Conformational geometry and vibrational frequencies of nucleic acid chains

Abstract Normal coordinate analysis of diethyl phosphate has been made, which predicts all observed Raman frequencies in the range 170–1300 cm −1 . The force constants from this calculation have been transferred to a vibrational calculation for a simplified model of the backbone of nucleic acids, which also involves the OPO 2 − O phosphate group and the C 5 ′C 4 ′C 3 ′linkage of the ribose. The coordinates of these atoms are those recently given by Arnott and Hukins, which place the ribose ring of B‐DNA in a C 3 ′‐ exo conformation. This simple polymer model appears to be able to describe adequately the frequency‐dependent changes observed in the Raman spectra arising from the backbone vibrations of nucleic acid in going from the B‐ to A‐form. The symmetric OPO diester stretch increases in frequency from about 787 cm −1 in the B‐form to 807 cm −1 in the A‐form. The increased frequency characteristic of the A‐form is due to the combining of the diester stretch with vibrations involving the C 5 ′, C 4 ′, and C 3 ′ nuclei. The frequency of the symmetric OPO diester stretch is shown to be very dependent on the conformation of the ribose ring, indicating that in polynucleotides the ribose ring takes on one of two rigid conformations: C 3 ′‐ endo for A‐form or C 3 ′‐ exo for B‐form and “disordered” polynucleotides. The calculation lends confirmation to the atomic coordinates of Arnott and Hukins since the use of other geometries with the same force constants failed to give results in agreement with experimental evidence. The calculations also demonstrate the lowering effect of hydration on the anionic PO stretching frequencies. Experimental results show that the 814‐cm −1 band observed in the spectra of 5′GMP gel arises from a different vibrational mode than that of the 814‐cm −1 band of A‐DNA.