Homopurine RP-stereodefined phosphorothioate analogs of DNA with hampered Watson–Crick base pairings form Hoogsteen paired parallel duplexes with (2′-OMe)-RNAs

Abstract

3′-O-(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of 5′-O-DMT-N⁶-methyl-deoxyadenosine and 5′-O-DMT-N²,N²-dimethyl-O⁶-diphenylcarbamoyl-deoxyguanosine (OTP-N^Y, N^Y = DMT-^m6dA or DMT-^m,m2dG^DPC) were synthesized, resolved onto pure P-diastereomers, and used in P-stereocontrolled synthesis of dinucleoside 3′,5,-phosphorothioates N^X_PST (N^X = ^m6dA or ^m,m2dG), in which the absolute configuration of the stereogenic phosphorus atom was established enzymatically. Diastereomerically pure OTP-N^Y and standard OTP-N (N = DMT-dA^Bz or DMT-dG^Bz,DPC) were used in the synthesis of chimeric R_P-stereodefined phosphorothioate oligomers ((R_P-PS)-DN(N^X)A) with hampered Watson–Crick base pairings. It was found that the ^m6dA units slightly reduce the thermodynamic stability of antiparallel duplexes formed with RNA and (2′-OMe)-RNA matrices, whereas ^m,m2dG units prevent their formation. The ^m6dA units stabilize (by up to 4.5 °C per modified unit) the parallel duplexes formed by (R_P-PS)-DN(N^X)A with Hoogsteen-paired (2′-OMe)-RNA templates compared to the analogous reference duplex containing only unmodified nucleobases. In contrast, the ^m,m2dG units destabilize such duplexes by up to 3 °C per modified unit. Both units prevent the formation of the corresponding parallel triplexes.