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

Abstract

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(G1T2G3C4G5Tg6G7T8T9T10G11T12)-3′; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5′-d(A13C14A15A16A17C18A19C20G21C22A23C24)-3′, forming the Tg6•A19 base pair, corresponding to the oxidative damage of thymine in DNA, or 5′-d(A13C14A15A16A17C18G19C20G21C22A23C24)-3′, forming the mismatched Tg6•G19 base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 °C, the equilibrium ratio of cis-5R,6S:trans-5R,6R epimers was 7:3 for the duplex containing the Tg6•A19 base pair. In contrast, for the duplex containing the Tg6•G19 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 A19 or G19. Thermodynamic measurements indicated a 13 °C reduction of Tm 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•G pair was more enthalpically favored than was the melting of the Tg•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-HafallaM. T.; AltamiranoA.; BasuA. K.; ChanM. K.; OcampoJ. E.; CummingsA.Jr.; BoorsteinR. J.; CunninghamR. P.; TeeborG. W.DNA Repair (Amst)2006, 5, 444−454].

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

“…The melting temperature (T m ) values of the Tg-containing DNA duplexes were 10˚C -11˚C lower in comparison with the corresponding duplexes without the Tg lesions ( Table 1). These results agree with the data reported in [10]. All the samples demonstrate a single reversible helix-coil transition.…”

“…Thymine glycol is known to remain in the Watson-Crick orientation with respect to the complementary adenine, although it disrupts hydrogen bonding interactions within the Tg/A pair [10]. The C5 methyl group at the 5R Tg is shown to protrude axially from the damaged pyrimidine ring and to hinder stacking with the 5'-adjacent base, especially with purine.…”

“…The C5 methyl group at the 5R Tg is shown to protrude axially from the damaged pyrimidine ring and to hinder stacking with the 5'-adjacent base, especially with purine. In the 3'-direction, stacking between Tg and the adjacent nucleotide pair is disrupted as well [10]. In addition, Tg causes destabilization of the 5'-neigboring nucleotide pair.…”

“…In medical studies, Tg can be used as a genetic biomarker of oxidative DNA damage along with other biomarkers such as 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG) [7]- [9]. There are four diastereomers of Tg because it contains two chiral carbon atoms, but Tg exists in solution as either the 5R cis-trans pair (5R,6S; 5R,6R) or the 5S cis-trans pair (5S,6R; 5S,6S) due to epimerization at the C6 position [10].…”

Self-assembling of dihydroxypropyl 5,6-dihydrothymine derivatives

“…Oxidation of the 5,6-double bond of thymidine generates two chiral centers at C(5) and C (6). The cis-5R, 6S form is generated as predominant product [12]. On the other hand, the reactivity of the pyrimidine ring has been considered as potential way for the intramolecular transformation of corresponding aliphatic nucleosides and for the synthesis new hetero bicyclic compounds [13].…”