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

• Published in: Nucleic acids research 1993-01, Vol.21 (3), p.569-576
• Main Authors: Fabian, H, Hoelzer, W, Heinemann, U, Sklenar, H, Welfle, H
• Format: Article
• Language: English
• ISSN: 0305-1048

In the crystal, d(GGGATCCC) sub(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 super(-1) and the spectral characteristics in the region 1200 to 1500 cm super(-1) clearly demonstrate the A-form as the dominant conformation. Bands at 691, 850, and 1080 cm super(-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 super(-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.