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Conformation of d (GGGATCCC) 2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling

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Item Type:Article
Title:Conformation of d (GGGATCCC) 2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling
Creators Name:Fabian, H., Hoelzer, W., Heinemann, U., Sklenar, H. and Welfle, H.
Abstract:In the crystal, d(GGGATCCC)2 forms an A-DNA double helix as known from a single crystal X-ray diffraction study. Accordingly, in the Raman spectra of crystals the A-family marker bands at 664, 705, 807 and 1101 cm-1 and the spectral characteristics in the region 1200 to 1500 cm-1 clearly demonstrate the A-form as the dominant conformation. Bands at 691, 850, and 1080 cm-1, however, indicate that a minor fraction of the octamer molecules in the crystal is in an unusual, still not unequivocally identified conformation possibly belonging to the B-family. In solution, the octamer is in B-like conformation as shown by the presence of B-DNA Raman marker bands at 685, 837, 1094 and 1421 cm-1. Molecular modelling techniques lead to three structures with slightly different B-form geometries as the lowest energies models when a sigmoidal dielectric function with the bulk dielectric constant epsilon = 78 and the value q = -0.5e for the effective phosphate charges was used in the calculations. An A-form structure bearing a strong resemblance to the experimentally determined crystal structure becomes the lowest energy model structure when the electrostatic parameters are changed to epsilon = 30 and q = -0.25e, respectively.
Keywords:Base Sequence, Computer Simulation, Crystallization, DNA, Molecular Models, Molecular Sequence Data, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Raman Spectrum Analysis, Solutions, X-Ray Diffraction
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:569-576
Date:11 February 1993
Official Publication:https://doi.org/10.1093/nar/21.3.569
PubMed:View item in PubMed

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