ALPHA-OLIGODEOXYRIBONUCLEOTIDE N3'-]P5' PHOSPHORAMIDATES - SYNTHESIS AND DUPLEX FORMATION

The synthesis and hybridization properties of novel nucleic acid analo gs, alpha-anomeric oligodeoxyribonucleotide N3'-->P5' phosphoramidates , are described, The alpha-3'-aminonucleoside building blocks used for oligonucleotide synthesis were synthesized from 3'-azido-3'-deoxythym idine or 3'-azido-2',3'-dideoxyuridine via acid catalyzed anomerizatio n or transglycosylation reactions, The base-protected alpha-5'-O-DMT-3 '-aminonucleosides were assembled into dimers and oligonucleotides on a solid support using the oxidative phosphorylation method, H-1 NMR an alysis of the alpha-N3'-->P5' phosphoramidate dimer structures indicat es significant differences in the sugar puckering of these compounds r elative to the beta-N3'-->P5' phosphoramidates and to the alpha-phosph odiester counterparts, Additionally, the ability of the alpha-oligonuc leotide N3'-->P5' phosphoramidates to form duplexes was studied using thermal denaturation experiments, Thus the N3'-->P5' phosphoramidate d ecamer containing only alpha-thymidine residues did not bind to poly(A ) and exhibited lower duplex thermal stability with poly(dA) than that for the corresponding beta-anomeric phosphoramidate counterpart, A mi xed base decamer alpha-CTTCTTCCTT formed duplexes with the RNA and DNA complementary strands only in a parallel orientation. Melting tempera tures of these complexes were significantly lower, by 34-47 or 15-25 d egrees C, than for the duplexes formed by the isosequential beta-phosp horamidates in antiparallel and parallel orientations respectively, In contrast, the alpha-decaadenylic N3'-->P5' phosphoramidate formed dup lexes with both RNA and DNA complementary strands with a stability sim ilar to that of the corresponding beta-anomeric phosphoramidate, Moreo ver, the self-complementary oligonucleotide alpha-ATATATATAT did not f orm an alpha:alpha homoduplex, These results demonstrate the effects o f 3'-aminonucleoside anomeric configuration on sugar puckering and con sequently on stability of the duplexes.