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

Abstract

Ultraviolet resonance Raman spectra of inosine and its deuterated species (C&d, N1-d and C&, Nl-deuterated derivatives) in aqueous solution have been collected (k,,, = 257 and 281 nm) and reported in the spectral region between 400 and 1800 cm-'. 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-mti 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(r1).

A UV resonance Raman investigation of poly(rI): Evidence for cation-dependent structural perturbations

“…The 1322 cm Ϫ1 mode arising from coupled C 8 OH bending and C 8 AN 7 ring stretching motions experiences a similar enhancement pattern. 24 Other vibrational modes occurring above 1500 cm Ϫ1 result from coupled ring-stretching and extracyclic hydrogenbending motions and are distinct with both excitation wavelengths. 724 1996 239 110 78 47 1322 142 48 136 477 446 139 45 25 1469 75 56 297 1214 969 323 109 63 1550 4994 645 332 805 362 272 409 346 1592 1644 96 170 722 524 190 92 41 1684 1629 168 45 19 52 47 As for dGMP, a localized inosine C 6 AO stretching mode occurring at 1684 cm Ϫ1 is best observed with 210 nm excitation ( Figure 3).…”

“…Earlier uv resonance Raman studies investigating hypoxanthine and inosine only used 281 and 257 nm as excitation wavelengths, and therefore the relative enhancement of the important carbonyl and ribose modes at shorter excitation wavelengths was not observed. 24,25 Figure 2 depicts spectra of IMP obtained with 210 and 250 nm excitation. The most intense band in the 250 nm excited spectrum, the 1469 cm Ϫ1 mode, results from coupled C 2 AN 3 bond stretching and N 1 H bending motions 24 and is not enhanced with 210 nm excitation ( Figure 3).…”

“…24,25 Figure 2 depicts spectra of IMP obtained with 210 and 250 nm excitation. The most intense band in the 250 nm excited spectrum, the 1469 cm Ϫ1 mode, results from coupled C 2 AN 3 bond stretching and N 1 H bending motions 24 and is not enhanced with 210 nm excitation ( Figure 3). The 1322 cm Ϫ1 mode arising from coupled C 8 OH bending and C 8 AN 7 ring stretching motions experiences a similar enhancement pattern.…”

“…The mode has considerable N 1 H bending character and the frequency shift is related to the weakening of the H bonds with temperature. 24 The observed frequency downshift with increased temperature in the UVRR spectra of both the Na ϩ and K ϩ forms of poly(rI) is strongly indicative of quadruplex formation at 4°C. Upon thermal denaturation the expected weakening of the interbase H bond between the C 6 AO and the N 1 H groups is observed in the intensity ratio of the 1550/1590 cm Ϫ1 bands, which decreases from 1.1 to 0.68.…”

“…Upon thermal denaturation the expected weakening of the interbase H bond between the C 6 AO and the N 1 H groups is observed in the intensity ratio of the 1550/1590 cm Ϫ1 bands, which decreases from 1.1 to 0.68. The 1550 cm Ϫ1 mode arises from a composite of ring stretching vibrations centered on the pyrimidine ring including C 6 ON 1 stretching motions (15%), 24 and the loss of intensity reflects in part the weakening of H bonds between the C 6 AO and N 1 H with increasing temperature.…”