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PubMed2006

Driven translocation of a polynucleotide chain through a nanopore: a continuous time Monte Carlo study.

Using the continuous time Monte Carlo method, we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have strong interaction with the pore, and depends on which end of the chain first enters the pore. Depending on this interaction, in both cases, the distribution of times for the chain to pass through the pore in our model is found to have three peaks, as observed in the experiment of Kasianowicz Brandin, Branton, and Deamer [Proc. Natl. Acad. Sci. USA 93, 13770 (1996)].

Computer Simulation↗
PubMed1993

Polynucleotide specificity of anti-reactive oxygen species (ROS) DNA antibodies.

Hydrogen peroxide in the presence of short wavelength UV light was able to induce alterations in native DNA fragments of 300 bp (ROS-DNA), thereby rendering it immunogenic in experimental animals. The specificity of induced antibodies was investigated by direct binding and competition ELISA. Inhibition studies revealed nearly 89% inhibition in the antibody binding by the immunogen and recognition of native B-, A- and allied conformations presented by various synthetic polynucleotides. Gel retardation assay reiterated the formation of immune complexes between induced antibodies and native and ROS-DNA fragments. It was observed that naturally occurring anti-DNA autoantibodies from systemic lupus erythematosus (SLE) sera recognize ROS-DNA. The comparison of the specificities of anti-DNA autoantibodies from 10 SLE patients showed a 20-50-fold preference for ROS-DNA over native DNA. These results demonstrate that anti-DNA antibodies can be induced by ROS-DNA, and that some of the autoimmune DNA binding antibodies found in SLE may result from response to reactive oxygen species.

Animals↗
PubMed1975

Polynucleotide kinase from rat-liver nuclei. Purification and properties.

A polynucleotide kinase, which catalyzes the phosphorylation of 5'-hydroxyl ends of deoxyribonucleic acid in the presence of adenosine triphosphate, has been purified 260-fold with a yield of 14% from 0.15 M NaCl extracts of rat liver nuclei. The purified enzyme has a pH optimum of 5.5. The enzyme is reversible inhibited by p-chloromercuribenzoate. The S0.5 value (ligand concentration required for a half-maximal activity) for ATP is 2.5 muM. A bivalent cation is essential for the reaction and S0.5 values for Mg2+, Ca2+ and Mn2+ are 3.3 mM, 4 mM and 0.05 mM respectively. Pyrophosphate remarkable inhibits the activity with I0.5 value (ligand concentration required for a half-maximal inhibition) of 0.2 mM, and sulfate, with I0.5 of 0.5 mM, whereas phosphate weakly inhibits the activity with I0.5 of about 20 mM. An apparent molecular weight of the purified enzyme is estimated to be 8 X 10(4) by gel filtration on a column of Sephadex G-150, and the Stokes radius of the enzyme molecule is shown to be about 0.36 nm. Sucrose density gradient centrifugation reveals that the enzyme has a sedimentation coefficient of about 4.4 S.

Adenosine Triphosphate↗
PubMed1977

Physicochemical properties of T4 polynucleotide kinase.

Some physicochemical properties of T4 polynucleotide kinase (EC2.7.1.78) have been studied. The enzyme is an oligomer of one polypeptide chain. The molecular weight of the monomer is 33000, as determined from the amino acid analysis. Phenylalanine is the N-terminal amino acid. Each monomer contains two --SH groups, one exposed and one more buried. Circular dichroic spectra suggest a high content of alpha-helical structure, 45--55%. Excitation at 280 nm gave a strong emission fluorescence spectrum with a maximum centering at 340 nm. Sedimentation studies suggested the enzymically active form to be a tetramer. High ionic strength (0.1 M KC1), spermine, and the substrates ATP and thymidine 3'-monophosphate were found to be essential factors in order to stabilize the protein in an oligomeric structure. The association constants for ATP, thymidine 3'-monphosphate, and P1 were determined fluorimetrically to be 7.9 x 105, 4.8 x 105, and 7.2 x 10(2) M-1 respectively.

Amino Acid Sequence↗
PubMed1978

Use of the T4 polynucleotide ligase in the joining of flush-ended DNA segments generated by restriction endonucleases.

Double-stranded DNA segments with completely base-paired ends were obtained by the action of various restriction endonucleases on phage and plasmid DNAs. These segments were joined covalently by the T4 polynucleotide ligase. The joining was monitored by the electron microscopy count of intramolecularly circularized segments. The highest extent of joining, close to 75%, was observed at 15-25 degrees C with the segments resulting from the action of the Bacillus subtilis (strain R) restriction endonuclease Bsu on the DNA of bacteriophage SPPI or of the plasmid pSC 101. The joining of double-stranded termini required about 10 times more enzyme than the short single-stranded termini produced by the Escherichia coli restriction endonuclease EcoRI. A shortened purification of the T4 ligase was found to give an enzyme devoid of interfacing nucleases.

Coliphages↗
PubMed1984

Interaction of the HB protein of Bacillus globigii with nucleic acids. Analysis of the binding to DNA and polynucleotides.

