Synthesis of a 1'-aminomethylthymidine and oligodeoxyribonucleotides with 1'-acylamidomethylthymidine residues.

Reported here is a 10-step synthesis of a phosphoramidite building block of 1'-aminomethylthymidine that starts from 2-deoxyribose. The framework of the branched aminonucleoside was elaborated from a known 1-cyano-1-bromo glycosyl donor, whose reaction with the silylated nucleobase furnished the 1'-cyanide, which was reduced to the desired aminomethylnucleoside. The N-allyloxycarbonyl (Alloc)-protected nucleoside was converted to a phosphoramidite building block and incorporated into the oligonucleotides 5'-GCAT*TATTAC-3', and 5'-GCAT*TAT*TAC-3', where T* denotes 1'-acylamidomethylthymidine residues. Removal of the Alloc protecting group and acylation with the residue of pyrene-1-yl-butanoic acid were achieved on support, using microwave irradiation to ensure full conversion. The UV-melting point of the duplex of the singly and doubly modified decamers with their fully complementary target sequence is 0.1-6.9 degrees C higher than that of the unmodified control duplex, depending on the salt concentration. This suggests that the aminomethyl linker may allow for the placing of a functional "payload" in the minor groove of DNA duplexes without disrupting the helix. Oligonucleotides thus endowed with functional modifications may become useful for biomedical applications.