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Plant Signaling & Behavior Mar 2011Pea mini-chromosome maintenance 6 (MCM6) single subunit (93 kDa) forms homohexamer (560 kDa) and contains an ATP-dependent and replication fork stimulated 3' to 5' DNA...
Pea mini-chromosome maintenance 6 (MCM6) single subunit (93 kDa) forms homohexamer (560 kDa) and contains an ATP-dependent and replication fork stimulated 3' to 5' DNA unwinding activity along with intrinsic DNA-dependent ATPase and ATP-binding activities [Plant Mol. Biol. 2010; DOI: 10.1007/s11103-010-9675-7]. Here, we have determined the effect of various DNA-binding agents, such as actinomycin, nogalamycin, daunorubicin, doxorubicin, distamycin, camptothecin, cyclophosphamide, ellipticine, VP-16, novobiocin, netropsin, cisplatin, mitoxantrone and genistein on the DNA unwinding and ATPase activities of the pea MCM6 DNA helicase. The results show that actinomycin and nogalamycin inhibited the DNA helicase (apparent Ki values of 10 and 1 μM, respectively) and ATPase (apparent Ki values of 100 and 17 μM, respectively) activities. Although, daunorubicin and doxorubicin also inhibited the DNA helicase activity of pea MCM6, but with less efficiency; however, these could not inhibit the ATPase activity. These results suggest that the intercalation of the inhibitors into duplex DNA generates a complex that impedes translocation of MCM6, resulting in the inhibitions of the activities. This study could be useful in our better understanding of the mechanism of plant nuclear DNA helicase unwinding.
Topics: Adenosine Triphosphatases; Camptothecin; Cisplatin; DNA Helicases; Dactinomycin; Daunorubicin; Ellipticines; Enzyme Inhibitors; Etoposide; Intercalating Agents; Mitoxantrone; Nogalamycin; Novobiocin; Pisum sativum; Plant Proteins
PubMed: 21336027
DOI: 10.4161/psb.6.3.13355 -
Nucleic Acids Research Mar 2000The solution structure and hydration of the chimeric duplex [d(CGC)r(aaa)d(TTTGCG)](2), in which the central hybrid segment is flanked by DNA duplexes at both ends, was...
The solution structure and hydration of the chimeric duplex [d(CGC)r(aaa)d(TTTGCG)](2), in which the central hybrid segment is flanked by DNA duplexes at both ends, was determined using two-dimensional NMR, simulated annealing and restrained molecular dynamics. The solution structure of this chimeric duplex differs from the previously determined X-ray structure of the analogous B-DNA duplex [d(CGCAAATTTGCG)](2)as well as NMR structure of the analogous A-RNA duplex [r(cgcaaauuugcg)](2). Long-lived water molecules with correlation time tau(c)longer than 0.3 ns were found close to the RNA adenine H2 and H1' protons in the hybrid segment. A possible long-lived water molecule was also detected close to the methyl group of 7T in the RNA-DNA junction but not with the other two thymines (8T and 9T). This result correlates with the structural studies that only DNA residue 7T in the RNA-DNA junction adopts an O4'-endo sugar conformation, while the other DNA residues including 3C in the DNA-RNA junction, adopt C1'-exo or C2'-endo conformations. The exchange rates for RNA C2'-OH were found to be approximately 5-20 s(-1). This slow exchange rate may be due to the narrow minor groove width of [d(CGC)r(aaa)d(TTTGCG)](2), which may trap the water molecules and restrict the dynamic motion of hydroxyl protons. The minor groove width of [d(CGC)r(aaa)d(TTTGCG)](2)is wider than its B-DNA analog but narrower than that of the A-RNA analog. It was further confirmed by its titration with the minor groove binding drug distamycin. A possible 2:1 binding mode was found by the titration experiments, suggesting that this chimeric duplex contains a wider minor groove than its B-DNA analog but still narrow enough to hold two distamycin molecules. These distinct structural features and hydration patterns of this chimeric duplex provide a molecular basis for further understanding the structure and recognition of DNA. RNA hybrid and chimeric duplexes.
Topics: Base Pairing; Base Sequence; Computer Simulation; DNA; Distamycins; Half-Life; Kinetics; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes; Protons; RNA; Solutions; Titrimetry; Water
PubMed: 10684926
DOI: 10.1093/nar/28.6.1322 -
Nucleic Acids Research Nov 2001The interactions of self-complementary oligonucleotides with a group of metal-mediated DNA-binding drugs, including chromomycin A(3), mithramycin and the novel compound...
