The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.

Four different crystals of d(CpGpCpGpCpG) have been solved by x-ray diffraction analysis and all form similar left-handed double helical Z-DNA molecules in the crystal lattice. Two different conformations are observed for the phosphates in the GpC sequences, as the phosphates are found either facing the helical groove or rotated away from it. The latter conformation is often found when hydrated magnesium ions are complexed to a phosphate oxygen atom. These different conformations may be used when right-handed B-DNA joins left-handed Z-DNA. Atomic coordinates and torsion angles are presented for both types of Z-DNA.

The structure of regenerated cellulose is shown by x-ray diffraction to be comprised of an array of antiparallel chain molecules. The determination was based on the intensity data from rayon fibers and utilized rigid-body least-squares refinement techniques. The unit cell is monoclinic with space group P2(1) and dimensions a = 8.01 A, b = 9.04 A, c = 10.36 A (fiber axis), and gamma = 117.1 degrees. Models containing chains with the same sense (parallel) or alternating sense (antiparallel) were refined against the intensity data. The only acceptable model contains antiparallel chains. The -CH2OH groups of the corner chain are oriented near to the gt position while those of the center chain are near to the tg position. Both chains possess an O3-H-O5' intramolecular hydrogen bond, and the center chain also has an O2'-H-O6 intramolecular bond. Intermolecular hydrogen bonding occurs along the 020 planes (o6-h-o2 bonds for the corner chains and O6-H-O3 bonds for the center chains) and also along the 110 planes with a hydrogen bond between the O2-H of the corner chain and the O2' of the center chain. This center-corner chain hydrogen bonding is a major difference between the native and regenerated structures and may account for the stability of the latter form.

No abstract

ABST4RACTThe structure of the tetramer d(CpGpCpG) has been solved by x-ray analysis in two different crystal forms with and without spermine cations. The molecules crystallize in hexagonal unit cells and they form a left-handed double helix of Z-DNA similar to that previously reported for the hexamer d(Cp~pCpGpCpG). In the crystal lattice the molecules stack together to form a virtually continuous left-handed double helix in which every fourth phosphate group is missing. The stacking of bases upon each other is similar to that seen in the hexamer. However, the base pairs have a slightly different orientation in that the cytosine residues are slightly removed from the axis of the molecule compared to the position they occupy in the hexamer. The structures are similar in two crystal forms with and without spermine cations. Most of our earlier knowledge of the organization of the DNA double helix came from fiber x-ray diffraction studies. These studies had the advantage that diffraction data are relatively easy to obtain but they had the substantial disadvantage that the data are limited in resolution and consequently the finer structural details are lost. It has been apparent for at least 7 years that fragments of nucleic acid double helices can be seen in a single crystal diffraction analysis which, in principle, can lead to atomic resolution data (1, 2). Our (Table 1). In addition, a fiber diffraction pattern of poly(dG-dC) has yielded a pattern consistent with a polymeric version of Z-DNA (7). In all of the crystals we find some slight modifications in the basic geometry of the left-handed helix. These variations can be seen because of the relatively high resolution of the crystal diffraction data. This emphasizes the fact that there is configurational variability in the left-handed double helix, a variability which no doubt will eventually be found when right-handed double-helical DNA is studied by these same methods. A major biological feature of double-helical DNA involves its interactions with small molecules and ions as well as with proteins, and all of these are likely to induce variations in conformation. Many of these configurational variations are sequence-dependent and therefore reflect the informational content of these long molecules. EXPERIMENTAL METHODSThe ammonium salt of the deoxy tetramer d(CpGpCpG), designated d(CG)2, was prepared by modification of the recently developed phosphotriester method (8,9). Two different crystal forms were obtained by using the vapor diffusion method with 5% isopropanol as the precipitating agent. Both crystal forms were obtained from solutions containing 30 mM sodium cacodylate buffer (pH 7.0), 15 mM MgCl2, and 2 mM d(CG)2. One solution also contained 10 mM spermine tetrachloride. The crystals grew in the form of hexagonal rods measuring up to 0.5 X 0.5 X 2.0 mm. They were mounted in sealed glass capillaries with a droplet of mother liquor, and three-dimensional data were collected to a resolution of 1.3 A by using a Picker diffractometer, although the data beyo...

No abstract

The structure of isotactic poly(2‐vinylpyridine) has been determined from x‐ray fiber data utilizing rigid‐body least‐squares refinement techniques. The polymer exists as a threefold helix with three chains passing through a hexagonal unit cell having the dimensions a = b = 15.49 Å and c = 6.56 Å (fiber axis) and space group P31 or P32. The asymmetric unit consists of three monomeric units (one in each chain), resulting in three crystallographically independent chains in the unit cell. The results show that two of the chains are interlocked through pyridine ring interactions whereas the third chain is less restricted. A statistical structure is proposed in which any two chains in the unit cell can be interlocked, provided they have the same sense. Such a situation permits a completely statistical structure in which half the chains in any crystallite are oriented upward and the other half downward.

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3 A resolution by x-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The cleft then acts as an elongated pair of jaws that draws the DNA between them by charge interactions involving the phosphates with the interior lysines and arginines. The jaws then close on the DNA strand through small conformation changes and the rotation of aromatic side-chains into position to stack upon the purines and pyrimidines. Complexes of the gene 5 protein with a variety of oligodeoxynucleotides have been formed and crystallized for x-ray diffraction analysis. The crystallographic parameters of four different unit cells indicate that the fundamental unit of the complex is composed of six gene 5 protein dimers. We believe this aggregate has 622 point group symmetry and is a ring formed by end to end closure of a linear array of six dimers. From our results we have proposed a double helical model for the gene 5 protein-DNA complex in which the protein forms a spindle or core around which the DNA is spooled. 5.0-A x-ray diffraction data from one of the crystalline complexes is currently being analyzed by molecular replacement techniques to obtain what we believe will be the first direct visualization of a protein-deoxyribonucleic acid complex approaching atomic resolution.