Research article summary (published 18 Oct 2009):

The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA.

Full Abstract

Oxidative damage to 5-methylcytosine in DNA, followed by deamination, yields thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, mispaired with deoxyguanosine. The structure of the 5R Tg.G mismatch pair has been refined using a combination of simulated annealing and isothermal molecular dynamics calculations restrained by NMR-derived distance restraints and torsion angle restraints in 5'-d(G(1)T(2)G(3)C(4)G(5)Tg(6)G(7)T(8)T(9)T(10)G(11)T(12))-3'.5'-d(A(13)C(14)A(15)A(16)A(17)C(18)G(19)C(20)G(21)C(22)A(23)C(24))-3'; Tg = 5R Tg. In this duplex the cis-5R,6S:trans-5R,6R equilibrium favors the cis-5R,6S epimer [Brown, K. L., Adams, T., Jasti, V. P., Basu, A. K., and Stone, M. P. (2008) J. Am. Chem. Soc. 130, 11701-11710]. The cis-5R,6S Tg lesion is in the wobble orientation such that Tg(6) O(2) is proximate to G(19) N1H and Tg(6) N3H is proximate to G(19) O(6). Both Tg(6) and the mismatched nucleotide G(19) remain stacked in the helix. The Tg(6) nucleotide shifts toward the major groove and stacks below the 5'-neighbor base G(5), while its complement G(19) stacks below the 5'-neighbor C(20). In the 3'-direction, stacking between Tg(6) and the G(7).C(18) base pair is disrupted. The solvent-accessible surface area of the Tg nucleotide increases as compared to the native Watson-Crick hydrogen-bonded T.A base pair. An increase in T(2) relaxation rates for the Tg(6) base protons is attributed to puckering of the Tg base, accompanied by increased disorder at the Tg.G mismatch pair. The axial vs equatorial conformation of the Tg(6) CH(3) group cannot be determined with certainty from the NMR data. The rMD trajectories suggest that in either the axial or equatorial conformations the cis-5R,6S Tg lesion does not form strong intrastrand hydrogen bonds with the imidazole N7 atom of the 3'-neighbor purine G(7). The wobble pairing and disorder of the Tg.G mismatch correlate with the reduced thermodynamic stability of the mismatch and likely modulate its recognition by DNA base excision repair systems.

Author information

Author/s: Brown, Kyle L (KL); Basu, Ashis K (AK); Stone, Michael P (MP);

Affiliation: Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA.

Grants: CA-55678 (Agency:NCI NIH HHS) ; ES-013324 (Agency:NIEHS NIH HHS)

Journal and publication information

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal: Biochemistry (Biochemistry), published in United States. (Language: eng)

Reference: 2009-Oct; vol 48 (issue 41) : pp 9722-33

Dates: Created 2009/10/13; Completed 2009/11/02;

PMID: 19772348, status: MEDLINE (last retrieval date: 11/2/2009, IMS Date: )

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

5-Methylcytosine - chemistry Base Pairing Chromatography, High Pressure Liquid - methods DNA - chemistry Deoxyguanosine - chemistry Kinetics

Magnetic Resonance Spectroscopy - methods Mass Spectrometry - methods Models, Molecular Oligodeoxyribonucleotides - chemistry; isolation & purification Protons Thymine - analogs & derivatives; chemistry

Associated Chemicals: Oligodeoxyribonucleotides (0) ; Protons (0) ; thymine glycol (2943-56-8) ; 5-Methylcytosine (554-01-8) ; Thymine (65-71-4) ; DNA (9007-49-2) ; Deoxyguanosine (961-07-9)

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