The interactions of self-complementary oligonucleotides with a group of metal-mediated DNA-binding drugs, including chromomycin A(3), mithramycin and the novel compound UK-1, were examined via electrospray ionization quadrupole ion trap mass spectrometry. Both chromomycin and mithramycin were shown to bind preferentially to GC-rich oligonucleotide duplexes in a 2:1 drug:metal ratio, while UK-1 was shown to bind in a 1:1 drug:metal stoichiometric ratio without a strong sequence preference. These trends were observed in the presence of Co(2+), Ni(2+) and Zn(2+), with the exception that chromomycin-Zn(2+) complexes were not readily observed. The binding stoichiometries as well as the sequence specificities are in agreement with literature reports for solution studies. Binding selectivities and stabilities of the complexes were also probed using electrospray ionization mass spectrometry. Both of the GC-rich oligomers 5'-GCGCGC-3' and 5'-GCGCATGCGC-3' exhibited a binding preference for chromomycin over mithramycin in the presence of Co(2+) and Ni(2+). Energy-variable collisionally activated dissociation of the complexes was employed to determine the stabilities of the complexes. The relative metal-dependent binding energies were Ni(2+) > Zn(2+) > Co(2+) for UK-1-oligomer complexes and Ni(2+) > Co(2+) for both mithramycin and chromomycin complexes.
Topics: Antineoplastic Agents; Base Sequence; Benzoxazoles; Binding Sites; Chromomycin A3; DNA; Distamycins; Dose-Response Relationship, Drug; Hydrogen-Ion Concentration; Metals; Molecular Weight; Nucleic Acid Synthesis Inhibitors; Oligodeoxyribonucleotides; Plicamycin; Spectrometry, Mass, Electrospray Ionization; Streptomyces; Substrate Specificity; Temperature; Thermodynamics
PubMed: 11691940
DOI: 10.1093/nar/29.21.e103 -
Nucleic Acids Research Jul 1985The binding sites of Hoechst 33258, netropsin and distamycin on three DNA restriction fragments from plasmid pBR322 were compared by footprinting with...
The binding sites of Hoechst 33258, netropsin and distamycin on three DNA restriction fragments from plasmid pBR322 were compared by footprinting with methidiumpropyl-EDTA X Fe(II) [MPE X Fe(II)]. Hoechst, netropsin and distamycin share common binding sites that are five +/- one bp in size and rich in A X T DNA base pairs. The five base pair protection patterns for Hoechst may result from a central three base pair recognition site bound by two bisbenzimidazole NHs forming a bridge on the floor of the minor groove between adjacent adenine N3 and thymine O2 atoms on opposite helix strands. Hydrophobic interaction of the flanking phenol and N-methylpiperazine rings would afford a steric blockade of one additional base pair on each side.
Topics: Base Sequence; Benzimidazoles; Binding Sites; Bisbenzimidazole; DNA; Distamycins; Netropsin
PubMed: 2410856
DOI: 10.1093/nar/13.13.4825 -
Evidence for structural deformation of the DNA helix by a psoralen diadduct but not by a monoadduct.Nucleic Acids Research Sep 1988We have investigated the structural change in a double-stranded DNA helix caused by covalent addition of a psoralen. A synthetic double-stranded DNA was constructed to...
We have investigated the structural change in a double-stranded DNA helix caused by covalent addition of a psoralen. A synthetic double-stranded DNA was constructed to contain either a psoralen furan-side monoadduct or an interstrand diadduct at a specific site. When the unmodified and psoralen modified DNAs were examined by electron microscopy in the presence of distamycin, which stiffens the DNA helix, the DNA containing the psoralen interstrand diadduct appeared bent (or kinked), whereas the furan-side monoadducted DNA appeared similar to the unmodified DNA. RecA protein from E. coli has been shown to preferentially bind UV (ultra violet) irradiated DNA presumably due to alterations in the normal DNA helical structure. Using a nitrocellulose filter binding assay, we have found that the psoralen interstrand diadduct enhances the binding of recA protein to the double-stranded DNA, whereas a furan-side monoadduct has little effect. Thus both the recA protein binding and the electron microscopic data suggest that a psoralen diadduct causes deformation of a DNA helix, most likely by kinking the helix, and that a monoadduct has little effect on the DNA helix structure.
