Abstract
Here we report that the poor binding of methylphos-phonate oligodeoxynucleosides (MP-ODNs) to their nucleic acid targets can be improved by additional inversion of the anomeric configuration (from β to α) in the sugar moieties to give a new class of analogs, MP α-oligonucleosides. MP α-dT 12 and MP 5′ α-d(TCTTAA-CCCACA) 3′ were synthesized and their ability to form hybrids with complementary single stranded (ss)DNA and ssRNA, as well as with double stranded (ds)DNA, was evaluated. The thermal stability of hybrids formed with MP α-analogs was compared with the affinity of phosphodiester (PO) and phosphorothioate (PS) β-and α-oligomers for their targets. Non-ionic MP α-oligo-nucleosides bound to their complementary DNA and RNA strands more tightly than their homologues with natural β-anomeric configuration did. With DNA target, MP α-oligomers formed duplexes more stable than the corresponding natural PO β-oligomer did. MP α-hetero-polymer hybridized to RNA target better than PS β-oligonucleotide did but the hybrid was less stable (∆T m-0.5_C per mod.) than the hybrid formed with the natural PO β-oligomer. Only MP α-dT 12 bound to dsDNA target at low salt concentration (0.1 M NaCl).