Vibrational analysis of nucleic acids .3. Conformation-dependent Raman markers of the phosphodiester backbone modeled by dimethyl phosphate

The dimethyl phosphate anion (CH3O)(2)PO2- is the simplest structural analogue of the phosphodiester backbone group in nucleic acids. Because of its simplicity, dimethyl phosphate is amenable to experimental and theoretical analyses of conformation-dependent vibrations of the diester (C-O-P-O-C) and dioxy (PO2-) linkages [Guan et al., Biophys. J., 66 (1994) 225; J. Phys. Chem., 99 (1995) 12054]. In the present work, we report the use of a previously developed generalized valence force field to determine the dependence of vibrational stretching frequencies of the dimethyl phosphate anion upon the conformational geometry of the phosphodiester moiety. Starting with the gauche-gauche C-O-P-O-C conformation (symmetry point group C-2), we have computed the frequency dependence of six diagnostic vibrational stretching modes upon stepwise rotation of each carbon linkage with respect to its phosphoester bond (O-P torsion). The computations show that both antisymmetric and symmetric phosphodiester (O-P-O) stretching vibrations are highly sensitive to C-O-P-O-C conformation, whereas the corresponding phosphodioxy (PO2-) stretching modes are relatively insensitive to conformation changes. The present calculations provide a theoretical basis for previously established empirical correlations which indicate that phosphodiester stretching modes are the definitive indicators of backbone conformation in the vibrational spectra of DNA and RNA.