Topics: Base Sequence; DNA; DNA Damage; Distamycins; Furocoumarins; Hydrogen-Ion Concentration; In Vitro Techniques; Microscopy, Electron; Molecular Sequence Data; Molecular Structure; Protein Binding; Rec A Recombinases; Structure-Activity Relationship
PubMed: 3174437
DOI: 10.1093/nar/16.18.8945 -
Biochemistry Sep 2011DNA sequence-dependent conformational changes induced by the minor groove binder, distamycin, have been evaluated by polyacrylamide gel electrophoresis. The distamycin... (Comparative Study)
Comparative Study
DNA sequence-dependent conformational changes induced by the minor groove binder, distamycin, have been evaluated by polyacrylamide gel electrophoresis. The distamycin binding affinity, cooperativity, and stoichiometry with three target DNA sequences that have different sizes of alternating AT sites, ATAT, ATATA, and ATATAT, have been determined by mass spectrometry and surface plasmon resonance to help explain the conformational changes. The results show that distamycin binds strongly to and bends five or six AT base pair minor groove sites as a dimer with positive cooperativity, while it binds to ATAT as a weak, slightly anticooperative dimer. The bending direction was evaluated with an in phase A-tract reference sequence. Unlike other similar monomer minor groove binding compounds, such as netropsin, the distamycin dimer changes the directionality of the overall curvature away from the minor groove to the major groove. This distinct structural effect may allow designed distamycin derivatives to have selective therapeutic effects.
Topics: Base Sequence; DNA-Binding Proteins; Distamycins; Nucleic Acid Heteroduplexes; Protein Binding; Protein Conformation; Protein Multimerization
PubMed: 21800847
DOI: 10.1021/bi201010g -
European Journal of Biochemistry Apr 1994We identify two high-affinity matrix-attachment regions (MAR elements) located in two introns of the human DNA topoisomerase I gene (TOP1). These intronic MAR elements,...
We identify two high-affinity matrix-attachment regions (MAR elements) located in two introns of the human DNA topoisomerase I gene (TOP1). These intronic MAR elements, designated MI and MII, are specifically bound by the nuclear matrix and partition with scaffolds in vitro. One of these MAR elements, MII, is part of a genomic region which is hypersensitive for endogenous nucleases. We have sequenced both DNA elements and have characterized their mode of binding to the nuclear matrix. Experiments with the minor-groove-binding ligands distamycin and chromomycin indicate that the A+T-rich regions, most likely homopolymeric A tracts, are responsible for binding of these DNA elements to the nuclear matrix. MII contains an alu-like element and a segment of curved DNA. Analysis of subfragments of MII show that the curved DNA region itself shows only weak nuclear-matrix binding, and that the high-affinity binding sites are located on subfragments on the 5' side of the curved DNA. In addition, we found that the alu-like sequence does not contribute significantly to the binding of MII and of subfragments of MII to nuclear-matrix proteins. Comparing the distribution of repetitive sequences in the cloned parts of human DNA topoisomerase I gene with the location of high-affinity matrix-binding sites we find no evidence that repetitive DNA may be located close to MAR elements as has been previously suggested.
Topics: Binding Sites; Chromomycins; DNA; DNA Topoisomerases, Type I; Deoxyribonuclease BamHI; Deoxyribonuclease I; Deoxyribonucleases, Type II Site-Specific; Distamycins; Humans; Introns; Molecular Sequence Data; Nuclear Matrix; Nucleic Acid Conformation; Repetitive Sequences, Nucleic Acid
PubMed: 8168528
DOI: 10.1111/j.1432-1033.1994.tb18753.x -
Antimicrobial Agents and Chemotherapy Jun 1972The antibiotics congocidine and distamycin A inhibited the replication of Shope fibroma and vaccinia viruses in BSC(1) cells. Treatment of infected cultures with...
The antibiotics congocidine and distamycin A inhibited the replication of Shope fibroma and vaccinia viruses in BSC(1) cells. Treatment of infected cultures with congocidine for a 12-hr period resulted in an irreversible inhibitory effect on virus development. A longer period of treatment with the antibiotic also resulted in inhibition of the residual infectious virions present in the treated cells. Distamycin A inhibited the replication of poxviruses, but its inhibitory effect was reversed when the antibiotic was removed from the infected cells even as long as 24 hr after treatment. The inhibitory effect of distamycin A and its reversibility resembled the antipoxvirus activity of rifampin.
