Ordered water structure around a B-DNA dodecamer. A quantitative study.

The crystal structure of the double-helical B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved and refined independently in three forms: (1) the parent sequence at room temperature; (2) the same sequence at 16 K; and (3) the 9-bromo variant C-G-C-G-A-A-T-TBrC-G-C-G at 7 degrees C in 60% (v/v) 2-methyl-2,4-pentanediol. The latter two structures show extensive hydration along the phosphate backbone, a feature that was invisible in the native structure because of high temperature factors (indicating thermal or static disorder) of the backbone atoms. Sixty-five solvent peaks are associated with the phosphate backbone, or an average of three per phosphate group. Nineteen other molecules form a first shell of hydration to base edge N and O atoms within the major groove, and 36 more are found in upper hydration layers. The latter tend to occur in strings or clusters spanning the major groove from one phosphate group to another. A single spermine molecule also spans the major groove. In the minor groove, the zig-zag spine of hydration that we believe to be principally responsible for stabilizing the B form of DNA is found in all three structures. Upper level hydration in the minor groove is relatively sparse, and consists mainly of strings of water molecules extending across the groove, with few contacts to the spine below. Sugar O-1' atoms are closely associated with water molecules, but these are chiefly molecules in the spine, so the association may reflect the geometry of the minor groove rather than any intrinsic attraction of O-1' atoms for hydration. The phosphate O-3' and O-5' atoms within the backbone chain are least hydrated of all, although no physical or steric impediment seems to exist that would deny access to these oxygen atoms by water molecules.

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60% methylpentanediol at 20 and at 7 degrees C. The first three forms show a 14-19 degrees bend in overall helix axis, but the fourth is straight and unbent. Detailed comparisons of the various forms have led to a better understanding of helix geometry and bending. Structural principles can be understood best if organized under four headings: 1) intrinsic geometry of the sugar rings, 2) stacking and relative motion of base pairs, 3) geometry of the connecting phosphate backbone, and 4) mechanics of bending in B-DNA. The observed bending is neither completely localized nor smooth and continuous, but an intermediate compromise that can be termed "annealed kinking."

The anatomy of A-, B-, and Z-DNA.

Recent advances in DNA synthesis methods have made it possible to carry out single-crystal x-ray analyses of double-stranded DNA molecules of predetermined sequence, with 4 to 12 base pairs. At least one example has been examined from each of the three known families of DNA helix: A, B, and Z. Each family has its own intrinsic restrictions on chain folding and structure. The observed solvent positions in these crystal structures have confirmed earlier fiber and solution measurements, and have led to proposals explaining the transitions from B to A and from B to Z helices. Prospects are improving for an understanding of the mode of bending of DNA in chromatin, and the way in which specific DNA sequences are recognized by drug molecules and repressor proteins.

The crystal structure of auramine perchlorate: correlation of the results with specular reflection spectroscopy.

The x-ray analysis of auramine perchlorate has been performed in order to establish the orientation of the cationic chromophoric group in the crystal for comparison with the orientation that was proposed on the basis of specular reflection studies. The compound crystallizes with two molecules per unit cell in space group P1 and cell parameters a = 8.86 A, b = 9.69 A, c = 11.27 A, alpha = 97 degrees 40', beta = 99 degrees 34', and gamma = 106 degrees 16'. The orientation of the chromophore is in good agreement with the crystal model. Other features of the structure are the hydrogen bonding scheme of the perchlorate ion, the highly distorted chromophoric group, and the planar dimethylamine substituents.