NMR Structures of Damaged DNA

Lukin, Mark; Santos, Carlos de los

doi:10.1021/cr0404646

Cited by 152 publications

(107 citation statements)

References 542 publications

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“…Because the bent conformation is established by only two interactions, with Arg294 and Thr239, the structure supports the hypothesis that Rad14 binds to DNA structures that are easily bendable or which already adopt a bent conformation before Rad14 binding. In this respect, our structures also explain the observed binding of XPA/Rad14 to DNA with bulges (34) because such DNA structures are also kinked (44). The structures furthermore explain the observed cooperativity of the Rad14/XPA binding event that is also visible in our gel shift experiments (Fig.…”

Section: Dna Bending and The Lesion Recognition Motifsupporting

confidence: 78%

“…CPD lesions, on the other hand, are not recognized by Rad14, likely, because these lesions are less efficiently accommodated in a sharply kinked structure. Indeed, it is known that CPD lesions hardly influence the duplex structure and its stability (44). More importantly, however, is the fact that the stiff four-membered ring cyclobutane structure of the CPD lesion points into the major groove, which might block bending into this groove.…”

Section: Discussionmentioning

confidence: 99%

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Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

Koch

Kuper

Gasteiger

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Nucleotide excision repair (NER) is responsible for the removal of a large variety of structurally diverse DNA lesions. Mutations of the involved proteins cause the xeroderma pigmentosum (XP) cancer predisposition syndrome. Although the general mechanism of the NER process is well studied, the function of the XPA protein, which is of central importance for successful NER, has remained enigmatic. It is known, that XPA binds kinked DNA structures and that it interacts also with DNA duplexes containing certain lesions, but the mechanism of interactions is unknown. Here we present two crystal structures of the DNA binding domain (DBD) of the yeast XPA homolog Rad14 bound to DNA with either a cisplatin lesion (1,2-GG) or an acetylaminofluorene adduct (AAF-dG). In the structures, we see that two Rad14 molecules bind to the duplex, which induces DNA melting of the duplex remote from the lesion. Each monomer interrogates the duplex with a β-hairpin, which creates a 13mer duplex recognition motif additionally characterized by a sharp 70°DNA kink at the position of the lesion. Although the 1,2-GG lesion stabilizes the kink due to the covalent fixation of the crosslinked dG bases at a 90°angle, the AAF-dG fully intercalates into the duplex to stabilize the kinked structure.

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Section: Dna Bending and The Lesion Recognition Motifsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

Koch

Kuper

Gasteiger

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…[13][14][15][16] NMR solution studies of bulky carcinogen-DNA adducts have provided considerable insights into adduct conformations. 17,18 An intriguing finding is the importance of base sequence context in governing the conformations of such DNA adducts. Indeed, equilibria between different adduct conformations can be governed by the sequences of adjacent base pairs, and even next nearest neighbors can influence the balance of populations in different conformers.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair

Cai

Patel

Geacintov

et al. 2007

Journal of Molecular Biology

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The nucleotide excision repair (NER) machinery excises a variety of bulky DNA lesions, but with varying efficiencies. The structural features of the DNA lesions that govern these differences are not well understood. An intriguing model system for studying structure-function relationships in NER is the major adduct derived from the reaction of the highly tumorigenic metabolite of benzo [a]pyrene, (+)-anti-benzo[a]pyrene diol epoxide, with the exocyclic amino group of guanine ((+)-trans-anti-[BP]-N 2 -dG, or G*). The rates of incision of the stereochemically identical lesions catalyzed by the prokaryotic UvrABC system was shown to be greater by a factor of 2.3±0.3 in the TG*T than in the CG*C sequence context [Biochemistry 46 (2007) 7006-7015]. Here we employ molecular dynamics simulations to elucidate the origin of the greater excision efficiency in the TG*T case and, more broadly, to delineate structural parameters that enhance NER. Our results show that the BP aromatic ring system is 5′-directed along the modified strand in the B-DNA minor groove in both sequence contexts. However, the TG*T modified duplex is much more dynamically flexible, featuring more perturbed and mobile Watson-Crick hydrogen bonding adjacent to the lesion, a greater impairment in stacking interactions, more dynamic local roll/ bending, and more minor groove flexibility. These characteristics explain a number of experimental observations concerning the (+)-trans-anti-[BP]-N 2 -dG adduct in double-stranded DNA with the TG*T sequence context: its conformational heterogeneity in NMR solution studies, its highly flexible bend, and its lower thermal stability. By contrast, the CG*C modified duplex is characterized by a single BP conformation and a rigid bend. While current recognition models of bulky lesions by NER factors have stressed the importance of impaired Watson-Crick pairing/ stacking and bending, our results highlight the likelihood of an important role for the local dynamics in the vicinity of the lesion.

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“…FAFmodified DNA duplexes equilibrate between S and B conformations, and S/B population ratios are modulated significantly by the 3′-flanking sequence (G > A > C > T). 1 H NMR and crystallographic studies have provided detailed atomic resolution views of bulky DNA adducts (2,3). However, they are not well-suited for studying multiple conformations in dynamic equilibriums, as is the case for AF.…”

Section: Adduct [N-(2′-deoxyguanosin-8-yl)-2-aminofluorene] (mentioning

confidence: 99%

“…Although the mechanisms of mutagenesis have been studied extensively, the conformational aspects underlying replication and repair efficiencies are not well-understood (3)(4)(5). A case in point is the strong hepatocarcinogen N-acetyl-2-aminofluorene, which reacts with DNA to produce two major C8-substituted dG adducts in vivo: an aminofluorene (AF) 1 Figure 1A) and an acetylaminofluorene (AAF) adduct [N-(2′-deoxyguanosin-8-yl)-2-acetylaminofluorene] (6).…”

Section: Introductionmentioning

confidence: 99%

Fluorescence Probing of Aminofluorene-Induced Conformational Heterogeneity in DNA Duplexes

Jain

Reshetnyak²,

Gao³

et al. 2008

Chem. Res. Toxicol.

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Fluorescence spectroscopy was used to study carcinogen-induced conformational heterogeneity in DNA duplexes. The fluorophore 2-aminopurine (AP) was incorporated adjacent (5′) to the lesion (G*) in eight different DNA duplexes [d(5′-CTTCTPG*NCCTC-3′):d(5′-GAGGNXTAGAAG-3′), G* = FAF adduct, P = AP, N = G, A, C, T, and X = C, A] modified by FAF [N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene], a fluorine-tagged model DNA adduct derived from the potent carcinogen 2-aminofluorene. Steady-state measurements showed that fluorescence intensity and Stern-Volmer constants (K sv ) derived from acrylamide quenching experiments decreased for all carcinogen-modified duplexes relative to the controls, which suggests greater AP stacking in the duplex upon adduct formation. Conformation-specific stacking of AP with the neighboring adduct was evidenced by a sequence-dependent variation in fluorescence intensity, position of emission maximum, degree of emission quenching by acrylamide, and temperature-dependent spectral changes. The magnitude of stacking was in the order of FAF residue in base-displaced stacked (S) > minor groove wedged (W) > major groove B type (B). This work represents a novel utility of AP in probing adduct-induced conformational heterogeneities in DNA duplexes.

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NMR Structures of Damaged DNA

Cited by 152 publications

References 542 publications

Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair

Fluorescence Probing of Aminofluorene-Induced Conformational Heterogeneity in DNA Duplexes

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