400796-40-9Relevant academic research and scientific papers
A new method for the synthesis of oligodeoxyribonucleotides containing 4-N-alkoxycarbonyldeoxycytidine derivatives and their hybridization properties
Kobori, Akio,Miyata, Kenichi,Ushioda, Masatoshi,Seio, Kohji,Sekine, Mitsuo
, p. 476 - 485 (2002)
Oligodeoxyribonucleotides incorporating 4-N-alkoxycarbonyldeoxycytidine derivatives were synthesized on polystyrene-type ArgoPore resins having a new benzyloxy(diisopropyl)silyl linker, by use of ZnBr2 as the detritylating agent. The first 3′-terminal thymidine could be attached to the resin by successive in situ reactions of 5′-O-DMTr-thymidine with diisopropylsilanediyl ditriflate and an ArgoPore resin containing hydroxyl groups. The use of this new silanediyl-type linker allowed release of the DNA chain from the resin by treatment with TBAF under neutral conditions. The Tm experiments apparently showed that incorporation of 4-N-alkoxycarbonyldeoxycytidines into DNA strands resulted in higher hybridization affinity with the complementary DNA strands than that of 4-N-acyldeoxycytidines. In addition, comparable Tm studies using oligodeoxyribonucleotides incorporating acyl (RC(O)-) groups and alkoxyacyl (RO(CH2)nC(O)-) groups having the same chain length show that the latter tend to exhibit higher Tm values than the former. It turned out that 4-N-alkoxycarbonyldeoxycytidines can form base pairs not only with deoxyguanosine but also with deoxyadenosine. Based on the ab initio calculations of the hydrogen bond energies of the possible base pairs formed between 4-N-methoxycarbonyl-1-methylcytosine and 9-methyladenine and the NMR analysis of the base-pairs of 15N-labeled 4-N-alkoxycarbonyldeoxycytidines with deoxyadenosine derivatives, we conclude that the base pair involves two unique hydrogen bonds between the cytosyl 4-NH group and the adenyl N1 atom and between the O atom of the ester group and the adenyl 6-NH group.
