Oligonucleotides containing a new type of acyclic, achiral nucleoside analogue: 1-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]thymine

An achiral, acyclic nucleoside analogue has been incorporated once or twice in oligodeoxyribonucleotides by the phosphoramidite method, and conditions found which allow deprotection of the oligonucleotides containing a sensitive modified allylic unit. The binding affinity of the modified oligonucleotides towards complementary DNA and RNA was reduced compared to unmodified DNA (ΔTm −2 to −6.5 °C). An oligonucleotide with two modifications at the 3′-end showed considerable resistance towards cleavage with a 3′-exonuclease.