Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5 R -thymine glycol lesion and structure of the cis -(5 R ,6 S ) thymine glycol epimer in the 5′-GTgG-3′ sequence: destabilization of two base pairs at the lesion site

Abstract

The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of epimers paired opposite adenine in the 5′-GTgG-3′ sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) epimer Tg and A are inserted into the helix, remaining in the Watson–Crick alignment. The Tg N3H imine and A N6 amine protons undergo increased solvent exchange. Stacking between Tg and the 3′-neighbor G•C base pair is disrupted. The solvent accessible surface and T2 relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH3 group is favored; propeller twisting of the Tg•A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3′-neighbor guanine alleviate steric clash with the 5′-neighbor base pair. Tg also destabilizes the 5′-neighbor G•C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.

Thymidine Glycol: The Effect on DNA Structure and DNA Binding by Site-Specific Proteins

“…In addition, Tg causes destabilization of the 5'-neigboring nucleotide pair. An NMR structure of a duplex DNA containing Tg in the sequence 5'-ATgA-3' suggests that the Tg lesion is largely extrahelical [48], while in the sequence 5'-GTgG-3', Tg remains either stacked or partially stacked within the double helix [49]. According to our data, the extent of the alterations in the CD spectra induced by Tg depends on the number of the A/T pairs flanking the damaged site.…”

“…Thus, the Tg position in the duplex II can be considered partially extrahelical (Figure 1(c)), as it is observed by NMR in [48]. The Tg also destabilizes its 5'-neighboring G/C pair [49].…”

Structural Characterization of Viral Ortholog of Human DNA Glycosylase NEIL1 Bound to Thymine Glycol or 5-Hydroxyuracil-containing DNA

“…A local conformational perturbation may also be at play here. The presence of (5R,6S)-Tg within double-stranded DNA is known to hinder proper stacking of the 5Ј base, especially when that base is a purine (45,59,60). Furthermore, the nature of the base opposite the lesion was shown to modulate repair of Tg by human NEIL1 (49); Tg occupies the wobble position when mispaired with G (61) and is excised much more rapidly than Tg:A (49).…”

Interactions between cigarette smoking and XPC-PAT genetic polymorphism enhance bladder cancer risk

“…genetic polymorphism enhance bladder cancer risk Interestingly, emerging evidence suggests an additional role for XPC concerning removal of oxidative damage (15) and regulation of the cell cycle for DNA damage response (16). Mutations in this gene result in Xeroderma pigmentosum, a rare autosomal recessive disorder characterized by increased sensitivity to sunlight and the development of skin cancer at an early age (17).…”