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The Biochemical Journal Mar 1973The polynucleotide kinase reaction was used in analyses of complex mixtures of oligodeoxynucleotides which were fractionated by various two-dimensional nucleotide...
Nucleotide sequence analysis with polynucleotide kinase and nucleotide "mapping" methods. 5'-Terminal sequences of deoxyribonucleic acid from bacteriophages lambda and 424.
The polynucleotide kinase reaction was used in analyses of complex mixtures of oligodeoxynucleotides which were fractionated by various two-dimensional nucleotide ;mapping' procedures. Parallel ionophoretic analyses on DEAE-cellulose paper, pH2, and AE-cellulose paper, pH3.5, of venom phosphodiesterase partial digests of 5'-terminally labelled oligonucleotides enabled the sequence of the nucleotides to be deduced uniquely. A ;diagonal ionophoresis' method has been used with mixtures of nucleotides. Application of these methods to 5'-terminally labelled DNA from bacteriophage lambda gave the terminal sequences pA-G-G-T-C-G and pG-G-G-C-G. Identical 5'-terminal sequences were found with DNA from bacteriophage 424.
Topics: Adenine Nucleotides; Adenosine Triphosphate; Animals; Autoradiography; Base Sequence; Coliphages; Cytosine Nucleotides; DNA, Viral; Deoxyribonucleases; Deoxyribonucleotides; Electrophoresis, Paper; Endonucleases; Escherichia coli; Guanine Nucleotides; Hydrogen-Ion Concentration; Mutation; Oligonucleotides; Pancreas; Phosphoric Diester Hydrolases; Phosphorus Isotopes; Phosphotransferases; Polynucleotides; Snakes; Species Specificity; Thymine Nucleotides; Venoms
PubMed: 4352720
DOI: 10.1042/bj1310569 -
Nucleic Acids Research Jul 2000Abasic (AP) sites constitute a common form of DNA damage, arising from the spontaneous or enzymatic breakage of the N-glycosyl bond and the loss of a nucleotide base. To...
Abasic (AP) sites constitute a common form of DNA damage, arising from the spontaneous or enzymatic breakage of the N-glycosyl bond and the loss of a nucleotide base. To examine the effects of such damage on DNA structure, especially in the vicinity of the abasic sugar, four 1.5 ns molecular dynamics simulations of double-helical DNA dodecamers with and without a single abasic (tetrahydrofuran, X) lesion in a 5'-d(CXT) context have been performed and analyzed. The results indicate that the abasic site does not maintain a hole or gap in the DNA, but instead perturbs the canonical structure and induces additional flexibility close to the abasic site. In the apurinic simulations (i.e., when a pyrimidine is opposite the AP site), the abasic sugar flipped in and out of the minor groove, and the gap was water filled, except during the occurrence of a novel non-Watson-Crick C-T base pair across the abasic site. The apyrimidinic gap was not penetrated by water until the abasic sugar flipped out and remained extrahelical. Both AP helices showed kinks of 20-30 degrees at the abasic site. The Watson-Crick hydrogen bonds are more transient throughout the DNA double helices containing an abasic site. The abasic sugar displayed an unusually broad range of sugar puckers centered around the northern pucker. The increased motion of the bases and backbone near the abasic site appear to correlate with sequence-dependent helical stability. The data indicate that abasic DNA contorts more easily and in specific ways relative to unmodified DNA, an aspect likely to be important in abasic site recognition and hydrolysis.
Topics: Apurinic Acid; Base Pairing; Carbohydrate Metabolism; Carbohydrates; Computer Simulation; DNA; Endodeoxyribonucleases; Hydrogen Bonding; Models, Molecular; Nucleic Acid Conformation; Phosphates; Polynucleotides; Rotation; Solvents; Static Electricity; Substrate Specificity; Water
PubMed: 10871413
DOI: 10.1093/nar/28.13.2613 -
Journal of Chemical Information and... Jan 2014In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers I: Proteins. J. Chem. Inf. Model. 2013, DOI:...