Topics: Amidines; Anti-Bacterial Agents; Cells, Cultured; Distamycins; Fibroma Virus, Rabbit; Guanidines; Poxviridae; Pyrroles; Virus Replication
PubMed: 4376908
DOI: 10.1128/AAC.1.6.483 -
Journal of Alzheimer's Disease : JAD 2014Tau protein has been proposed as a trigger of Alzheimer's disease once it is hyperphosphorylated. However, the role that native tau forms play inside the neuronal...
Tau protein has been proposed as a trigger of Alzheimer's disease once it is hyperphosphorylated. However, the role that native tau forms play inside the neuronal nucleus remains unclear. In this work we present results concerning the interaction of tau protein with double-stranded DNA, single-stranded DNA, and also with a histone-DNA complex. The tau-DNA interaction results in a structure resembling the beads-on-a-string form produced by the binding of histone to DNA. DNA retardation assays show that tau and histone induce similar DNA retardation. A surface plasmon resonance study of tau-DNA interaction also confirms the minor groove of DNA as a binding site for tau, similarly to the histone binding. A residual binding of tau to DNA in the presence of Distamycin A, a minor groove binder, suggests the possibility that additional structural domains on DNA may be involved in tau interaction. Finally, DNA melting experiments show that, according to the Zipper model of helix-coil transition, the binding of tau increases the possibility of opening the DNA double helix in isolated points along the chain, upon increasing temperature. This behavior is analogous to histones and supports the previously reported idea that tau could play a protective role in stress situations. Taken together, these results show a similar behavior of tau and histone concerning DNA binding, suggesting that post-translational modifications on tau might impair the role that, by modulating the DNA function, might be attributable to the DNA-tau interaction.
Topics: Animals; Cattle; DNA; Histones; Humans; Microscopy, Electron, Transmission; Oligonucleotides; Protein Binding; Protein Processing, Post-Translational; Surface Plasmon Resonance; Thermodynamics; Time Factors; tau Proteins
PubMed: 24254705
DOI: 10.3233/JAD-131415 -
Journal of Neurochemistry Jan 1999Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin, a neurotransmitter that has been implicated in many psychiatric illnesses. The...
Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin, a neurotransmitter that has been implicated in many psychiatric illnesses. The mechanism of transcriptional regulation of the human TPH gene is largely unknown. We have identified a negative regulatory element located between nucleotides -310 and -220 in the human TPH (hTPH) gene. Electromobility shift analyses performed with the -310/-220 hTPH probe and nuclear extract from P815-HTR (a TPH-expressing cell line) revealed two slow migrating protein-DNA complexes, designated I and II. CCAAT displacement protein (CDP/Cut) is involved in complex I formation as shown in electromobility shift analysis, using consensus oligonucleotide competitor and antibody. Mutations in the CDP/Cut binding site not only disrupted the CDP-DNA complex but also disrupted the second complex, suggesting that the core binding sequences of the two proteins are overlapping. The functional importance of these protein-DNA interactions was assessed by transiently transfecting wild-type and mutant pTPH/luciferase reporter constructs into P815-HTR cells. Mutations in the core CDP/Cut site resulted in an approximately fourfold increase in relative luciferase activities. Because CDP/Cut has been shown to repress transcription of many target genes, we speculate that disruption of the CDP/Cut binding was responsible, at least in part, for the activation of hTPH gene.
Topics: Amino Acid Sequence; Animals; Antiviral Agents; DNA Methylation; DNA Probes; DNA-Binding Proteins; Distamycins; Electron Transport Complex II; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Neoplastic; Homeodomain Proteins; Mast-Cell Sarcoma; Mice; Molecular Sequence Data; Multienzyme Complexes; NAD(P)H Dehydrogenase (Quinone); Nuclear Proteins; Oxidoreductases; Protein Binding; Regulatory Sequences, Nucleic Acid; Repressor Proteins; Succinate Dehydrogenase; Transcription, Genetic; Tryptophan Hydroxylase; Tumor Cells, Cultured
PubMed: 9886051
DOI: 10.1046/j.1471-4159.1999.0720029.x