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

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'-deoxyadenosine. 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 (chi) and the sugar pucker conformation.

Interpretation of DNA Vibration Modes: III - The Behaviour of the Sugar Pucker Vibration Modes as a Function of its Pseudorotation Parameters

“…As far as the DNA vibration mode analysis is concerned, we have performed recently a substantial study of the nucleosidicvibrations as a function of the glycosidic torsion angle (1,2). The calculated results could reproduce very well the Raman peak and infrared band shifts observed upon the right-to right-and right-to left-handed conformational transitions.…”

“…As far as the position of the 05' terminal is concerned, 3 privileged situations namely: gauche-gauche (y = 60°) gauche-trans (y = 180°) and trans-gauche (y = 300°) have been taken into consideration, where y represents the torsion angle defined by the four atoms C3'-C4'-C5'-05' (Figures 1 b and lc ). The F matrix elements for the sugar pucker is equivalent to that used in our previous investigations on the nucleosidic and nucleotidic vibrational analyses (1)(2)(3)12,13). It is mainly based on the reliable force field proposed by Eyster and Prohofsky in their valuable work on the furanose ring modes in pure and deuterated species (16).…”

“…The present investigation is based on a reliable simplified valence force field, tested previously on mononucleosides and mononucleotides (12,13), as well as on the nucleosidic residues involved in the double-helical chain constitution (1)(2)(3). Moreover, Downloaded by [Rutgers University] at 23: 11 10 April 2015 as an extension of our study, additional work has been carried out in order to assign the phosphate backbone contribution to the vibrational spectra as appearing in the DNA right-handed conformation (14).…”

Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

“…The D 2 O absorbance between 1300 and 1200 cm À1 obscures the PO 2 À asymmetric stretch, which normally occurs around 1220 cm À1 . Absorptions near 1076, 1055, 1022, 972, 945 and 895 cm À1 are ascribed to deoxyribose [30][31][32][33][34].…”

“…Tables 1 and 2 list the observed absorption and VCD peaks of the free deoxyoctanucleotides and their corresponding daunomycin complexes. Absorptions of DNA and individual components have been investigated previously [25][26][27][28][29][30][31][32][33][34][35]. Assignments based on ab initio derived harmonic force field calculations have been made for nucleobases, deoxyribose, phosphate, and for several deoxyoctanucleotides [36][37][38][39][40][41][42][43].…”