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Zalpha, an N-terminal domain of human double-stranded RNA adenosine deaminase (ADAR1), was found to interact with Z-DNA. It was determined whether Zalpha can stabilize the left-handed Z conformation adapted by unaltered, linear alternating (dGdC) polymer including the methylated form. The influence of Zalpha on short, methylated and unmethylated deoxycytidine-deoxyguanosine oligonucleotides was also studied. Results showed that Zalpha recognizes and binds to unaltered poly(dGdC) and also short d(CG)n oligonucleotide sequences.

A 16-amino acid oligopeptide forms a stable [Beta]-sheet structure in water. In physiological solutions it is able to self-assemble to form a macroscopic matrix that stains with Congo red. On raising the temperature of the aqueous solution above 70[degrees]C, an abrupt structural transition occurs in the CD spectra from a [Beta]-sheet to a stable [Alpha]-helix without a detectable random-coil intermediate. With cooling, it retained the [Alpha]-helical form and took several weeks at room temperature to partially return to the [Beta]-sheet form. Slow formation of the stable [Beta]-sheet structure thus shows kinetic irreversibility. Such a formation of very stable [Beta]-sheet structures is found in the amyloid of a number of neurological diseases. This oligopeptide could be a model system for studying the protein conformational changes that occurs in scrapie or Alzheimer disease. The abrupt and direct conversion from a [Beta]-sheet to an [Alpha]-helix may also be found in other processes, such as protein folding and protein-protein interaction. Furthermore, such drastic structure changes may also be exploited in biomaterials designed as sensors to detect environmental changes.

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been determined by X-ray diffraction analysis of single crystals to 2.3 Å resolution using six isomorphous heavy-atom derivatives. The essentially globular monomer appears to consist of three secondary structural elements, a radically twisted three-stranded antiparallel β sheet and two distinct anti-parallel β loops, which are joined by short segments of extended polypeptide chain. The molecule contains no α-helix. A long groove, or arch, 30 Å in length is formed by the underside of the twisted β sheet and one of the two β ribbons. We believe this groove to be the DNA binding region, and this is supported by the assignment of residues on its surface implicated in binding by solution studies. These residues include several aromatic amino acids which may intercalate or stack upon the bases of the DNA. Two monomers are maintained as a dimer by the very close interaction of symmetry related β ribbons about the molecular dyad. About six residues at the amino and carboxyl terminus are in extended conformation and both seem to exhibit some degree of disorder. The amimo-terminal methionine is the locus for binding the platinum heavy-atom derivatives and tyrosine 26 for attachment of the major iodine substituent. © 1979.

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.

DNA fragments with stretches of cytosine residues can fold into four-stranded structures in which two parallel duplexes, held together by hemiprotonated cytosine[center dot][cytosine.sup.+] (C[center dot][C.sup.+]) base pairs, intercalate into each other with opposite polarity. The structural details of this intercalated DNA quadruplex have been assessed by solution NMR and single crystal x-ray diffraction studies of cytosine-rich sequences, including those present in metazoan telomeres. A conserved feature of these structures is the absence of stabilizing stacking interactions between the aromatic ring systems of adjacent C[center dot][C.sup.+] base pairs from intercalated duplexes. Effective stacking involves only the exocyclic keto groups and amino groups of the cytidine bases. The apparent absence of stability provided by stacking interactions between the bases in this intercalated DNA has prompted us to examine the available structures in detail, in particular with regard to unusual features that could compensate for the lack of base stacking. In addition to base-on-deoxyribose stacking and intra-cytidine C - H...O hydrogen bonds, this analysis reveals the presence of a hitherto unobserved, systematic intermolecular C - H...O hydrogen bonding network between the deoxyribose sugar moieties of antiparallel backbones in the four-stranded molecule.

Agarose-encapsulated, metabolically active, permeabilized nuclei for human hematopoietic cell lines were analyzed for Z-DNA formation in the beta-globin gene cluster. Biotinylated monoclonal antibodies against Z-DNA were diffused into the nuclei and cross-linked to DNA. After digestion, the fragments that had formed Z-DNA were isolated. Five of the seventeen regions with Z-DNA motifs in the 73-kb region were found in the Z formation.

The three-dimensional (3D) structures of many DNA-binding proteins have been solved, and the mechanism of sequence-specific DNA recognition is largely understood. In contrast, little is known about the recognition systems [...], The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs. The crystal structure of regA was determined at 1.9 A resolution; the protein was shown to have an a-helical core and two regions with antiparallel β sheets. One of these β sheets has four antiparallel strands and has some sequence homology to RNP-1 and RNP-2, which are believed to be RNA-binding motifs and are found in a number of known RNA-binding proteins. Structurally guided mutants may help to uncover the basis for this variety of RNA interaction.

X-ray crystallographic analysis of the four-stranded intercalated DNA d(C4) at a resolution of 2.3 angstrom units shows that d(C4) consists of two intercalated complexes linked by hemiprotonated cytosine-cytosine base pairs. The duplexes have parallel strands and two of them exhibit an opposite orientation. The d(C4) molecule also contains a 12.4 angstrom unit, slow, right-handed twist between the cytosine-cytosine base pairs and a 3.1 angstrom unit base stacking distance.

Analysis of the crystal structure of d(C3T) at 1.4 angstrom resolution reveals the presence of a four-stranded intercalated complex containing two intercalated parallel-stranded duplexes that are connected by cytosine-protonated cytosine base pairs. The molecule is asymmetric, having a flat, lath-like appearance, with the covalently bonded cytosine having a right-handed twist of 17.1 degrees. The phosphate groups on one of the flat side are rotated far from the molecule's center and bridging water molecules that bind the NH of cytosine and a phosphate group of the opposite chain retain the orientation of these phosphate groups. The structure exhibits microheterogeneism with the cytosine hemiprotonating at pH 7.

Genetic-mutational studies and structural investigation helped dissect the domain of HAP2 that mediates subunit association in the heteromeric CCAAT-binding complex. Protein-protein association is mediated by an extremely short site in HAP2. An alpha-helix configuration is likely for this domain.

A study of the left-handed Z-DNA duplex pure-spermine form X-ray crystal structure reveals that a hitherto unknown second intrahelix spermine molecule and two hydrated sodium ions are present at a temperature of -110 degrees Celsius. The second spermine molecule is mainly found within the duplexes' minor grooves of the crystal lattice. The intrahelix spermine molecule reduces cross-groove electrostatic repulsion within the Z-DNA helix and enhances stability.