Fluorescence of the phenylalanine residues of the HB protein of Baccillus globigii was found to be quenched upon binding to nucleic acids. Using this phenomenon, the binding properties were investigated on the basis of an approach published recently. The stoichiometric numbers were about 10 basepairs per bound protein molecule for double-stranded DNA and about 10 bases for single-stranded polynucleotides, independent of salt concentration. Cooperativity parameters were in the range of 50-250. Binding constants were about 5 X 10(6) M-1 (at 0.1 M NaCl) and decreased with increasing salt concentration. From the salt dependence it is inferred that about one Na+ ion is displaced upon binding of a protein molecule to DNA. Therefore the binding site should contain one positively charged amino acid residue. The protein was found to bind with comparable strength to double-stranded and single-stranded DNA as well as to poly(rA). Hence it is concluded that the HB protein does not belong to the category of 'melting proteins'.

Bacillus↗
PubMed1968

Autocorrelation functions of noisy electron micrographs of stained polynucleotide chains.

Polyuridylic acid was deposited on carbon films in the presence of the thallous salt of mercury-p-dihydroquinone-O,O-diacetic acid under conditions leading to attachment of one of these molecules to each nucleotide. In electron micrographs of the stained polynucleotide chain, detail was obscured by the noise resulting from the substrate. Optically obtained autocorrelation functions of the distribution of density along the strands revealed peaks suggesting a structural regularity of 8 angstroms; this was interpreted as the internucleotide spacing.

Hydroquinones↗
PubMed1969

Antibodies to polynucleotides: distribution in human serums.

Hemagglutination procedures were used to determine the distribution of antibodies to native DNA, single-stranded DNA, and double-stranded RNA. Antibodies to all three polynucleotides were found in a high percentage of the serums of patients with systemic lupus erythematosus. Antibodies to native DNA occurred almost exclusively in serums of patients in the active stages of systemic lupus erythematosus, whereas antibodies to single-stranded DNA were observed in the serums of patients with several diseases and of some normal individuals.

Antibody Formation↗
PubMed1986

The mechanism of binding of a polynucleotide chain to pancreatic ribonuclease.

The crystalline complex of pancreatic ribonuclease (RNase) with oligomers of d(pA)4 has been solved by x-ray diffraction methods and refined by standard procedures to a conventional crystallographic R factor of 0.22 at 2.5 angstrom resolution. The asymmetric unit is a complex of one RNase molecule associated with four d(pA)4 oligomers. Although the DNA in this complex is segmented, and therefore shows some discontinuities, it nevertheless traces a continuous path 12 nucleotides in length that passes through the active site cleft of the enzyme and over the surface of the protein. The DNA makes a series of eight to nine electrostatic bonds between its phosphate groups and lysine and arginine residues on the protein, as well as specific chemical interactions at the active site. The path described by the sequence of nucleotides is likely to be that taken by an extended polynucleotide chain when it is bound by the enzyme.

Animals↗
PubMed1971

Quantitative aspects of deoxyribonucleic acid renaturation: base composition, state of chromosome replication, and polynucleotide homologies.

The base composition of a deoxyribonucleic acid (DNA) sample affects its intrinsic rate of renaturation. In agreement with the information of Wetmur and Davidson, it was established that high guanosine plus cytosine (GC) DNA renatures faster than expected from analytical measurement of its molecular weight. A calculated correction factor of 1.8% of the observed C(0)t(.5) is required for every mole per cent GC difference from 51% GC. The correction factor is now established in the range of 32 to 65% GC. Renaturation of DNA mixtures prepared from pairs of organisms has been studied. When no similarity existed between the two organisms, the observed C(0)t(.5) of the mixture was the sum of the independently determined C(0)t(.5) values. Lack of additivity was correlated with similarities in polynucleotide sequence of the reassociating DNA molecules. A quantitative relationship was formulated to relate C(0)t(.5) values of renatured DNA mixtures to per cent binding ("homology"). Finally, it was demonstrated that DNA prepared from log-phase cells renatures faster than stationary-phase DNA and also departs from theoretical second-order kinetics.

Autoradiography↗
PubMed1972

Polynucleotide sequence divergence among strains of Escherichia coli and closely related organisms.

Polynucleotide sequence similarity tests were carried out to determine the extent of divergence present in a number of Escherichia coli strains, obtained from diverse human, animal, and laboratory sources, and closely related strains of Shigella, Salmonella, and the Alkalescens-Dispar group. At 60 C, relative reassociation of deoxyribonucleic acid (DNA) from the various strains with E. coli K-12 DNA ranged from 100 to 36%, with the highest level of reassociation found for three strains derived from K-12, and the lowest levels for two "atypical" E. coli strains and S. typhimurium. The change in thermal elution midpoint, which indicates the stability of DNA duplexes, ranged from 0.1 to 14.5 C, with thermal stability closely following the reassociation data. Reassociation experiments performed at 75 C, at which temperature only the more closely related DNA species form stable duplexes, gave similar indications of relatedness. At both temperatures, Alkalescens-Dispar strains showed close relatedness to E. coli, supporting the idea that they should be included in the genus Escherichia. Reciprocal binding experiments with E. coli BB, 02A, and K-12 yielded different reassociation values, suggesting that the genomes of these strains are of different size. The BB genome was calculated to be 9% larger than that of K-12, and that of 02A 9% larger than that of BB. Calculation of genome size for a series of E. coli strains yielded values ranging from 2.29 x 10(9) to 2.97 x 10(9) daltons. E. coli strains and closely related organisms were compared by Adansonian analysis for their relatedness to a hypothetical median strain. E. coli 0128a was the most closely related to this median organism. In general, these data compared well with the data from reassociation experiments among E. coli strains. However, anomalous results were obtained in the cases of Shigella flexneri, S. typhimurium, and "atypical" E. coli strains.

