Vibrational modes of A-DNA,B-DNA,and A-RNA backbones: An application of a green-function refinement procedure

Normal vibrational analysis was carried out for DNA molecules in both A and B conformations as well as for A-RNA. A simplified backbone model was examined and expanded to include the backbone phosphate-group and the ribose ring. We applied the new force-constant refinement procedure discussed in the preceeding paper [Van Zandt, L. L., Lu, K.-C. & Prohofsky, E. W. (1977) Biopolymers, 16 , 2481–90] to fit some observed frequencies in the Raman spectra for all three nucleic acids with the same set of force constants. The results indicate that the observed frequency shift can be attributed to the conformational change solely. We ignored the second-order differences in force constants for the different geometries. The agreement between the observed and calculated frequencies derived from the final refined set of force constants is good and apparently justifies this assumption. Two modes previously assigned to the symmetric diester O-P-O stretch and the symmetric dioxy O‥P‥O stretch are actually fitted. They are mainly backbone phosphate-group modes. The refined ribose-ring force-constants were transferred to the calculation of the vibrational spectrum of tetrahydrofuran. The overall agreement is again good. We discuss these calculations and the resulting normal modes. We also discuss the application of the Green-function refinement scheme and several strategies adopted to bias the convergence of the procedure.