Molecular structure of (m5 dC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA

The hexamer (m5 dC-dG)3 has been synthesized and its three-dimensional structure determined by a single crystal X-ray diffraction analysis. The structure has been refined to a final R value of 15.6% at 1.3 A resolution. The molecule forms a left-handed Z-DNA helix which is similar to the unmethylated Z-DNA structure. The presence of the methyl group has resulted in slight changes in the twist angle between successive base pairs and modification of some of the interatomic contacts. Methylation of cytosine in the C5 position is associated with a relative destabilization of the B-DNA structure and a stabilization through hydrophobic bonding of the Z-DNA structure.

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA

The deoxynucleotide fragment d(GpGpCpCpGpGpCpC) was synthesized and crystallized, and its three-dimensional structure was determined by x-ray diffraction techniques to a resolution of 2.25 A. The molecule forms a right-handed double helix in which the two base pairs at either end of the molecule are in the conventional A-DNA conformation, while the central four base pairs have a modified form in which alternate residues have sugar conformations that are closer to those in B-DNA than in A-DNA. The molecules have an intermolecular contact in which the planar terminal guanine . cytosine base pair lies on the flat minor groove surface of the A-DNA helix.

The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions

The laser-Raman spectra of crystalline d(CpGpCpGpCpG) and of aqueous poly(dG-dC).poly(dG-dC) in high salt (4M NaCl) and low salt (0.1M NaCl) solutions have been measured and compared. The spectra of the crystal and the high-salt solution show a striking congruence, which indicates clearly that the high-salt form of the aqueous polymer has the left-handed Z-DNA structure of the crystalline oligomer. These two spectra differ substantially from that of the low-salt form of the polymer, which has been found previously to have spectral characteristics of the B-form of DNA. The high salt spectrum shows a unique line due to guanine residues at 625 cm-1 which should be useful for qualitative and possibly quantitative assessment of the amount of Z-structure present in a sample of DNA.

Crystallographic studies of snake venom proteins from Taiwan cobra (Naja nana atra). Cardiotoxin-analogue III and phospholipase A2

Orthorhombic crystals of cardiotoxin-analogue III from Taiwan cobra have been grown from 2-methyl-2,4-pentanediol solution. The space group is P222 with 2 molecules/asymmetric unit. Several different crystal forms of phospholipase A2 from Taiwan cobra have been produced with or without Ca2+ ion. One of them, grown from 30 mM sodium cacodylate buffer (pH 6 to 7) and 30% 2-methyl-2,4-pentanediol with 20 mg/ml of protein, diffracts well to 2 A resolution. It crystallizes in space group P3112 or P3212 with 2 molecules/asymmetric unit, but it can be related to a quasi-cubic space group P213.

Molecular structure of an anticancer drug-DNA complex: daunomycin plus d(CpGpTpApCpG)

The structure of the crystalline daunomycin-d(CpGpTpApCpG) complex has been solved by x-ray diffraction analysis. The DNA forms a six-base-pair right-handed double helix with two daunomycin molecules intercalated in the d(CpG) sequences. The daunomycin aglycone chromophore is oriented at right angles to the long dimension of the DNA base pairs and the cyclohexene ring rests in the minor groove. Substituents on this ring have hydrogen bonding interactions to the base pairs above and below the intercalation site. These appear to be specific for anthracycline antibiotics. The amino sugar lies in the minor groove of the double helix without bonding to the DNA. The DNA double helix is distorted in a novel manner in accommodating the drug.

Biochemical and structural studies of the tetragonal crystalline modification of the Escherichia coli elongation factor Tu

The tetragonal crystalline form of the trypsin-treated Escherichia coli protein elongation factor Tu has been analyzed by biochemical and x-ray crystallographic techniques. The crystals contain two tightly associated polypeptide fragments of molecular weight 36,000 and 6,500 which represent 97% of the native enzyme. The crystals do not contain a short internal polypeptide fragment of 14 amino acids which dissociates from the native enzyme following mild trypsin digestion. The short fragment has been implicated in the aminoacyl-tRNA binding function and its location has been determined. The structure of the modified enzyme in the P4(3)2(1)2 crystal form has been determined to 5 A resolution by x-ray diffraction methods. The protein consists of two domains: the larger domain exhibits considerable alpha helical characteristics and the smaller domain has no identifiable secondary structural features. The relationship between the double domain structure of the enzyme and its biochemical properties is discussed.

The tetramer d(CpGpCpG) crystallizes as a left-handed double helix

The 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(CpGpCpGpCpG). 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.

X-ray diffraction studies on crystalline complexes of the gene 5 DNA-unwinding protein with deoxyoligonucleotides

Complexes of the gene 5 protein with a variety of oligodeoxynucleotides, ranging in length from two to eight and having several different sequences, have been formed and crystallized for x-ray diffraction analysis. The crystallographic parameters of four different unit cells, all of which are based on hexagonal packing arrangements, indicate that the fundamental unit of the complex is composed of 12 gene 5 monomers.

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.

Atomic resolution analysis of a 2:1 complex of CpG and acridine orange

Cytidylyl-3', 5'-guanosine and acridine orange crystallize in a highly-ordered triclinic lattice which diffracts X-rays to 0.85 angstrom resolution. The crystal structure has been solved and refined to a residual factor of 9.5%. The two dinucleoside phosphate molecules form an antiparallel double helix with the acridine orange intercalated between them. The two base pairs of the double helical fragment have a twist angle of 10 degrees and it is found to have a C3' endo-(3', 5')-C2' endo mixed sugar puckering along the nucleotide backbone as has been observed for other simple intercalator complexes. Twenty-five water molecules have been located in the lattice together with a sodium ion. The intercalator double helical fragments form sheets which are held together by van der Waals interactions in one direction and hydrogen bonding interactions in the other. The crystal lattice contains aqueous channels in which sixteen water molecules are hydrogen bonded to the nucleotide, none to the intercalator, five water molecules are coordinated about the sodium ion and four water molecules bind solely to other water molecules. The bases in the base pairs have a dihedral angle of 7 to 8 degrees between them.

