α-Oligodeoxyribonucleotide N3'→P5' phosphoramidates: Synthesis and duplex formation

Abstract

The synthesis and hybridization properties of novel nucleic acid analogs, α-anomeric oligodeoxyribonucleotide N3'→P5' phosphoramidates, are described. The α-3'-aminonucleoside building blocks used for oligonucleotide synthesis were synthesized from 3'-azido-3'-deoxythymidine or 3'-azido-2',3'-dideoxyuridine via acid catalyzed anomerization or transglycosylation reactions. The base-protected α-5'-O-DMT-3'-aminonucleosides were assembled into dimers and oligonucleotides on a solid support using the oxidative phosphorylation method. 1H NMR analysis of the α-N3'→P5' phosphoramidate dimer structures indicates significant differences in the sugar puckering of these compounds relative to the β-N3'→P5' phosphoramidates and to the α-phosphodiester counterparts. Additionally, the ability of the α-oligonucleotide N3'→P5' phosphoramidates to form duplexes was studied using thermal denaturation experiments. Thus the N3'→P5' phosphoramidate decamer containing only α-thymidine residues did not bind to poly(A) and exhibited lower duplex thermal stability with poly(dA) than that for the corresponding β-anomeric phosphoramidate counterpart. A mixed base decamer α-CTTCTTCCTT formed duplexes with the RNA and DNA complementary strands only in a parallel orientation. Melting temperatures of these complexes were significantly lower, by 34-47 or 15-25°C, than for the duplexes formed by the isosequential β-phosphoramidates in antiparallel and parallel orientations respectively. In contrast, the α-decaadenylic N3'→P5' phosphoramidate formed duplexes with both RNA and DNA complementary strands with a stability similar to that of the corresponding β-anomeric phosphoramidate. Moreover, the self-complementary oligonucleotide α-ATATATATAT did not form an α:α homoduplex. These results demonstrate the effects of 3'-aminonucleoside anomeric configuration on sugar puckering and consequently on stability of the duplexes.