Synthesis and hybridizing properties of P-stereodefined chimeric [PS]-{DNA:RNA) and [PS]-{DNA:(2 '-OMe)-RNA) oligomers

Oxathiaphospholane derivatives of 2'-OMe-ribonucleosides and 2'-O-TBDMS-ribonucleosides (N-M-OTP and N-T-OTP, respectively; nucleobase protected) were synthesized and separated into pure P-diastereomers. X-ray analysis showed the R-P absolute configuration of the phosphorus atom in the fast-eluting diastereomer of (T)A-OTP. The fast- and slow-eluting P-diastereomers of N-M-OTP and N-T-OTP were used in the solid-phase synthesis of phosphorothioate dinucleotides ((NPST)-N-M and NPST, respectively), which were subsequently hydrolyzed with R-P-selective phosphodiesterase svPDE and S-P-selective nuclease P1 to determine the absolute configuration of the phosphorus atoms. P-Stereodefined phosphorothioate ([PS]) 10-mer chimeric oligomers [PS]-{DNA:(2'-OMe)-RNA} and isosequential [PS]-{DNA:RNA} containing two N-M(PS) or N-PS units were synthesized. Melting experiments performed for their complexes with Watson-Crick paired DNA matrix showed that N-M(PS) or N-PS units decrease the thermal stability of the duplexes (Delta T-m = -0.5 divided by -5.5 degrees C per modification) regardless of the absolute configuration of the P-atoms. When the (2'-OMe)-RNA matrix was used an increase in T-m was noted in all cases (Delta T-m = +1 divided by +7 degrees C per modification). The changes in thermal stability of the duplexes formed by [PS]-chimeras with DNA and (2'-OMe)-RNA matrices do not correlate with the absolute configuration of the phosphorus atoms.