Vibrational analysis of nucleic acids. III. Conformation-dependent Raman markers of the phosphodiester backbone modeled by dimethyl phosphate

Raman and Raman optical activity (ROA) analysis of RNA structural motifs

“…The introduction of a mismatched base pair is expected to disrupt the native A-type helix, leading to the decrease in intensity of this Raman band for the Mismatch RNA compared to that of the Hairpin RNA, and for the EMCV RNA compared to the Bulge RNA. A similar decrease in intensity is observed for the Raman band recorded at $1047 cm À1 , originating from P-O stretching [34], although the decrease in intensity for the EMCV RNA relative to the Bulge RNA is greater than for that observed for the Raman band at $813 cm À1 . The Raman band recorded at $1098 cm À1 , assigned to PO 2 À stretching [34] and as stated above used as an internal standard for intensity normalisation, shows a greater intensity in the spectrum of the Bulge RNA compared to that of the Hairpin and Mismatch RNA, with this increase due to the addition of the seven extra residues in the pyrimidine-rich bulge.…”

Vibrational Analysis of Phosphorothioate DNA: II. The POS Group in the Model Compound Dimethyl Phosphorothioate [(CH3O)2(POS)]-

“…In particular, the vibrational modes of the phosphodiester group have been shown to be sensitive to the conformation (A-, B-and Z-forms) of the nucleic acid backbone [6,7]. A number of experimental and theoretical studies on model compounds (for example, dimethyl phosphate anion, DMP) that mimic the DNA/RNA backbone have been reported [8][9][10][11][12][13]. Brown and Peticolas [14] have performed the normal coordinate analysis of the diethyl phosphate model compound to predict and compare the experimentally determined Raman modes of the C3' -endo and C3' -exo sugar puckers of A-and B-form DNA.…”

Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium

“…Vibrational spectroscopy has proved useful for the elucidation of the structural changes subsequent to the binding of metal cations to phosphate groups and has been widely applied in studies of nucleic acids [10] and lipid bilayers [11,12]. Experimental data obtained for metal-diethyl phosphate systems suggest that the presence of metal cations induces shifts of the most intense PO 2 Ϫ stretches observed in both infrared (IR) and Raman spectra [13].…”