Vibrational mode assignments of the subunits involved in poly-riboinosinic acid helical structures : from hypoxanthine base to riboinosinic residue

Abstract

Ultraviolet resonance Raman spectra of hypoxanthine base as well as inosine, along with their deuterated species, have been collected in neutral aqueous solution (λexc = 257 and 281 nm) in the spectral region between 400 and 1800 cm−1. The observed vibrational modes have been assigned by a normal mode analysis which rests on previous work on the vibrational assignments of hypoxanthine nucleic base and furanose ring with various geometries. Normal mode analysis has been carried out on inosine by using three different nucleoside conformations, as determined from X-ray studies of molecular crystals. The most striking features of the present work are : i) the assignments of inosine vibrational modes are very different from those of the hypoxanthine base, and ii) : the best fit between measured and calculated vibrational wavenumbers and their isotopic shifts upon selective deuterations has been obtained for inosine structures containing an N-type sugar (C3′-endo) associated with a low-anti base. In addition, we have tested the reliability of this force field in the case of inosine residues involved in a canonical A-RNA helical structure, by comparing the calculated wavenumbers of the most characteristic vibrational modes with those observed in off- and on-resonance Raman spectra of poly(rI).