Low‐Temperature conformation of Mg2+‐Poly(U) in D2O as revealed by IR and Raman Spectroscopy and by normal‐mode analysis treatment

Abstract

AbstractInfrared and Raman spectra of the Mg2+ salt of poly(U) in D2O were recorded in the 1600‐1800 cm−1 region and between 1 and 20C. The ir spectra showed a melting curve similar to the uv melting curves with a temperature of transition of about 6.5°C. This spectral change is assumed to be associated with the formation of the secondary structure of Mg2+‐poly(U) in D2O at this temperature. Three double‐helical and two triple‐helical structures were used as inputs to compute the normal modes of vibration. A double‐helical structure was found to give the best agreement with the observations. Knowledge of the C=0 eigenvectors, and of the expression for transition probability from quantum mechanics, was used to explain the so far unanswered question of H. T. Miles [(1964) Proc. Natl. Acad. Sci. USA 51, 1104–1109; (1980) Biomolecular Structure, Conformation, Function and Evolution, Pergamon, Oxford, pp. 251–264] as to why there is an increase in the ir vibrational wave number of a carbonyl band when that group is H‐bonded to another polynucleotide chain in a helix. Such considerations also explain why a predicted band at about 1648 cm−1 is not to be seen in the ir spectra but is present in the Raman spectra. The model incorporating the CO transition dipole‐dipole coupling interaction is able to explain also the observed higher intensity of the higher wave‐number ir band. The experimental results demonstrate that the complete picture of vibrational dynamics of Mg2+‐poly(U) in D2O is obtained only by looking simultaneously at ir and Raman spectra and not at only one of them. Weak ir bands were found to be as useful as the strong ones in understanding structure and vibrational dynamics. On the bases of our ir and Raman spectra, of the normal‐mode analyses, and of the literature data, it is concluded that Mg2+‐poly(U) in D2O is present in a double‐helical structure at temperatures below the temperature of transition, whereby the uracil residues are paired according to arrangement (a) (see Fig. 1). This structure is rodlike and arises by refolding of one poly(U) chain. The computations show that no normal mode is associated with a single CO group vibration; all CO group vibrations are heavily mixed motions of various CO groups.