Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins

Qian Ruan, Tongming Liu, Alexander Kolbanovskiy, Yang Liu, Jian Ren, Milan Skorvaga, Yue Zou, Joshua Lader, Brijesh Malkani, Shantu Amin, Bennett Van Houten, Nicholas Geacintov

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)7006-7015
Number of pages10
JournalBiochemistry
Volume46
Issue number23
DOIs
StatePublished - Jun 12 2007

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DNA Adducts
Benzo(a)pyrene
Epoxy Compounds
Guanine
Base Pairing
DNA Repair
Repair
Nucleotides
Activation energy
Arrhenius plots
Temperature
DNA
Bacilli
Conformations
Proteins
Nuclear magnetic resonance
Substrates
Bacillus
benzo(a)pyrene N2-dG adduct
IgA receptor

ASJC Scopus subject areas

  • Biochemistry

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Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. / Ruan, Qian; Liu, Tongming; Kolbanovskiy, Alexander; Liu, Yang; Ren, Jian; Skorvaga, Milan; Zou, Yue; Lader, Joshua; Malkani, Brijesh; Amin, Shantu; Van Houten, Bennett; Geacintov, Nicholas.

In: Biochemistry, Vol. 46, No. 23, 12.06.2007, p. 7006-7015.

Research output: Contribution to journalArticle

Ruan, Q, Liu, T, Kolbanovskiy, A, Liu, Y, Ren, J, Skorvaga, M, Zou, Y, Lader, J, Malkani, B, Amin, S, Van Houten, B & Geacintov, N 2007, 'Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins', Biochemistry, vol. 46, no. 23, pp. 7006-7015. https://doi.org/10.1021/bi700294k
Ruan, Qian ; Liu, Tongming ; Kolbanovskiy, Alexander ; Liu, Yang ; Ren, Jian ; Skorvaga, Milan ; Zou, Yue ; Lader, Joshua ; Malkani, Brijesh ; Amin, Shantu ; Van Houten, Bennett ; Geacintov, Nicholas. / Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. In: Biochemistry. 2007 ; Vol. 46, No. 23. pp. 7006-7015.
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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.",
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AU - Liu, Tongming

AU - Kolbanovskiy, Alexander

AU - Liu, Yang

AU - Ren, Jian

AU - Skorvaga, Milan

AU - Zou, Yue

AU - Lader, Joshua

AU - Malkani, Brijesh

AU - Amin, Shantu

AU - Van Houten, Bennett

AU - Geacintov, Nicholas

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