76
references.pmid: 16464005
references.citation: J Mol Biol. 1998 Sep 18;282(2):331-43
references.pmid: 9735291
references.citation: Biopolymers. 1982 May;21(5):995-7
references.pmid: 7082773
references.citation: Biophys J. 2002 Dec;83(6):3446-59
references.pmid: 12496111
references.citation: J Mol Biol. 2000 Jan 7;295(1):71-83
references.pmid: 10623509
references.citation: Nucleic Acids Res. 2007;35(5):1555-68
references.pmid: 17287290
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
references.pmid: 9736707
references.citation: Cell Res. 2008 Jan;18(1):184-97
references.pmid: 18157156
references.citation: Biochimie. 1999 Jan-Feb;81(1-2):39-44
references.pmid: 10214908
references.citation: Nucleic Acids Res. 1989 Mar 11;17(5):1797-803
references.pmid: 2928107
references.citation: Proc Natl Acad Sci U S A. 1988 Mar;85(6):1763-7
references.pmid: 3162306
references.citation: Carcinogenesis. 1995 Feb;16(2):357-65
references.pmid: 7859369
references.citation: Chem Res Toxicol. 1998 Apr;11(4):381-8
references.pmid: 9548810
references.citation: Nucleic Acids Res. 1998 Apr 15;26(8):1906-26
references.pmid: 9518483
references.citation: Nucleic Acids Res. 1995 Jun 25;23(12):2314-9
references.pmid: 7610061
references.citation: J Mol Biol. 1995 Mar 17;247(1):34-48
references.pmid: 7897660
references.citation: Biochemistry. 1998 Apr 7;37(14):4993-5000
references.pmid: 9538018
references.citation: Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1914-8
references.pmid: 1311854
references.citation: Nucleic Acids Res. 1992 Dec 11;20(23):6167-76
references.pmid: 1475180