Solvent distribution in crystals of B- and Z-oligomers.
Two crystal structures of deoxyoligomers were refined to high resolution using the programs NUCLIN and NUCLSQ developed for refining the structure of yeast aspartic acid tRNA. The B form oligomer is the dodecamer d(5'OH-C-G-C-G-A-A-T-T-C-G-C-G-3'OH) solved by Dickerson and coworkers in 1981; the data used for the refinement are those deposited in the Brookhaven Data Bank. The crystal structure of the Z form hexamer d(5'OH-5BrC-G-5BrC-G-5BrC-G-3'OH) was resolved in Strasbourg. During the refinement each compound exhibits a different behaviour. Over sixty water molecules were located for each oligomer. The distribution of water molecules is typical of each helical form. Probably due to disorder, the hydration of the B form is not extensive. The minor groove of the B form presents the "spine of hydration" much discussed by Dickerson and coworkers. The Z form hexamer presents its most extended hydration network in the deep cavernous groove corresponding to the minor groove. Intermolecular contacts occur in both oligomers in the minor groove: in the B form through twisted guanine-guanine hydrogen bonding, and in the Z form through base-base stacking and the water network. The role and importance of solvent structure for DNA structure is discussed in the light of the results presented.
D003460:Crystallization; D004247:DNA; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D012997:Solvents
D009838:Oligodeoxyribonucleotides; D012997:Solvents; D004247:DNA