In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers I: Proteins. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400541d), we introduce a new algorithm for structure classification of biopolymeric structures based on main-chain dihedral angles. The DISICL algorithm (short for DIhedral-based Segment Identification and CLassification) classifies segments of structures containing two central residues. Here, we introduce the DISICL library for polynucleotides, which is based on the dihedral angles ε, ζ, and χ for the two central residues of a three-nucleotide segment of a single strand. Seventeen distinct structural classes are defined for nucleotide structures, some of which--to our knowledge--were not described previously in other structure classification algorithms. In particular, DISICL also classifies noncanonical single-stranded structural elements. DISICL is applied to databases of DNA and RNA structures containing 80,000 and 180,000 segments, respectively. The classifications according to DISICL are compared to those of another popular classification scheme in terms of the amount of classified nucleotides, average occurrence and length of structural elements, and pairwise matches of the classifications. While the detailed classification of DISICL adds sensitivity to a structure analysis, it can be readily reduced to eight simplified classes providing a more general overview of the secondary structure in polynucleotides.
Topics: Algorithms; Biopolymers; Computational Biology; Computer Simulation; Databases, Nucleic Acid; Models, Molecular; Multiprotein Complexes; Nucleic Acid Conformation; Polynucleotides; Software
PubMed: 24364355
DOI: 10.1021/ci400542n -
Nucleic Acids Research Apr 1980Polynucleotides containing adenosine and 8-azidoadenosine or inosine and 8-azidoinosine residues have been prepared from mixtures of nucleoside diphosphates using...
Polynucleotides containing adenosine and 8-azidoadenosine or inosine and 8-azidoinosine residues have been prepared from mixtures of nucleoside diphosphates using polynucleotide phosphorylase from Escherichia coli. These copolymers can form complexes with polyuridylic or polycytidylic acids respectively. Single stranded poly(adenylic, 8-azidoadenylic acid) [poly(A,z8A)] has been used as a photoaffinity reagent to explore the subunit topography of RNA polymerase from E. coli.
Topics: Adenosine; Adenosine Monophosphate; Affinity Labels; Azides; Binding Sites; DNA-Directed RNA Polymerases; Escherichia coli; Inosine; Inosine Monophosphate; Inosine Nucleotides; Kinetics; Poly C; Poly U; Polyribonucleotide Nucleotidyltransferase; Polyribonucleotides; Protein Binding; Transcription, Genetic
PubMed: 7001370
DOI: 10.1093/nar/8.7.1675 -
Analytical Cellular Pathology... 2013Interactions of cationic tetrakis (N, N', N″, N‴- tetramethyltetra-3, 4-pyridinoporphyrazinatozinc (II) (Zn (tmtppa)) with synthetic polynucleotides, poly (G-C) and...
Interactions of cationic tetrakis (N, N', N″, N‴- tetramethyltetra-3, 4-pyridinoporphyrazinatozinc (II) (Zn (tmtppa)) with synthetic polynucleotides, poly (G-C) and poly (A-T), and calf thymus DNA have been characterized in 7.5 mM phosphate buffer of pH 7.2 by UV-Vis absorption and fluorescence spectroscopy. The appearance of hypochromicity more than 30% in UV-Vis spectra of porphyrazine due to interaction of both poly (G-C) and poly (A-T) indicates interaction similar to that of porphyrazine with DNA. The binding constants were determined from the changes in the Q-band maximum of the porphyrazine spectra at various poly (G-C) and DNA concentrations. The values of K were 2.5×10⁶ M⁻¹, 2.5×10⁶ M⁻¹ and 2.5×10⁵ M⁻¹ for poly (G-C), poly (A-T) and DNA, respectively, at 25°C. The thermodynamic parameters (ΔG°, ΔH°, ΔS°) were calculated using the van't Hoff equation at various temperatures. The enthalpy and entropy changes were determined to be 41.14 kJ mol⁻¹ and 260.50 J mol⁻¹·K⁻¹ for poly (G-C) and 53.59 kJ mol⁻¹ and 285.46 J mol⁻¹·K⁻¹ for DNA at 25°C. The positive and large values of the entropy and enthalpy suggest that both hydrophobic and electrostatic interactions may play an important role in the stabilization of the complex formation. The binding of polynucleotides to porphyrazine quenches fluorescence emission of ethidium bromide (EB), and the quenching process obeys linear Stern-Volmer relationship. The results reviled groove-binding mode of porphyrazine for both AT- and GC-rich polynucleotides of DNA.
