alpha -oligodeoxyribonucleotide N3' arrow right P5' phosphoramidates: Synthesis and duplex formation

• Published in: Nucleic acids research 1998-02, Vol.26 (4), p.1099-1106
• Main Authors: Pongracz, K, Gryaznov, S M
• Format: Article
• Language: English
• ISSN: 0305-1048

The synthesis and hybridization properties of novel nucleic acid analogs, alpha -anomeric oligodeoxyribonucleotide N3' arrow right P5' phosphoramidates, are described. The alpha -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 alpha -5'-O-DMT-3'-aminonucleosides were assembled into dimers and oligonucleotides on a solid support using the oxidative phosphorylation method. super(1)H NMR analysis of the alpha -N3' arrow right P5' phosphoramidate dimer structures indicates significant differences in the sugar puckering of these compounds relative to the beta -N3' arrow right P5' phosphoramidates and to the alpha -phosphodiester counterparts. Additionally, the ability of the alpha -oligonucleotide N3' arrow right P5' phosphoramidates to form duplexes was studied using thermal denaturation experiments. Thus the N3' arrow right P5' phosphoramidate decamer 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 mixed base decamer alpha -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 degree C, than for the duplexes formed by the isosequential beta -phosphoramidates in antiparallel and parallel orientations respectively. In contrast, the alpha -decaadenylic N3' arrow right P5' phosphoramidate formed duplexes with both RNA and DNA complementary strands with a stability similar to that of the corresponding beta -anomeric phosphoramidate. Moreover, the self-complementary oligonucleotide alpha -ATATATATAT did not form an alpha : alpha homoduplex. These results demonstrate the effects of 3'-aminonucleoside anomeric configuration on sugar puckering and consequently on stability of the duplexes.