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

Abstract

A systematic study of the sugar pucker characteristic vibration modes as a function of its geometrical conformations, has been performed. The present investigation is based on the Wilson GF method and a non-redundant valence force field. The calculated results allow to assign the modes arising mainly from the sugar motions and present in quasi whole vibrational spectra related to the right or left-handed double-helices (i.e., 1050 cm-1, 960 cm-1 and 890 cm-1). Moreover, the conformation dependent modes as those at 860 cm-1 and around 810 cm-1 (A form) as well as the one located around 830 cm-1 (B form) are interpreted by the present investigation. The possibility of the interaction of the latter modes with the phosphate group motions along the DNA double-helical chains are also discussed.

Conformational analysis of the telomerase RNA pseudoknot hairpin by Raman spectroscopy

“…The second peak located at z812 cm À1 ( Fig. 2A) derives its intensity primarily from the phosphodiester group, n s (O-P-O) symmetric stretching O-P-O vibrational mode (Small et al 1972;Trulson et al 1987;Dohy et al 1989;Abdelkafi et al 1998). In addition, this mode is coupled with C39-endo ribose vibrations (Small et al 1972).…”

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

“…Worth noting is the appearance of a negative shoulder in VCD at $1110 cm À1 corresponding to a shoulder in absorption in the same position, which can be assigned to a vibration involving P- 34,46]. The absence of any major effects on both types of spectra in this region upon complex formation suggests only minor rearrangement of the sugar-phosphate backbone structure upon intercalation.…”

“…Of these, only the 972 cm À1 absorption has a corresponding VCD feature, which in CGCG may be likened to a negative band at the same position. The former group has contributions from displacements associated with the P-O 50 -C 50 -C 40 linkage [34], i.e., vibrational modes of the sugar-phosphate backbone. No distinctive assignments are available for the latter group, but it is plausible that these absorptions arise from non-canonical B structures.…”

“…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].…”