Stacking and stability of RNA duplexes containing fluorobenzene and fluorobenzimidazole nucleosides.

Six different fluorobenzene or fluorobenzimidazole ribonucleosides and one abasic site were incorporated in oligoribonucleotides. Individual contributions of base stacking and solvation of the modified nucleosides could be determined. In fluorobenzene.fluorobenzimidazole-modified base pairs a duplex stabilizing force was found that points to a weak F...H hydrogen bond. The lipophilicity of the unprotected nucleosides were investigated by determination of 1-octanol water partition coefficients.