Synthesis and characteristics of modified DNA fragments containing thymidine glycol residues

Abstract

Chemical synthesis of a series of modified oligodeoxyribonucleotides containing one or two residues of thymidine glycol (5,6-dihydro-5,6-dihydroxythymidine), the main product of oxidative DNA damage, is described. The thermal stability of DNA duplexes containing thymidine glycol residues was studied using UV spectroscopy. Introduction of even one thymidine glycol residue into the duplex structure was shown to result in its significant destabilization. Data on the interaction of DNA methyltransferases and type II restriction endonucleases with DNA ligands containing oxidized thymine were obtained for the first time. Introduction of a thymidine glycol residue into the central degenerate position of the recognition site of restriction endonuclease SsoII was found to result in an increase in the initial hydrolysis rate of the modified duplex in comparison with that of the unmodified structure. The affinity of C5-cytosine methyltransferase SsoII for the DNA duplex bearing thymidine glycol was found to be twofold higher than for the unmodified substrate. However, such a modification of the DNA ligand prevents its methylation. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://www.maik.ru.

DNA Polymerases β and λ Bypass Thymine Glycol in Gapped DNA Structures

“…Complementary oligodeoxynucleotides were annealed in equimolar amounts by heating a water solution to 80 °C (for Tg-containing oligos) and to 95 °C (for native DNA substrates) for 10 min, followed by slow cooling to room temperature. The stability of Tg-containing oligos at this temperature was investigated previously (4). The oligonucleotide substrates used in the study are presented in the Table 1.…”

“…The synthesis of the 34-mer oligodeoxynucleotide containing thymidine glycol was performed as described ,, . The automatic oligonucleotide synthesis technique was applied to incorporate the thymidine glycol residue into a certain position of the oligonucleotide strand.…”

“…After the oligonucleotide synthesis and deprotection step, the purity of modified oligonucleotides was confirmed by reverse-phase high-performance liquid chromatography, polyacrylamide gel electrophoresis, and MALDI-TOF MS. Epimerization was not observed. Studies on the stability of Tg-containing oligonucleotides have been previously reported . Modified oligonucleotides were not degraded under the conditions used for their synthesis and purification.…”

“…Unlike normal DNA bases, Tg is nonplanar and induces strongly pronounced distortion in regular DNA structure. Moreover, it dramatically changes the thermodynamic properties of the DNA duplex , . Tg is a poor mutagenic lesion because it generally pairs with correct A .…”

Is Thymidine Glycol Containing DNA a Substrate of E. coli DNA Mismatch Repair System?

“…The oligonucleotides containing the thymidine glycol residue (5R, 6S-stereoisomer) in a specified position were prepared as described in [34] . The oligodeoxyribonucleotides (unmodified as well as containing Alexa-488 or Alexa-594 dyes) were provided by Eurogentec (Belgium).…”