G. J. Quigley

Molecular structure of a left-handed double helical DNA fragment at atomic resolution.

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.

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions. The molecule is also stabilized by considerable stacking of the planar purines and pyrimidines. This tertiary structure explains, in a simple and direct fashion, chemical modification studies of transfer RNA. Since most of the tertiary interactions involve nucleotides which are common to all transfer RNA s, it is likely that this three-dimensional structure provides a basic pattern of folding which may help to clarify the three-dimensional structure of all transfer RNAs.

Three-Dimensional Structure of Yeast Phenylalanine Transfer RNA: Folding of the Polynucleotide Chain

At 4 � resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 � apart. These peaks are probably associated with the phosphate groups, while lower levels of electron density between segments of adjacent polynucleotide chains are interpreted as arising from hydrogen-bonded purine-pyrimidine base pairs. It is possible to trace the entire polynucleotide chain with only two minor regions of ambiguity. The polynucleotide chain has a secondary structure consistent with the cloverleaf conformation; however, its folding is different from that proposed in any model. The molecule is made of two double-stranded helical regions oriented at right angles to each other in the shape of an L. One end of the L has the CCA acceptor; the anticodon loop is at the other end, and the dihydrouridine and TψC loops form the corner.

A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences.

The ease with which a particular DNA segment adopts the left‐handed Z‐conformation depends largely on the sequence and on the degree of negative supercoiling to which it is subjected. We describe a computer program (Z‐hunt) that is designed to search long sequences of naturally occurring DNA and retrieve those nucleotide combinations of up to 24 bp in length which show a strong propensity for Z‐DNA formation. Incorporated into Z‐hunt is a statistical mechanical model based on empirically determined energetic parameters for the B to Z transition accumulated to date. The Z‐forming potential of a sequence is assessed by ranking its behavior as a function of negative superhelicity relative to the behavior of similar sized randomly generated nucleotide sequences assembled from over 80,000 combinations. The program makes it possible to compare directly the Z‐forming potential of sequences with different base compositions and different sequence lengths. Using Z‐hunt, we have analyzed the DNA sequences of the bacteriophage phi X174, plasmid pBR322, the animal virus SV40 and the replicative form of the eukaryotic adenovirus‐2. The results are compared with those previously obtained by others from experiments designed to locate Z‐DNA forming regions in these sequences using probes which show specificity for the left‐handed DNA conformation.

G.T wobble base-pairing in Z-DNA at 1.0 Å atomic resolution: the crystal structure of d(CGCGTG)

The DNA oligomer d(CGCGTG) crystallizes as a Z‐DNA double helix containing two guanine‐thymine base pair mismatches of the wobble type. The crystal diffracts to 1 A resolution and the structure has been solved and refined. At this resolution, a large amount of information is revealed about the organization of the water molecules in the lattice generally and more specifically around the wobble base pairs. By comparing this structure with the analogous high resolution structure of d(CGCGCG) we can visualize the structural changes as well as the reorganization of the solvent molecules associated with wobble base pairing. There is only a small distortion of the Z‐DNA backbone resulting from introduction of the GT mismatched base pairs. The water molecules cluster around the wobble base pair taking up all of the hydrogen bonding capabilities of the bases due to wobble pairing. These bridging water molecules serve to stabilize the base‐base interaction and, thus, may be generally important for base mispairing either in DNA or in RNA molecules.

Interactions of Quinoxaline Antibiotic and DNA.: The Molecular Structure of a Triostin A—d(GCGTACGC) Complex

The crystal structure of a DNA octamer d(GCGTACGC) complexed to an antitumor antibiotic, triostin A, has been solved and refined to 2.2 A resolution by x-ray diffraction analysis. The antibiotic molecule acts as a true bis intercalator surrounding the d(CpG) sequence at either end of the unwound right-handed DNA double helix. As previously observed in the structure of triostin A-d(CGTACG) complex (A.H.-J. Wang, et. al., Science, 225, 1115-1121 (1984)), the alanine amino acid residues of the drug molecule form sequence-specific hydrogen bonds to guanines in the minor groove. The two central A.T base pairs are in Hoogsteen configuration with adenine in the syn conformation. In addition, the two terminal G.C base pairs flanking the quinoxaline rings are also held together by Hoogsteen base pairing. This is the first observation in an oligonucleotide of. Hoogsteen G.C base pairs where the cytosine is protonated. The principal functional components of a bis-intercalative compound are discussed.

