Structure of hybrid backbone methylphosphonate DNA heteroduplexes: Effect of R and S stereochemistry

Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridization abilities are observed between the R_p and S_p diastereomers. Chirally pure methylphosphonate deoxyribooligonucleotides were synthesized, and the solution structures of duplexes formed between a single strand heptanucleotide methylphosphonate, d(Cp_MeCp_MeAp_MeAp _MeAp_MeCp_MeA), hybridized to a complementary octanucleotide, d(TpGpTpTpTpGpGpC), were studied by NMR spectroscopy. Stereochemistry at the methylphosphonate center for the heptanucleotide was either RpRpRpRpRpRp (R_p stereoisomer) or RpRpRpSpRpRp (S_p stereoisomer, although only one of the six methylphosphonate centers has the S_p stereochemistry). The results show that the methylphosphonate strands in the heteroduplexes exhibit increased dynamics relative to the DNA strand. Substitution of one chiral center from R_p to S_p has a profound effect on the hybridization ability of the methylphosphonate strand. Sugars in the phosphodiester strand exhibit C_2′ endo sugar puckering while the sugars in the methyl phosphonate strand exhibit an intermediate C_4′ endo puckering. Bases are well stacked on each other throughout the duplex. The hybridization of the methylphosphonate strand does not perturb the structure of the complementary DNA strand in the hetero duplexes. The sugar residue 5′ to the S_p chiral center shows A-form sugar puckering, with a C_3′-endo conformation. Minor groove width in the R_p stereoisomer is considerably wider, particularly at the R_p vs S_p site and is attributed to either steric interactions across the minor groove or poorer metal ion coordination within the minor groove.