Preliminary molecular replacement results for a crystalline gene 4 protein-deoxyoligonucleotide complex

Complexes of the gene 5 protein from bacteriophage fd with a variety of oligodeoxynucleotides, ranging in length from two to eight and comprised of several different sequences, have been formed and crystallized for X-ray diffraction analysis. The crystallographic parameters of four different unit cells, all of which are based on hexagonal packing arrangements, 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-helix model for the gene 5 protein-DNA complex in which the protein forms a spindle or core around which the DNA is spooled. Currently 5.0-A X-ray diffraction data from one of the crystalline complexes is being analyzed by molecular replacement techniques to obtain a direct image of the protein-nucleic acid complex.

Molecular structure of a double helical DNA fragment intercalator complex between deoxy CpG and a terpyridine platinum compound

The crystal structure of a complex containing deoxy CpG and a terpyridine platinum compound (TPH) shows a DNA double helical fragment with TPH intercalated between two Watson-Crick GC base pairs. The DNA unwinding angle is 23 degrees and the pucker of the deoxyribose rings differ at the 3' and 5' ends.

Sterol synthesis. Chemical synthesis, structure determination and metabolism of 14 alpha-methyl-5 alpha-cholest-7-en-3 beta, 15 beta-diol and 14 alpha-methyl-5 alpha-cholest-7-en-3 beta, 15 alpha-diol

14alpha-Methyl-5alpha-cholest-7-en-3beta,15beta-diol and 14alpha-methyl-5alpha-cholest-7-en-3beta,15alpha-diol have been prepared by chemical synthesis. Unequivocal establishment of these structures was based upon X-ray crystallographic analysis of 3beta-p-bromobenzoyloxy-14alpha-methyl-5alpha-cholest-7-en-15beta-ol and was supported by other spectroscopic data. Spectroscopic data were presented for the following compounds prepared in this study: 3beta-benzoyloxy-5alpha-cholest-8(14)-en-15-one, 3beta-benzoyloxy-14alpha-methyl-5alpha-cholest-7-en-15-one, 3beta-benzoyloxy-14alpha-methyl-5alpha-cholest-7-en-15beta-ol, 14alpha-methyl-5alpha-cholest-7-en-3beta, 15beta-diol, 14alpha-methyl-5alpha-cholest-7-en-3beta, 15alpha-cholest-7-en-15beta-diol, 14alpha-methyl-5alpha-cholest-7-en-3beta, 15alpha-diol, 3beta, 15alpha-bis-benzoyloxy-14alpha-methyl-5alpha-cholest-7-ene, 3beta-p-bromobenzoyloxy-14alpha-methyl-5alpha-cholest-7-en-15beta-ol and 3beta, 15beta-bis-p-bromobenzoyloxy-14alpha-methyl-5alpha-cholest-7-ene. Studies of the metabolism of [16-3H]-14alpha-methyl-5alpha-cholest-7-en-3beta, 15beta-diol and [16-3H]-14 alpha-methyl-5 alpha-cholest-7-en-3beta, 15alpha-diol in liver homogenates of female rats indicated that only the 3beta, 15beta-diol was convertible to cholesterol.

Hydrogen bonding in yeast phenylalanine transfer RNA

Further analysis of the three-dimensional electron density map of yeast phenylalanine tRNA is presented. Attention is focused on the several types of unique hydrogen bonding that are found in the molecule and a number of sections of the electron density map are presented. These sections are compared with an electron density map of a dinucleoside phosphate. The bases in the helical stem regions are all involved in Watson-Crick hydrogen bonding interactions with the exception of the guanine-uracil base pair. Several additional tertiary hydrogen bonding interactions are described.

Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles

The atomic coordinates of yeast phenylalanine transfer RNA (tRNA) as well as the torsion angles of the polynucleotide chain are presented as derived from an x-ray diffraction analysis of orthorhombic crystals. A comparison is made between the coordinates obtained from analysis of monoclinic crystals of the same material. It is concluded that the molecule has substantially the same form in the orthorhombic and the monoclinic lattices, except for differences found between residues at the 3' end of the polynucleotides chain. A number of observations are made concerning hydrogen bonding interactions which may account for many of the residues conserved in all tRNA sequences.

The general structure of transfer RNA molecules

The three-dimensional structure of yeast phenylalanine tRNA serves as a useful basis for understanding the tertiary structure of all tRNAs. A large number of tRNA sequences have been surveyed and some general conclusions are drawn. There are only a few regions in the molecule in which there are differences in the number of nucleotides; and the structure of yeast phenylalanine tRNA can accommodate these differences by forming or enlarging protuberances on the surface of the basic framework molecule. The nature and distribution of the differences in number of nucleotides are surveyed and possible hydrogen bonding interactions are discussed for a number of tRNA classes. The two most significant features of the molecule are the large number of stacking interactions which are seen to include most of the nucleotides in the molecule and the system of specific hydrogen bonding interactions. It is likely that these stabilizing elements are preserved in all tRNA structures.

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 RNA's.