Probing for DNA damage with β-hairpins

Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

Yang Liu, Dara Reeves, Konstantin Kropachev, Yuqin Cai, Shuang Ding, Marina Kolbanovskiy, Alexander Kolbanovskiy, Judith L. Bolton, Suse Broyde, Bennett Van Houten, Nicholas E. Geacintov

Research output: Contribution to journalArticle

Abstract

Nucleotide excision repair (NER) is an important prokaryotic and eukaryotic defense mechanism that removes a large variety of structurally distinct lesions in cellular DNA. While the proteins involved are completely different, the mode of action of these two repair systems is similar, involving a cut-and-patch mechanism in which an oligonucleotide sequence containing the lesion is excised. The prokaryotic and eukaryotic NER damage-recognition factors have common structural features of β-hairpin intrusion between the two DNA strands at the site of the lesion. In the present study, we explored the hypothesis that this common β-hairpin intrusion motif is mirrored in parallel NER incision efficiencies in the two systems. We have utilized human HeLa cell extracts and the prokaryotic UvrABC proteins to determine their relative NER incision efficiencies. We report here comparisons of relative NER efficiencies with a set of stereoisomeric DNA lesions derived from metabolites of benzo[. a]pyrene and equine estrogens in different sequence contexts, utilizing 21 samples. We found a general qualitative trend toward similar relative NER incision efficiencies for ∼65% of these substrates; the other cases deviate mostly by ∼30% or less from a perfect correlation, although several more distant outliers are also evident. This resemblance is consistent with the hypothesis that lesion recognition through β-hairpin insertion, a common feature of the two systems, is facilitated by local thermodynamic destabilization induced by the lesions in both cases. In the case of the UvrABC system, varying the nature of the UvrC endonuclease, while maintaining the same UvrA/B proteins, can markedly affect the relative incision efficiencies. These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER.

Original languageEnglish (US)
Pages (from-to)684-696
Number of pages13
JournalDNA Repair
Volume10
Issue number7
DOIs
StatePublished - Jul 15 2011

Fingerprint

DNA Adducts
DNA Repair
DNA Damage
Repair
Nucleotides
DNA
Endonucleases
Benzo(a)pyrene
In Vitro Techniques
Cell Extracts
HeLa Cells
Thermodynamics
Oligonucleotides
Horses
Metabolites
Estrogens
Proteins
Substrates
Processing

Keywords

  • Benzo[a]pyrene
  • Equilenin
  • Human
  • NER
  • Prokaryotic

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Probing for DNA damage with β-hairpins : Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro. / Liu, Yang; Reeves, Dara; Kropachev, Konstantin; Cai, Yuqin; Ding, Shuang; Kolbanovskiy, Marina; Kolbanovskiy, Alexander; Bolton, Judith L.; Broyde, Suse; Van Houten, Bennett; Geacintov, Nicholas E.

In: DNA Repair, Vol. 10, No. 7, 15.07.2011, p. 684-696.

Research output: Contribution to journalArticle

Liu, Yang ; Reeves, Dara ; Kropachev, Konstantin ; Cai, Yuqin ; Ding, Shuang ; Kolbanovskiy, Marina ; Kolbanovskiy, Alexander ; Bolton, Judith L. ; Broyde, Suse ; Van Houten, Bennett ; Geacintov, Nicholas E. / Probing for DNA damage with β-hairpins : Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro. In: DNA Repair. 2011 ; Vol. 10, No. 7. pp. 684-696.
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abstract = "Nucleotide excision repair (NER) is an important prokaryotic and eukaryotic defense mechanism that removes a large variety of structurally distinct lesions in cellular DNA. While the proteins involved are completely different, the mode of action of these two repair systems is similar, involving a cut-and-patch mechanism in which an oligonucleotide sequence containing the lesion is excised. The prokaryotic and eukaryotic NER damage-recognition factors have common structural features of β-hairpin intrusion between the two DNA strands at the site of the lesion. In the present study, we explored the hypothesis that this common β-hairpin intrusion motif is mirrored in parallel NER incision efficiencies in the two systems. We have utilized human HeLa cell extracts and the prokaryotic UvrABC proteins to determine their relative NER incision efficiencies. We report here comparisons of relative NER efficiencies with a set of stereoisomeric DNA lesions derived from metabolites of benzo[. a]pyrene and equine estrogens in different sequence contexts, utilizing 21 samples. We found a general qualitative trend toward similar relative NER incision efficiencies for ∼65{\%} of these substrates; the other cases deviate mostly by ∼30{\%} or less from a perfect correlation, although several more distant outliers are also evident. This resemblance is consistent with the hypothesis that lesion recognition through β-hairpin insertion, a common feature of the two systems, is facilitated by local thermodynamic destabilization induced by the lesions in both cases. In the case of the UvrABC system, varying the nature of the UvrC endonuclease, while maintaining the same UvrA/B proteins, can markedly affect the relative incision efficiencies. These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER.",
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