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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 |
| ISSN: | 0305-1048 |
| Publisher: | Oxford University Press |
| Volume: | 21 |
| Number: | 3 |
| 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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