Oligonucleotides bearing an aliphatic amino group at the C5-position of deoxyuridine (ULNH2TCCCA, TULNH2CCCA, ULNH2CCACTT, where L = -CH2-, -CH2OCH2CH2- or -CH2NHCOCH2CH2-) have been synthesized. The photoactive (p-azidotetrafluorobenzamido, 2-nitro-5-azidobenzamido, or p-azidobenzamido), alkylating [4-[N-(2-chloroethyl)-N-methylamino]benzyl], or intercalating [N-(2-hydroxyethyl)phenazinium] groups were attached to the amino linker of oligonucleotides. The Tm values were determined for the duplexes formed by the above oligonucleotide derivatives. The alkylating group does not change the melting temperature of the corresponding duplex. The duplex stability is increased a little in the case of photoactive groups. The influence of the phenazinium residue on the duplex stability strongly depends on its location in the oligonucleotide. The spacer length between the C5 atom of deoxyuridine and the photoactive or phenazinium group was shown to influence the complementary duplex stability.