Topics: Animals; Cations; Cattle; DNA; Humans; Polynucleotides
PubMed: 24473094
DOI: 10.3233/ACP-140086 -
Journal of Bacteriology Feb 1968Deoxyribonucleic acids (DNA's) extracted from organisms presently placed in the genus Brucella (B. abortus, B. melitensis, B. neotomae, and B. suis) possessed very...
Deoxyribonucleic acids (DNA's) extracted from organisms presently placed in the genus Brucella (B. abortus, B. melitensis, B. neotomae, and B. suis) possessed very similar polynucleotide sequences. Unlabeled, single-stranded DNA fragments from B. abortus, B. melitensis, B. neotomae, and B. suis were equally effective in competing with the interaction of corresponding radiolabeled, single-stranded DNA fragments with their homologous DNA-agars. Unlabeled fragments of B. ovis, however, did not compete as effectively as the homologous, unlabeled DNA's, and this organism, therefore, had a detectably different polynucleotide composition. The mole percentages of guanine plus cytosine in Brucella DNA's (56 to 58%) were also similar. DNA's from Francisella tularensis, Escherichia coli, and the slow loris did not compete.
Topics: Brucella; Brucella abortus; Chemical Phenomena; Chemistry, Physical; Cytosine; DNA, Bacterial; Escherichia coli; Francisella tularensis; Guanine; Nucleic Acid Denaturation; Phosphorus Isotopes; Polynucleotides
PubMed: 4966546
DOI: 10.1128/jb.95.2.444-448.1968 -
Nucleic Acids Research Nov 1998Mammalian DNA ligase III exists as two distinct isoforms denoted alpha and beta. Both forms possess a motif that is homologous to the putative zinc finger present in...
Mammalian DNA ligase III exists as two distinct isoforms denoted alpha and beta. Both forms possess a motif that is homologous to the putative zinc finger present in poly(ADP-ribose) polymerase. Here, the role of this motif in the binding and ligation of nicked DNA and RNA substrates in vitro has been examined in both isoforms. Disruption of the putative zinc finger did not affect DNA ligase III activity on nicked DNA duplex, nor did it abolish DNA ligase III-alpha activity during DNA base excision repair in a cell-free assay. In contrast, disruption of this motif reduced 3-fold the activity of both DNA ligase III isoforms on nicked RNA present in RNA/DNA homopolymers. Furthermore, whereas disruption of the motif did not prevent binding of DNA ligase III to nicked DNA duplex, binding to nicked RNA homopolymers was reduced approximately 10-fold. These results suggest that the putative zinc finger does not stimulate DNA ligase III activity on simple nicked DNA substrates, but indicate that this motif can target the binding and activity of DNA ligase III to nicked RNA homopolymer. The implications of these results to the cellular role of the putative zinc finger are discussed.
Topics: Amino Acid Sequence; Animals; Base Sequence; Catalytic Domain; DNA; DNA Ligase ATP; DNA Ligases; DNA Primers; DNA Repair; DNA-Binding Proteins; Escherichia coli; In Vitro Techniques; Molecular Sequence Data; Mutagenesis, Site-Directed; Poly-ADP-Ribose Binding Proteins; Polynucleotides; RNA; Recombinant Proteins; Substrate Specificity; X-ray Repair Cross Complementing Protein 1; Xenopus Proteins; Zinc Fingers
PubMed: 9776738
DOI: 10.1093/nar/26.21.4804 -
Journal of Bacteriology Jun 1973Polynucleotide sequence relationships between two reference Vibrio parahaemolyticus strains isolated from Japanese and American gastroenteritis patients were...
