Molecular conformations and 8-CH exchange rates of purine ribo- and deoxyribonucleotides: investigation by Raman spectroscopy.

Abstract

AbstractThe rate of deuterium exchange of the 8‐CH group in a purine deoxyribonucleotide, is the same as the 8‐CH exchange rate in the corresponding purine ribonucleotide, with the exception of 5′‐nucleotides of guanine. The observed 20% slower rate of 8‐CH exchange in 5′‐dGMP versus 5′‐rGMP, over the temperature range 50–80°C, are attributable to differences in molecular conformation, including differences in ring puckering of the furanose substituents. Minor differences in 8‐CH exhange rates are observed between 5′‐and cyclic (3′:5′)‐deoxyribonucleotides of a given purine, which are similar to those observed previously between corresponding 5′‐ and cyclic ribonucleotides that have been attributed to the charge difference of their respective phosphate groups [Ferreira, S. A. & Thomas, G. J., Jr. (1981) J. Raman Spectrosc. 11, 508–514]. The coupling of guanine and furanose ring structures in the 5′‐nucleotides is also evident from the vibrational frequencies of the guanine ring, which are strongly dependent on the pucker of the attached furanose moiety. Raman difference spectroscopy clearly reveals the dependence of purine nucleotide spectra on sugar‐ring pucker. In the case of GMP, the guanine characteristic ring breathing mode near 600–700 cm−1 depends for its exact position and intensity on the proportion of C3′‐endo (668 cm−1) and C2′‐endo (682 cm−1) conformers in equilibrium with one another. The Raman intensity ratio I(668)/I(682) is proposed as a measure of the conformer ratio C3′‐endo/C2′‐endo in 5′‐dGMP with possible application also to nucleic acids. Among cyclic nucleotides, differences in spectra of deoxyribo‐ and ribo‐ forms also appear to be related to differences of molecular conformation.