Synthesis and thermodynamic studies of oligonucleotides containing the two isomers of thymine glycol

Thymine glycol is a major type of base damage, which is formed in DNA by reactive oxygen species. I describe the synthesis of oligonucleotides containing the 5S isomer of thymine glycol, which was not obtained by the oxidation of the oligonucleotides. Before the 5S isomer was synthesized, a building block without the protection of the tertiary hydroxy function at the C5 position of thymine glycol was tested by the use of the previously reported 5R isomer. In the presence of imidazole, migration of the silyl group between the C5 and C6 positions was observed, while the result of the oligonucleotide synthesis was identical to the case of the fully protected building block. Therefore, oligonucleotides containing the (5S)-thymine glycol were synthesized with the disilylated building block. In contrast to the 5R derivative, two products were detected in the HPLC analysis of the crude mixture after deprotection. Analysis by matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry revealed that the larger peak was the desired oligonucleotide, and it was found that the by-product was completely degraded by a short treatment with ammonium hydroxide at room temperature. I also report the application of oligonucleotides containing each isomer of thymine glycol to thermodynamic analyses of base-pair formation. The thermodynamic parameters obtained for the duplexes containing either the (5R)- or (5S)-thymine glycol indicated that the thymine glycol cannot form a base-pair with any nucleobase, regardless of the configuration at the C5 position.