Anita D. Gunjal

Sugar-thioacetamide backbone in oligodeoxyribonucleosides for specific recognition of nucleic acids.

The amide linkage being shorter than the natural phosphate linkage, an additional atom is introduced into oligodeoxyribonucleosides (ODNs) with sugar-thioacetamide backbone that show very good RNA recognition properties.

Spectroscopic and enzymatic characterization of 2′–5′ and 3′–5′ RNA hexamers AACCUU synthesised by phosphotriester approach in solution using 2′-t-butyldimethylsilyl protection☆

Abstract Comparative 1 H, 31 P NMR and CD spectroscopic results and enzymatic cleavage of single stranded RNA hexamers which have identical base sequence (AACCUU) but are regioisomeric at the internucleotide phosphate linkages (2′–t′, 3′–5′ and their covalent hybrid) are presented. The 31 P NMR results revealed significant differences in local phosphate backbone conformation among these isomers, with 2′–5′ isomer exhibiting maximum heterogeneity as compared to the 3′–5′ isomer, the analogous DNA hexamer and the covalent hybrid hexamer. In contrast to this, there are no appreciable differences in the overall base-base stacking as seen in the CD spectra of 2′–5′ and 3′–5′ isomers. All RNA hexamers were synthesised by solution phase phosphotriester chemistry with t-butyldimethylsilyl (TBDMS) as 2′-O-protecting group. The fully protected oligorobomers were deprotected in two steps: (i) saturated anhydrous MeOHNH 3 for phosphate and amino deprotections and (ii) TBAF for removal of 2′-O-TBDMS group. Use of sat. MeOHNH 3 (instead of aq. NH 3 ) prevents 2′–3′ internucleotide phosphate migrations, chain fragmentations and 5′-terminal modifications by neighbouring group participation (NGP). The retention of isomeric integrity and absence of 5′-terminal modification in the final products was established by digestion with several nucleases.