Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA. Sequence-specific cationic stabilization of B form DNA

Abstract

Synchrotron radiation diffraction data for phage T2 CsDNA fibres have been used to determine the co-ordinates of the caesium ions in crystalline B form DNA. The R value is 0.16 for an optimized structure. The caesium ions are distributed equally between the narrow and wide grooves of B DNA and are located close to the dyad axes lying between the planes of adjacent base-pairs. On the wide-groove side the cations are separated from the nearest phosphate atoms by a hydration layer one to two water molecules thick. In the narrow groove the cations are directly co-ordinated to the base atoms and, for six out of ten possible DNA stacking types, form chelation complexes: O-2(Pyr)-Cs+-O-2(Pyr), O-2(Pyr)-Cs+-N-3(Pur) or N-3(Pur)-Cs+-N-3(Pur), which stabilize the B conformation. The steric properties of such complexes as estimated for different base sequences and for different ions are consistent with the structural behaviour of double-helical polynucleotides with different base sequences, as experimentally observed.