Synthesis and properties of oligonucleotides containing 5-substituted pyrimidine nucleoside

Abstract

Our recent study on the oligodeoxyribonucleotide (ODN) containing 5-substituted pyrimidine nucleosides is described. 5-Substituted 2′-deoxyuridine derivatives and 5-substituted arabinofuranosyluracil derivatives were synthesized from 2,2′-anhydro-5-methoxycarbonylmethyluridine, which was synthesized from arabinoaminooxazoline and dimethyl α-bromomethylfumarate. Modified ODNs bearing these nucleoside analogs were prepared chemically by pre-synthetic modification method or post-synthetic modification method. Effect of 5-substituent groups on DNA/DNA or DNA/RNA duplexes was investigated by measuring the melting behaviors. Some of these modified ODNs are expected as antisense ODNs since these could induce RNase H activity and impart stability against nuclease. Also, 5-substituted 2′-deoxyuridine analog triphosphates served as substrates of thermophilic family B DNA polymerases in a primer extension reaction or PCR, to give the modified ODNs. 5-Methoxycarbonylmethyl-2′-deoxyuridine residues incorporated into DNA by PCR could be used to post-synthetic derivatization. This finding is useful for in vitro selection of the functionalized DNA.