Polynucleotide sequence relationships between two reference Vibrio parahaemolyticus strains isolated from Japanese and American gastroenteritis patients were investigated by use of (32)P-DNA/DNA reassociation in free solution. In addition, these strains were similarly compared with 22 other strains of estuarine and marine vibrios, including 11 strains previously identified as V. parahaemolyticus (2 Japanese, 1 of unknown location, and 8 American strains obtained from diverse geographical locations and sources in North America), 3 strains of V. alginolyticus, and 8 of Vibrio spp. Deoxyribonucleic acid (DNA) from the Japanese and American gastroenteritis isolates showed high relative levels of intraspecific duplex formation (92 to 93%) when reassociated, reciprocally, at 60 C. Heterologous DNA duplexes exhibited thermal elution midpoint [Tm(e)] values comparable to those obtained from homologous duplexes (88.0) when thermally eluted from hydroxyapatite, thus indicating high base-pair complementarity. Other V. parahaemolyticus strains showed DNA homologies of 85% or greater, with correspondingly high Tm(e) values (86.0 to 88.0) for the heteroduplexes formed. DNA of two of three V. alginolyticus strains (ATCC 17749 and 166-70) was 55 to 60% homologous to reference V. parahaemolyticus DNA preparations; Vibrio sp. strain 5144 (originally classified as V. parahaemolyticus biotype 2 and subsequently as V. alginolyticus strain 5144) showed only 24 to 26% DNA homology to the same reference DNA. These data provide evidence that Vibrio sp. strain 5144 is genetically distinct from the other V. alginolyticus strains used in this study. Three bioluminescent strains thought to be closely related to V. parahaemolyticus demonstrated only 24 to 31% DNA homology to the reference V. parahaemolyticus DNA. These data firmly establish the existence in some Atlantic and Gulf Coast estuaries of organisms genetically very similar to V. parahaemolyticus, the causative agent of "shirasu" food poisoning in Japan.
Topics: Base Sequence; Culture Media; DNA, Bacterial; DNA, Single-Stranded; Japan; Nucleotides; Phosphorus Isotopes; Polynucleotides; Temperature; United States; Vibrio
PubMed: 4712574
DOI: 10.1128/jb.114.3.916-927.1973 -
Proceedings of the National Academy of... Jun 1961
Topics: DNA; Polynucleotides; Protein Structure, Secondary
PubMed: 13770642
DOI: 10.1073/pnas.47.6.791 -
Nucleic Acids Research Apr 1980The reactions between purified anti-poly A. poly U and-poly I. poly C. antibodies (IgG and IgM), and synthetic and natural polynucleotides were visualized at the...
The reactions between purified anti-poly A. poly U and-poly I. poly C. antibodies (IgG and IgM), and synthetic and natural polynucleotides were visualized at the molecular level. This was achieved by the use of fine tungsten bidirectional shadowing of molecules adsorbed onto thin carbon films, combined with dark field electron microscopic observation. A progression was observed from monogamous multivalency (binding of a single multifunctional antigen molecule with several combining sites of the same antibody molecule simultaneously) (Crothers and Metzger, 1972, Immunochemistry, 9, 341-357), to aggregation. Different types of figures were observed, among which loops formed by the coiling of the antigen around a single IgM molecule were very frequently seen. The tendency of IgG antibodies to bind cooperatively to certain antigens was also noted. In contrast, cross-links were seldom encountered. The cross-reactivity of different polynucleotides was also assessed by a quantitative analysis. The length of antigen associated to an antibody molecule (either IgG or IgM) was also measured.
Topics: Animals; Antibodies; Antigen-Antibody Complex; Cell Line; Immunoglobulins; Mice; Microscopy, Electron; Models, Molecular; Nucleic Acid Conformation; Plasmacytoma; Poly A-U; Poly I-C
PubMed: 7433130
DOI: 10.1093/nar/8.8.1805