Sharanabasava B. Rajur

The synthesis of oligodeoxynucleotides containing 2-thiothymine and 5-methyl-4-pyrimidinone base analogues

Abstract A procedure is described for the Preparation of two thymidine analogues in which the O 2 -carbonyl is deleted (d H 2 T) or converted to an O 2 -thione (ds 2 T). The phosphoramidites of these nucleosides have been synthesized and used to incorporate the analogues site-specifically into oligodeoxynucleotide sequences.

Synthesis and properties of a hoechst-like minor-groove binding agent tethered to an oligodeoxynucleotide

A small Hoechst-like DNA groove-binding fluorophore carrying a terminal bromoacetimido linker has been synthesized. Individual diastereomeric oligodeoxynucleotide dodecamers containing a thiol-based linker attached to an internucleotide phosphoramidate within a sequence of dA-dT residues were each covalently labeled with the new fluorophore. One isomer of the DNA-fluorophore conjugate (Isomer B) hybridizes to the complementary single-stranded target DNA and the presence of the tethered fluorophore results in both increased duplex stability and an enhanced fluorescent signal, presumably due to the fluorophore binding in the dA-dT rich minor groove. Duplex stability is increased by 2-3 degrees C and the fluorescence quantum yield for the fluorophore increases four-fold. In contrast, the other diastereomer (Isomer A) exhibits reduced helix stability (approximately 2 degrees C) and only slight changes in fluorescence intensity upon hybridization.