title: Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins.
abstract: The influence of DNA base sequence context on the removal of a bulky benzo[a]pyrene diol epoxide-guanine adduct, (+)-trans-B[a]P-N2-dG (G*), by UvrABC nuclease from the thermophilic organism Bacillus caldotenax was investigated. The lesion was flanked by either T or C in otherwise identical complementary 43-mer duplexes (TG*T or CG*C, respectively). It was reported earlier that in the CG*C context, a dominant minor groove adduct structure was observed by NMR methods with all Watson-Crick base pairs intact, and the duplex exhibited a rigid bend. In contrast, in the TG*T context, a highly flexible bend was observed, base pairing at G*, and two 5'-base pairs flanking the adduct were impaired, and multiple solvent-accessible adduct conformations were observed. The TG*T-43-mer duplexes are incised with consistently greater efficiency by UvrABC proteins from B. caldotenax by a factor of 2.3 +/- 0.3. The rates of incisions increase with increasing temperature and are characterized by linear Arrhenius plots with activation energies of 27.0 +/- 1.5 and 23.4 +/- 1.0 kcal/mol for CG*C and TG*T duplexes, respectively. These values reflect the thermophilic characteristics of the UVrABC nuclease complex and the contributions of the different DNA substrates to the overall activation energies. These effects are consistent with base sequence context-dependent differences in structural disorder engendered by a loss of local base stacking interactions and Watson-Crick base pairing in the immediate vicinity of the lesions in the TG*T duplexes. The local weakening of base pairing interactions constitutes a recognition element of the UvrABC nucleotide excision repair apparatus.
authors.affiliation: Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, USA.
authors.forename: Qian
authors.initials: Q
authors.lastname: Ruan
authors.forename: Tongming
authors.initials: T
authors.lastname: Liu
authors.forename: Alexander
authors.initials: A
authors.lastname: Kolbanovskiy
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.forename: Jian
authors.initials: J
authors.lastname: Ren
authors.forename: Milan
authors.initials: M
authors.lastname: Skorvaga
authors.forename: Yue
authors.initials: Y
authors.lastname: Zou
authors.forename: Joshua
authors.initials: J
authors.lastname: Lader
authors.forename: Brijesh
authors.initials: B
authors.lastname: Malkani
authors.forename: Shantu
authors.initials: S
authors.lastname: Amin
authors.forename: Bennett
authors.initials: B
authors.lastname: Van Houten
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
mesh_terms: D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide / Q000737:chemistry*; D001483:Base Sequence; D002151:Calorimetry; D004247:DNA / Q000737:chemistry*; D018736:DNA Adducts; D004260:DNA Repair; D004706:Endodeoxyribonucleases / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D018736:DNA Adducts; D029968:Escherichia coli Proteins; D009838:Oligodeoxyribonucleotides; D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide; D004247:DNA; D004706:Endodeoxyribonucleases; C036385:endodeoxyribonuclease uvrABC