Synthesis of fluorobenzene and benzimidazole nucleic-acid analogues and their influence on stability of RNA duplexes

Six different ribonucleoside phosphoramidites with fluorobenzenes or fluoro benzimidazoles as base analogues, one abasic site, and inosine were synthes ized and incorporated into oligoribonucleotides. The oligomers were investi gated by means of UV and CD spectroscopy to assess the contribution of H-bo nding, base stacking, and solvation to the stability of the RNA duplex. CD Spectra show that the incorporation of modified nucleosides does not lead t o changes in the structure of RNA. The T-m differences determined are based on changes in base stacking and solvation. Individual contributions of bas e stacking and solvation of the modified nucleosides could be determined. I n fluorobenzene . fluorobenzimidazole-modified base pairs, a duplex-stabili zing force was found that points to a weak F ... H H-bond.