Interconversion of the cis-5R,6S- and trans-5R,6R-Thym ine Glycol Lesions in Duplex DNA

• Published in: Journal of the American Chemical Society Vol. 130; no. 35; pp. 11701 - 11710
• Main Authors: Brown, Kyle L, Adams, Travis, Jasti, Vijay P, Basu, Ashis K, Stone, Michael P
• Format: Journal Article
• Language: English
• Published: 03-09-2008
• ISSN: 0002-7863
• DOI: 10.1021/ja8016544

Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, is formed in DNA by the reaction of thymine with reactive oxygen species. The 5R Tg lesion was incorporated site-specifically into 5'-d(G super(1)T super(2)G super(3)C super(4)G5 Tg super(6) G super(7)T super(8)T super(9)T super(10)G super(11) T super(12))-3'; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5'-d(A super(13)C super(14)A super(15)A super(16) >A super(17)C super(18) A super(19) C super(20)G super(21)C super(22)A super(23)C super(24))-3', forming the Tg super(6) times A super(19) base pair, corresponding to the oxidative damage of thymine in DNA, or 5'-d(A super(13)C super(14)A super(15)A super(16)A super(17)C super(18) G super(19) C super(20)G super(21)C super(22)A super(23)C super(24))-3', forming the mismatched Tg super(6) times G super(19) base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 degree C, the equilibrium ratio of cis-5R,6S:trans-5R,6R epimers was 7:3 for the duplex containing the Tg super(6) times A super(19) base pair. In contrast, for the duplex containing the Tg super(6) times G super(19) base pair, the cis-5R,6S:trans-5R,6R equilibrium favored the cis-5R,6S epimer; the level of the trans-5R,6R epimer remained below the level of detection by NMR. The data suggested that Tg disrupted hydrogen bonding interactions, either when placed opposite to A super(19) or G super(19). Thermodynamic measurements indicated a 13 degree C reduction of T sub(m) regardless of whether Tg was placed opposite dG or dA in the complementary strand. Although both pairings increased the free energy of melting by 3 kcal/mol, the melting of the Tg times G pair was more enthalpically favored than was the melting of the Tg times A pair. The observation that the position of the equilibrium between the cis-5R,6S and trans-5R,6R thymine glycol epimers in duplex DNA was affected by the identity of the complementary base extends upon observations that this equilibrium modulates the base excision repair of Tg [ Ocampo-Hafalla M. T. ; Altamirano A. ; Basu A. K. ; Chan M. K. ; Ocampo J. E. ; Cummings A. Jr. ; Boorstein R. J. ; Cunningham R. P. ; Teebor G. W. DNA Repair (Amst)2006, 5, 444-454 ].