P-stereocontrolled synthesis of oligo(nucleoside N3′→O5′ phosphoramidothioate)s – opportunities and limitations

3′-N-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5′-O-DMT-3′-amino-2′,3′-dideoxy-ribonucleosides ((N)OTP-N), that bear a 4,4-unsubstituted, 4,4-dimethyl, or 4,4-pentamethylene substituted oxathiaphospholane ring, were synthesized. Within these three series, (N)OTP-N differed by canonical nucleobases (i.e., Ade(Bz), Cyt(Bz), Gua(iBu), or Thy). The monomers were chromatographically separated into P-diastereomers, which were further used to prepare N(NPS)N′ dinucleotides (3), as well as short P-stereodefined oligo(deoxyribonucleoside N3′→O5′ phosphoramidothioate)s (NPS-) and chimeric NPS/PO- and NPS/PS-oligomers. The condensation reaction for (N)OTP-N monomers was found to be 5–6 times slower than the analogous OTP derivatives. When the 5′-end nucleoside of a growing oligomer adopts a C3′-endo conformation, a conformational ‘clash’ with the incoming (N)OTP-N monomer takes place, which is a main factor decreasing the repetitive yield of chain elongation. Although both isomers of N(NPS)N′ were digested by the HINT1 phosphoramidase enzyme, the isomers hydrolyzed at a faster rate were tentatively assigned the R(P) absolute configuration. This assignment is supported by X-ray analysis of the protected dinucleotide (DMT)dG(iBu)(NPSMe)T(OAc), which is P-stereoequivalent to the hydrolyzed faster P-diastereomer of dG(NPS)T.