Effect of the Terminal Amino Group of a Linker Arm and Its Length at the C5 Position of a Pyrimidine Nucleoside on the Thermal Stability of DNA Duplexes

2′-Deoxyuridine derivatives bearing a substituent at the C5-position, which has a different chain length and a different functional group (methyl or amino), were synthesized and incorporated into oligodeoxyribonucleotides. The effect of the substituent groups in the major groove on the stability of the duplexes was investigated by UV melting experiments. It was found that the stabilization of these duplexes by a terminal amino group depended on the length of a linker arm.