From nucleic base to polynucleotide: A vibrational analysis of the repetitive subunits involved in poly(rl) strands

Abstract

AbstractUltraviolet resonance Raman spectra of inosine and its deuterated species (C8‐d, Nl‐d and C8‐, Nl‐deuterated derivatives) in aqueous solution have been collected (λexc = 257 and 281 nm) and reported in the spectral region between 400 and 1800 cm−1. The observed vibrational modes have been assigned using the Wilson GF method with an empirical harmonic valence force field and a non‐redundant set of internal co‐ordinates. This normal mode analysis is based on previous work on the vibrational assignments of the hypoxanthine nucleic base and the furanose ring with various geometries. Here the analysis has been carried out 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; (ii) the best fit between measured and calculated vibrational wavenumbers and their isotopic shifts upon selective deuteration has been obtained from inosine structures containing an N‐type sugar (C3′‐endo) associated with a low‐anti base. In addition, we have tested the reliability of the 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).