Synthesis and characterization of oligodeoxynucleotides containing the two 5R and 5S diastereomers of (5′S,6S )-5′,6-cyclo-5,6-dihydrothymidine; radiation-induced tandem lesions of thymidine

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The insertion of the (5′S,5R,6S) and (5′S,5S,6S) diastereomers of 5′,6-cyclo-5,6-dihydrothymidine into oligonucleotides is described. Due to the poor reactivity of the 5′-OH group of this modified nucleoside, the preparation of its 3′-phosphoramidite synthon 8 required the use of the non-standard 5′-levulinyl protecting group. It was successfully applied to the solid-phase synthesis of various oligonucleotides ranging from 3 to 22 bases long in combination with conventional dimethoxytrityl mononucleoside phosphoramidite chemistry. Characterization of these modified DNA fragments by enzymic digestions and mass spectroscopic analyses confirmed the designated sequences and compositions.