title: Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate.
abstract: Raman and ir spectra are reported for diethyl phosphate [(CH3CH2O)2PO2-] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH313CH2O)2PO2-] and deuterium substituents on methyl and methylene carbons [(CH3CD2O)2PO2-, (CD3CH2O)2PO2-, (CD3CD2O)2PO2-]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O2-)-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group.
authors.affiliation: Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City 64110, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Guan
authors.forename: G J
authors.initials: GJ
authors.lastname: Thomas
mesh_terms: D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D009696:Nucleic Acids / Q000737:chemistry*; D010755:Organophosphates / Q000737:chemistry*; D014732:Vibration
chemical_list: D009696:Nucleic Acids; D010755:Organophosphates; C034789:diethyl phosphate; D004247:DNA