Base Sequence↗
PubMed1973

Polynucleotide sequence relationships among Japanese and American strains of Vibrio parahaemolyticus.

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.

Base Sequence↗
PubMed1977

Phylogenetic relationships of bacterial endosymbionts of Paramecium aurelia: polynucleotide sequence relationships of 51 kappa and its mutants.

Hydroxyapatite chromatographic procedures were used to investigate the deoxyribonucleic acid (DNA) sequence relationships of kappa of Paramecium tetraurelia stock 51 and the organisms that have been designated as mutants of 51 kappa. Of the "mutants" studied, only 51m43 kappa possessed a high percentage (89%) of DNA sequences homologous to those of 51 kappa. All other "mutant" strains possessed less than 25% polynucleotide sequence homology to 51 kappa DNA. The three strains of pi endosymbionts (51m1 pi, 51m43 pi, and 139 pi) share greater than 75% DNA sequence homology with each other and approximately 50% DNA sequence homology with 138 mu, the mate-killer endosymbiont found in P. octaurelia. Only 23% of the 51 kappa DNA sequences were found to be homologous with those of 51m1 kappa. The data indicate that of the "mutants" studied, only 51m43 kappa could be a mutant of 51 kappa. The pi endosymbionts comprise a closely related group of organisms that are also related to 138 mu but not to any of the kappas tested. The group of organisms designated as kappa appears to be comprised of at least two distinct phylogenetic groups.

Animals↗
PubMed1979

A new gene of Escherichia coli K-12 whose product participates in T4 bacteriophage late gene expression: interaction of lit with the T4-induced polynucleotide 5'-kinase 3'-phosphatase.

We isolated five Escherichia coli mutants deficient in their ability to support the late (replication-coupled) gene expression of T4 bacteriophage at 30 degrees C. These mutants, which we call Lit mutants, define at least one novel gene at 25 min on the E. coli map. They were selected in an attempt to obtain mutants which restrict the growth of T4 mutants deficient in polynucleotide 5'-kinase 3'-phosphatase but not that of wild-type T4 at 37 degrees C. Some of the mutants do have these phenotypes under some conditions. Studies of the block in T4 development in some of the E. coli mutants suggest that Lit mutants are affected in a gene product involved in the metabolism of deoxyribonucleic acid nicks or single-strand gaps. None of the Lit mutants is deficient in the major, bacterial, 3'-phosphatase activity in crude extracts.

Chromosome Mapping↗
PubMed2003

The Streptomyces coelicolor polynucleotide phosphorylase homologue, and not the putative poly(A) polymerase, can polyadenylate RNA.

A protein containing a nucleotidyltransferase motif characteristic of poly(A) polymerases has been proposed to polyadenylate RNA in Streptomyces coelicolor (P. Bralley and G. H. Jones, Mol. Microbiol. 40:1155-1164, 2001). We show that this protein lacks poly(A) polymerase activity and is instead a tRNA nucleotidyltransferase that repairs CCA ends of tRNAs. In contrast, a Streptomyces coelicolor polynucleotide phosphorylase homologue that exhibits polyadenylation activity may account for the poly(A) tails found in this organism.

Amino Acid Sequence↗
PubMed1987

Comparative study of synthetic oligonucleotide and cloned polynucleotide enterotoxin gene probes to identify enterotoxigenic Escherichia coli.

Escherichia coli isolated from 2,126 children in Thailand and the Philippines was examined for enterotoxin production and for DNA hybridization with synthetic oligonucleotide and cloned polynucleotide enterotoxin gene probes. A total of 233 infections with E. coli that were detected by one or more of these assays were identified. Of the infections, 75% (164/233) were identified by all three methods. An additional 18% (43/233) were identified by two of three methods. Isolates from 10% (19/183) of infections with E. coli that hybridized with both the oligonucleotide and cloned enterotoxin gene probes were nontoxigenic, as determined by the Y1 adrenal cell and suckling mouse assays. Although synthetic oligonucleotide probes to detect enterotoxigenic E. coli are more uniform and easier to use than cloned enterotoxin gene probes, the heat-labile toxin oligo probe used in this study did not identify 13% (11/87) of infections with E. coli that produced heat-labile toxin, as identified with the Y1 adrenal cell assay and the cloned enterotoxin gene probe. Synthetic oligonucleotide probes enable laboratories with only minimal equipment to use DNA hybridization assays to identify enterotoxigenic E. coli.

Bacterial Toxins↗