Comparative studies of high resolution Z-DNA crystal structures Part 1: Common hydration patterns of alternating dC-dG

The water structure in three crystal forms of the left-handed Z-DNA hexamer [d(CGCGCG)]2 has been analyzed. Several common motifs have been found in the first hydration shells. On the convex surface, the major groove of the left-handed conformation, water molecules bridge the guanine O-6 keto groups at GpC steps. Cytosine N-4 nitrogens of opposite strands are hydrated by tandem water molecules. At the bottom of the minor groove, a string of water molecules connects the cytosine O-2 keto groups. Across the minor groove guanine N-2 nitrogens are bridged to phosphate oxygens of cytosine and guanine residues by one or two water molecules. In contrast to the very regular geometry of the water structure around the bases, the arrangement of water molecules between phosphate groups appears to be less ordered. However, there is a strong correlation between the interphosphate distances and the number of water molecules or ions which link the phosphate groups. In all three structures various ions, such as sodium and magnesium ions, as well as the protonated amino and imino groups of the polycation spermine displace and replace water molecules in the first hydration shell. Nevertheless, the analysis reveals that numerous first hydration shell water molecules in Z-DNA crystals can be regarded as part of the DNA structure. Their positions and thermal parameters are generally independent of changes in the local crystallographic environment.

X-ray crystallographic studies of polymorphic forms of yeast phenylalanine transfer RNA

Abstract Yeast phenylalanine transfer RNA has been found to crystallize in five different crystal systems involving eight different space groups. The X-ray diffraction characteristics of these forms are described. One of the orthorhombic forms yields a diffraction pattern with higher resolution than either the hexagonal, the cubic or the monoclinic forms. One region of this orthorhombic diffraction pattern is particularly sensitive to X-ray exposure and to changes in the concentration of various solutes. The diffraction pattern from the cubic crystal form extends to a resolution of 3 A, and there are a number of strong reflections in the 3 to 4 A region which suggest that double-helical segments of the tRNA molecules are oriented along the 4-fold axes. Some comments are made regarding the nature of the polymorphism in the transfer RNA crystals.

Structure of 11-deoxydaunomycin bound to DNA containing a phosphorothioate.

The anthracyclines form an important family of cancer chemotherapeutic agents with a strong dependence of clinical properties on minor differences in chemical structure. We describe the X-ray crystallographic solution of the three-dimensional structure of the anthracycline 11-deoxydaunomycin plus d(CGTsACG). In this complex, two drug molecules bind to each hexamer duplex. Both the drug and the DNA are covalently modified in this complex in contrast with the three previously reported DNA-anthracycline complexes. In the 11-deoxydaunomycin complex the 11 hydroxyl group is absent and a phosphate oxygen at the TpA step has been replaced by a sulfur atom leading to a phosphorothioate with absolute stereochemistry R. Surprisingly, removal of a hydroxyl group from the 11 position does not alter the relative orientation of the intercalated chromophore. However, it appears that the phosphorothioate modification influenced the crystallization and caused the 11-deoxydaunomycin-d(CGTsACG) complex to crystallize into a different lattice (space group P2) with different lattice contacts and packing forces than the non-phosphorothioated DNA-anthracycline complexes (space group P4(1)2(1)2). In the minor groove of the DNA, the unexpected position of the amino-sugar of 11-deoxydaunomycin supports the hypothesis that in solution the position of the amino sugar is dynamic.

Unit cell transformations in yeast phenylalanine transfer RNA crystals

Abstract The orthorhombic unit cell of crystalline yeast phenylalanine transfer RNA has dimensions a = 33 A , b = 56 A and c = 161 A . When the mother liquor dries partially, a series of transformations takes place in which the a and b axes change very little but the c axis decreases abruptly first to 128 A and then to 109 A. In a closely related orthorhombic cell in a different space group the c axis is 104 A. Although there is some loss in resolution in these smaller unit cells, the over-all distribution of scattering intensity does not change substantially. This suggests that the tRNA molecules can slide together along the c axis without a substantial change in internal structure.