FT IR-VCD spectra of six octadeoxynucleotides

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

“…34 We have chosen the octamer structure as it was more convenient for the fragment selection and the CCT procedure than longer sequences and because the experimental VCD spectra of (dG-dC) 4 , (dG-dC) 20 , and poly(dG-dC) were essentially the same. 30,33,34 The main aim of this work was to verify if the CCT technique could reproduce the experimentally observed sign change of the VCD couplets for the two DNA helices with opposite handedness.…”

“…The computed spectra will be compared to the experimental results for the same set of octanucleotides measured earlier. 33 To highlight the effects of dynamical fluctuations and solvent influence, we restrain here to only two octamers with the largest difference in the base content, (CGCGCG CG)*(GCGCGCGC) octamer, abbreviated as CG, and (CGAATTCG)*(GCTTAAGC), abbreviated as CGAT.…”

“…24 First applications of the technique were mostly aimed at understanding the nature of nucleic acid VCD and establishing characteristic VCD signatures of different nucleic acid conformations, and were performed mainly by the groups of Keiderling in Chicago 6,[24][25][26][27][28][29] and Diem in New York. 14,18,19,[30][31][32] The group of Wieser in Calgary in 1995 expanded the use of VCD in nucleic acid field systematically investigating the effect of the base sequence variation on VCD spectra, 33 studying DNA and RNA interactions with metal ions 5,23,[34][35][36][37][38] and drugs, [39][40][41][42][43] and exploring atypical nucleic acid structures. 44 The pioneering work has been performed on home-built VCD instruments.…”

Intercalation of daunomycin into d(CG)4 oligomer duplex containing G·T mismatches by vibrational circular dichroism and infrared absorption spectroscopy

“…Its capabilities for structural elucidation of diverse DNA structures have been proven on several occasions by the pioneering work of the groups of T. Keiderling [22][23][24][25][26] and M. Diem, [27][28][29] and by results reported from our laboratory. [30][31][32] The typical VCD bands of DNA arise from vibrations involving the four DNA bases (1750-1450 cm À1 ) and the sugarphosphate backbone (1150-800 cm À1 ). The VCD features are structurally diagnostic and provide unique information about DNA structure and conformation.…”

“…The VCD couplets arising from PO 2 À vibrations are characteristic for the backbone structure, while those arising from the C-O stretching and sugar deformation modes can help distinguish between deoxyribose conformations. In addition to studying various DNA structures, VCD can be successfully applied to investigate nucleic acid interactions with various binding ligands such as intercalators, 30,31,33 minor groove binders and metal ions. 32 Due to its enhanced conformational sensitivity, VCD has been successfully applied to examine DNA interactions with the anticancer drug daunomycin.…”