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  • Polymer and Materials Science  (8)
  • protein-nucleic acid interactions  (2)
  • Life Sciences (General)  (1)
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  • 1
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 2 (1964), S. 399-413 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Titration studies of the 1 : 1 helical polynucleotide complex of polyinosinic acid and polycytidylic acid reveal that these two polymers form a complex when the polycytidylic acid is protonated near pH 3. Sedimentation studies show that the protonated complex also has a 1 : 1 stoichiometry. However, the protonated complex is more stable than the unprotonated neutral complex as judged by its thermal stability. The molecular structure of the protonated complex is not the same as the neutral form. Study of the kinetics of the reaction of the protonated complex with formaldehyde suggests that the amino group of cytosine is involved in hydrogen bonds which hold the polynucleotide strands together.
    Additional Material: 10 Ill.
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  • 2
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Both (dC-dG)4 and d(CGCATGCG) crystallize in hexagonal lattices and their three-dimensional structure has been solved by x-ray diffraction analysis. Both molecules are found to form Z-DNA, although the fine details of the structure cannot be visualized due to the statistical disordering of the molecules along the c-axis, which is brought about by the symmetry constraints of the space group. This represents the first time in which the unmodified dinucleotide sequences CpAp and TpGp have been found to form Z-DNA in a crystalline lattice.
    Additional Material: 1 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 34 (1994), S. 663-672 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A 16-residue amphiphilic oligopeptide (EAK16) with every other residue alanine and also containing glutamic acid and lysine (Ac-NH-AEAEAKAKAEAEAKAK-CONH2) is able to form an unusually stable β-sheet structure. The β-sheet structure is stable at very low concentrations in water and at high temperatures. Various pH changes at 1.5, 3, 7, and 11 had little effect on the stability of the β-sheet structure. The β-sheet structure was not altered significantly even in the presence of 0.1% SDS, 7 molar guanidine hydrochloride, or 8 molar urea. One of the structural characteristics of the EAK16 is its ionic self-complementarity in that ionic bonds and hydrogen bonds between Glu and Lys can form readily between two oligopeptide β-sheet structures. This structural feature is probably one of the factors that promotes its extreme stability. This is the first example of such an extended ionic self-complementarity in a protein structure. EAK16 and its related peptides may have applications as useful biomaterials. It also offers a good model for studying the mechanism of β-sheet formation. Because the oligopeptide can self-assemble to form a membranous structure, it may have relevance to origin of life research. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 18 (1979), S. 539-552 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The three-dimensional structure of putrescine diphosphate has been solved by x-ray diffraction analysis. The structure reveals the detailed interaction between the amino groups of putrescine and the phosphate residues in which hydrogen bonding and electrostatic forces play a predominant role. The structure serves as a useful model for understanding the interaction of amines with nucleic acids both in a sequence-specific and non-sequence-specific fashion. In particular, a model is proposed for the interaction of the E-amino group of lysine with regions of DNA containing adenine-thymine sequences.
    Additional Material: 7 Ill.
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  • 5
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe the crystal structure of an octameric DNA sequence, d(GGm5CCGGCC), at 2.25 Å resolution. The sequence contains one C5-methylated cytosine per DNA strand. This methylation corresponds to that utilized in vivo by the HaeIII restriction modification system. The present structure is compared to that of the unmethylated octamer solved previously as well as to other A-DNA crystal structures. It retains the characteristics seen in these other DNA molecules, i.e., reduced base-pair tilt angles and increased major groove width, indicating that the presence of the methyl groups does not drastically affect the A-DNA backbone conformation. The position of the methyl groups appears to block the major grove, thus preventing potential sequence-specific protein interactions. In addition, the presence of these hydrophobic substituents may enhance the overall stability of the A-DNA conformation.
    Additional Material: 9 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 95-101 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Unfractionated yeast transfer ribonucleic acid (tRNA) was reacted in aqueous acetone solution with the sulfhydryl spin-labeling reagnent, N-(l-oxyl-2,2,5,5-tetramethyl-3-Pyrrolidinyl)iodoacetamide. Whereas tRNA stripped of amino acids reacted only slowly, there were sites on tRNA charged with cysteine which combined rapidly with the reagent. The latter class of spin-label was quickly cleaved from the tRNA upon incubation in mildly alkaline solution (pH 8.0), suggesting that it was attached to the cysteinyl side chains. The paramagnetic resonance spectrum of column-purified spin-labeled cysteinyl tRNA showed that the spin-label was partially immobilized as a result of its interaction with the tRNA. When the tRNA was slowly heated, an abrupt increase occurred in the rotational mobility of the paramagnetic amino-acid side chain.
    Additional Material: 4 Ill.
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  • 7
    ISSN: 0006-3525
    Keywords: DNA crystallography ; i-motif ; intercalation ; crystal lattice and packing ; nucleic acids ; intermolecular interactions ; crystal engineering ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Condensation of single molecules from solution into crystals represents a transition between distinct energetic states. In solution, the atomic interactions within the molecule dominate. In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice - these are the packing interactions. The crystal structures of d(CCCT), d(TAACCC), d(CCCAAT), and d(AACCCC) have in common a four-stranded intercalated cytosine segment, built by stacked layers of cytosine · cytosine+ (C · C+) base pairs coming from two parallel duplexes that intercalate into each other with opposite polarity. The intercalated cytosine segments in these structures are similar in their geometry, even though the sequences crystallized in different space groups. In the crystals, adenine and thymine residues of the sequences are used to build the three-dimensional crystal lattice by elaborately interacting with symmetry-related molecules. The packing elements observed provide novel insight about the copious ways in which nucleic acid molecules can interact with each other - for example, when folded in more complicated higher order structures, such as mRNA and chromatin. © 1998 John Wiley & Sons, Inc. Biopoly 44: 257-267, 1997
    Additional Material: 5 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 10 (1971), S. 1795-1807 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two molecules of 1-methyl-5-fluorouracil complex with one molecule of 9-erthyl-2, -6-diaminopurine and crystsallize in a triclinic unit cell. The crystal structure was solves by analysis of 3-dimensional x-ray diffraction data. Asharpened Patterson map was used to dertermine the structure with apsuedo-heavy atom technique. The three molecule from a planar hydrogen bonded Watson-Crick pair with the purine while the other pyrimide forms hydrogen bond to adenine through the imdazole nitrogen. The network is compeleted by purine-purine hydrogen bond.
    Additional Material: 4 Ill.
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  • 9
    ISSN: 0091-7419
    Keywords: protein-nucleic acid interactions ; X-ray diffraction ; gene 5 protein ; molecular replacement ; DNA ; fd bacteriophage ; Life Sciences ; Molecular Cell Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: 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-Å 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.
    Additional Material: 6 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, N.Y. : Wiley-Blackwell
    Journal of Supramolecular Structure 10 (1979), S. 457-465 
    ISSN: 0091-7419
    Keywords: DNA binding protein ; gene 5 ; fd bacteriophage ; X-ray diffraction ; protein-nucleic acid interactions ; Life Sciences ; Molecular Cell Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3-Å 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 structure and binding mechanism as we visualize it appear to be fully consistent with evidence provided by physical-chemical studies of the protein in solution.
    Additional Material: 6 Ill.
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