Oligonucleotides Bearing a 5-Substituted Pyrimidine Nucleoside: Their Synthesis, Properties, and Application

5-Substituted 2'-deoxyuridine derivatives and 5-substituted arabinofuranosyluracil derivatives were synthesized from 2,2'-anhydro-5-methoxycarbonylmethyluridine. Introduction of the 5-substituted 2'-deoxyuridine analog into DNAs was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. Modified ODNs bearing the nucleoside analogs were prepared either by a pre-synthetic modification method or a post-synthetic modification method. Effect of the 5-substituent on thermal stability of duplexes was investigated by measuring the melting behaviors. The modified ODNs could induce RNase H activity and then would be useful as an antisense agent. 5- Substituted 2'-deoxyuridine analog triphosphates could serve as substrates of thermophilic family B DNA polymerases in a primer extension reaction or PCR, to give the corresponding modified ODNs. The 5-methoxycarbonylmethyl-2'- deoxyuridine residues incorporated into DNA by PCR could be used to the postsynthetic derivatization. The modified DNA prepared by PCR is useful for in vitro selection of the functionalized DNA.