Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion–base stacking interactions

Department of Chemistry, Department of Biology, New York University, New York, NY 10003, USA.
Nucleic Acids Research (Impact Factor: 9.11). 07/2011; 39(20):8752-64. DOI: 10.1093/nar/gkr537
Source: PubMed


The molecular basis of resistance to nucleotide excision repair (NER) of certain bulky DNA lesions is poorly understood. To
address this issue, we have studied NER in human HeLa cell extracts of two topologically distinct lesions, one derived from
benzo[a]pyrene (10R-(+)-cis-anti-B[a]P-N2-dG), and one from the food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (C8-dG-PhIP), embedded in either full or ‘deletion’ duplexes (the partner nucleotide opposite the lesion is missing).
All lesions adopt base-displaced intercalated conformations. Both full duplexes are thermodynamically destabilized and are
excellent substrates of NER. However, the identical 10R-(+)-cis-anti-B[a]P-N2-dG adduct in the deletion duplex dramatically enhances the thermal stability of this duplex, and is completely resistant
to NER. Molecular dynamics simulations show that B[a]P lesion-induced distortion/destabilization is compensated by stabilizing aromatic ring system–base stacking interactions.
In the C8-dG-PhIP-deletion duplex, the smaller size of the aromatic ring system and the mobile phenyl ring are less stabilizing
and yield moderate NER efficiency. Thus, a partner nucleotide opposite the lesion is not an absolute requirement for the successful
initiation of NER. Our observations are consistent with the hypothesis that carcinogen–base stacking interactions, which contribute
to the local DNA stability, can prevent the successful insertion of an XPC β-hairpin into the duplex and the normal recruitment
of other downstream NER factors.

    • "Thus, this type of repeat is highly efficient at eliciting mutations that involve DNA strand breaks (insertions and deletions;Table 2 ), but not mutations that originate from errorprone repair, such as translesion DNA synthesis. On the one hand, this behavior may depend on the high stacking interactions characteristic of homo(purine@BULLETpyrimidine) runs, which disfavor DNA repair [Yang, 2006; Reeves et al., 2011; Ding et al., 2012; Jain et al., 2013b] and, hence may provide limited opportunities for misincorporation at a basic sites. On the other hand, triplex-formation does not provide duplex substrates with potential mismatches, as for direct repeat and inverted repeats (Fig. 3), which are efficiently repaired. "
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    ABSTRACT: Missense/nonsense mutations and micro-deletions/micro-insertions (<21bp) represent ∼76% of all mutations causing human inherited disease, and their occurrence has been associated with sequence motifs (direct, inverted and mirror repeats; G-quartets) capable of adopting non-B DNA structures. We found that a significant proportion (∼21%) of both micro-deletions and micro-insertions occur within direct repeats, and are explicable by slipped misalignment. A novel mutational mechanism, DNA triplex formation followed by DNA repair, may explain ∼5% of micro-deletions and micro-insertions at mirror repeats. Further, G-quartets, direct and inverted repeats also appear to play a prominent role in mediating missense mutations, whereas only direct and inverted repeats mediate nonsense mutations. We suggest a mutational mechanism involving slipped strand mispairing, slipped structure formation and DNA repair, to explain ∼15% of missense and ∼12% of nonsense mutations yielding perfect direct repeats from imperfect repeats, or the extension of existing direct repeats. Similar proportions of missense and nonsense mutations were explicable by hairpin/loop formation and DNA repair, yielding perfect inverted repeats from imperfect repeats. We also propose a model for single base-pair substitution based on one-electron oxidation reactions at G-quadruplex DNA. Overall, the proposed mechanisms provide support for a role for non-B DNA structures in human gene mutagenesis. This article is protected by copyright. All rights reserved.
    No preview · Article · Oct 2015 · Human Mutation
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    • "The importance of perturbations of the normal DNA base stacking interactions by DNA lesions, such as one containing a crosslink between guanine and thymine in DNA duplexes (73), as well as the potential stabilizing effects associated with interactions between aromatic rings of carcinogens with DNA bases has been considered recently (69,71,74); evidence was presented that weakened van der Waals stacking interactions correlate with enhanced NER susceptibility whereas enhanced stacking interactions result in diminished excision efficiencies. Accordingly, we evaluated the van der Waals stacking interaction energies for all simulated base-displaced structures. "
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    ABSTRACT: Nucleotide excision repair (NER) efficiencies of DNA lesions can vary by orders of magnitude, for reasons that remain unclear. An example is the pair of N-(2′-deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF) and N-(2′-deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) adducts that differ by a single acetyl group. The NER efficiencies in human HeLa cell extracts of these lesions are significantly different when placed at G1, G2 or G3 in the duplex sequence (5′-CTCG1G2CG3CCATC-3′) containing the NarI mutational hot spot. Furthermore, the dG-C8-AAF adduct is a better substrate of NER than dG-C8-AF in all three NarI sequence contexts. The conformations of each of these adducts were investigated by Molecular dynamics (MD) simulation methods. In the base-displaced conformational family, the greater repair susceptibility of dG-C8-AAF in all sequences stems from steric hindrance effects of the acetyl group which significantly diminish the adduct-base stabilizing van der Waals stacking interactions relative to the dG-C8-AF case. Base sequence context effects for each adduct are caused by differences in helix untwisting and minor groove opening that are derived from the differences in stacking patterns. Overall, the greater NER efficiencies are correlated with greater extents of base sequence-dependent local untwisting and minor groove opening together with weaker stacking interactions.
    Full-text · Article · Aug 2012 · Nucleic Acids Research
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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.
    Full-text · Article · Jul 2011 · DNA repair
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