RNA duplex formation by oligodeoxynucleotides containing C-5 alkyne and C-5 thiazole substituted deoxyuridine analogs

Abstract

The binding affinity of methyl substituted C-5 propyne and C-5 thiazole ODNs for RNA was assessed by thermal denaturation analysis (Tm). The results indicate that increased size of the alkyne substituent lead to decreased affinity, but certain methyl substitutions on the thiazole lead to higher affinity complexes with RNA. The increased affinity of methylthiazole ODNs to RNA was dependent on the position of the methyl substituent with 5-methylthiazole ODN (2h) exhibiting the highest Tm. The 5-methylthiazole group likely increases hydrophobic interactions with adjacent base pairs in the canonical double helix.