Interpretation of DNA Vibration Modes II-The Adenosine and Thymidine Residues Involved in Oligonucleotides and Polynucleotides

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Abstract
Normal coordinate analysis of the adenosine and thymidine residues involved in the right- and left-handed conformations of oligonucleotides and polynucleotides has been performed. The valence force field, employed in this work, allowed recently to reproduce the vibrational spectra of 2′-deoxythymidine and 2′-deoxyadcnosine. The calculated wavenumbers based on a non-redundant set of internal coordinates have been compared to the Raman and infrared peak positions arising from A, B, C, D and Z conformations, in the 1550-1250 cm−1 and 800–600 cm−1 spectral regions: i.e. characteristic of adenosine and thymidine residues. Moreover, a systematic study has been performed on the evolution of the vibrational wavenumbers as a function of the glycosidic angle (χ) and the sugar pucker conformation.