1
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Ranasinghe M, Fogg JM, Catanese DJ, Zechiedrich L, Demeler B. Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:267-280. [PMID: 37501021 PMCID: PMC10530205 DOI: 10.1007/s00249-023-01671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of several months without aggregation or degradation, and with excellent reproducibility. The sedimentation and diffusion coefficients of linearized and nicked minicircle DNA demonstrated a highly homogeneous sample, and increased with temperature, indicating a decrease in friction. The sedimentation of linearized DNA was the slowest; supercoiled DNA sedimented the fastest. With increasing temperature, the supercoiled samples shifted to slower sedimentation, but sedimented faster than nicked minicircles. These results suggest that negatively supercoiled DNA becomes less compact at higher temperatures. The supercoiled minicircles, as purified from bacteria, displayed heterogeneity. Therefore, supercoiled DNA isolated from bacteria is unsuitable as a molecular standard. Linear and nicked samples are well suited as a molecular standard for AUC and have exceptional colloidal stability in an AUC cell. Even after sixty experiments at different speeds and temperatures, measured over the course of 4 months, all topological states of DNA remained colloidal, and their concentrations remained essentially unchanged.
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Affiliation(s)
- Maduni Ranasinghe
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Daniel J Catanese
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, 59812, USA.
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2
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Ramirez P, Leavitt JC, Gill JJ, Mateos M. Preliminary Characterization of Phage-Like Particles from the Male-Killing Mollicute Spiroplasma poulsonii (an Endosymbiont of Drosophila). Curr Microbiol 2022; 80:6. [PMID: 36445499 DOI: 10.1007/s00284-022-03099-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/24/2022] [Indexed: 11/30/2022]
Abstract
Bacteriophages are vastly abundant, diverse, and influential, but with few exceptions (e.g. the Proteobacteria genera Wolbachia and Hamiltonella), the role of phages in heritable bacteria-arthropod interactions, which are ubiquitous and diverse, remains largely unexplored. Despite prior studies documenting phage-like particles in the mollicute Spiroplasma associated with Drosophila flies, genomic sequences of such phage are lacking, and their effects on the Spiroplasma-Drosophila interaction have not been comprehensively characterized. We used a density step gradient to isolate phage-like particles from the male-killing bacterium Spiroplasma poulsonii (strains NSRO and MSRO-Br) harbored by Drosophila melanogaster. Isolated particles were subjected to DNA sequencing, assembly, and annotation. Several lines of evidence suggest that we recovered phage-like particles of similar features (shape, size, DNA content) to those previously reported in Drosophila-associated Spiroplasma strains. We recovered three ~ 19 kb phage-like contigs (two in NSRO and one in MSRO-Br) containing 21-24 open reading frames, a read-alignment pattern consistent with circular permutation, and terminal redundancy (at least in NSRO). Although our results do not allow us to distinguish whether these phage-like contigs represent infective phage-like particles capable of transmitting their DNA to new hosts, their encoding of several typical phage genes suggests that they are at least remnants of functional phage. We also recovered two smaller non-phage-like contigs encoding a known Spiroplasma toxin (Ribosome Inactivating Protein; RIP), and an insertion element, suggesting that they are packaged into particles. Substantial homology of our particle-derived contigs was found in the genome assemblies of members of the Spiroplasma poulsonii clade.
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Affiliation(s)
- Paulino Ramirez
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA.,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Justin C Leavitt
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA. .,Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA.
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3
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Fogg JM, Judge AK, Stricker E, Chan HL, Zechiedrich L. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 2021; 12:5683. [PMID: 34584096 PMCID: PMC8478907 DOI: 10.1038/s41467-021-25936-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
DNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.
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Affiliation(s)
- Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
- Department of Pharmacology and Chemical Biology, Houston, TX, USA
| | - Allison K Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
| | - Erik Stricker
- Department of Molecular Virology and Microbiology, Houston, TX, USA
| | - Hilda L Chan
- Graduate Program in Immunology and Microbiology, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Houston, TX, USA.
- Graduate Program in Immunology and Microbiology, Houston, TX, USA.
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4
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Douglas ME, Ali FA, Costa A, Diffley JF. The mechanism of eukaryotic CMG helicase activation. Nature 2018; 555:265-268. [PMID: 29489749 PMCID: PMC6847044 DOI: 10.1038/nature25787] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/29/2017] [Indexed: 12/17/2022]
Abstract
The initiation of eukaryotic DNA replication occurs in two discrete stages: first, the minichromosome maintenance (MCM) complex assembles as a head-to-head double hexamer that encircles duplex replication origin DNA during G1 phase; then, 'firing factors' convert each double hexamer into two active Cdc45-MCM-GINS helicases (CMG) during S phase. This second stage requires separation of the two origin DNA strands and remodelling of the double hexamer so that each MCM hexamer encircles a single DNA strand. Here we show that the MCM complex, which hydrolyses ATP during double-hexamer formation, remains stably bound to ADP in the double hexamer. Firing factors trigger ADP release, and subsequent ATP binding promotes stable CMG assembly. CMG assembly is accompanied by initial DNA untwisting and separation of the double hexamer into two discrete but inactive CMG helicases. Mcm10, together with ATP hydrolysis, then triggers further DNA untwisting and helicase activation. After activation, the two CMG helicases translocate in an 'N terminus-first' direction, and in doing so pass each other within the origin; this requires that each helicase is bound entirely to single-stranded DNA. Our experiments elucidate the mechanism of eukaryotic replicative helicase activation, which we propose provides a fail-safe mechanism for bidirectional replisome establishment.
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Affiliation(s)
- Max E. Douglas
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT
| | - John F.X. Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT
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5
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Sutthibutpong T, Harris SA, Noy A. Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA. J Chem Theory Comput 2015; 11:2768-75. [PMID: 26575569 DOI: 10.1021/acs.jctc.5b00035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thana Sutthibutpong
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
| | - Sarah A. Harris
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
| | - Agnes Noy
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
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6
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Cebrián J, Kadomatsu-Hermosa MJ, Castán A, Martínez V, Parra C, Fernández-Nestosa MJ, Schaerer C, Martínez-Robles ML, Hernández P, Krimer DB, Stasiak A, Schvartzman JB. Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules. Nucleic Acids Res 2014; 43:e24. [PMID: 25414338 PMCID: PMC4344484 DOI: 10.1093/nar/gku1255] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We systematically varied conditions of two-dimensional (2D) agarose gel electrophoresis to optimize separation of DNA topoisomers that differ either by the extent of knotting, the extent of catenation or the extent of supercoiling. To this aim we compared electrophoretic behavior of three different families of DNA topoisomers: (i) supercoiled DNA molecules, where supercoiling covered the range extending from covalently closed relaxed up to naturally supercoiled DNA molecules; (ii) postreplicative catenanes with catenation number increasing from 1 to ∼15, where both catenated rings were nicked; (iii) knotted but nicked DNA molecules with a naturally arising spectrum of knots. For better comparison, we studied topoisomer families where each member had the same total molecular mass. For knotted and supercoiled molecules, we analyzed dimeric plasmids whereas catenanes were composed of monomeric forms of the same plasmid. We observed that catenated, knotted and supercoiled families of topoisomers showed different reactions to changes of agarose concentration and voltage during electrophoresis. These differences permitted us to optimize conditions for their separation and shed light on physical characteristics of these different types of DNA topoisomers during electrophoresis.
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Affiliation(s)
- Jorge Cebrián
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Maridian J Kadomatsu-Hermosa
- Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción, P.O. Box 2111, SL. San Lorenzo, Paraguay
| | - Alicia Castán
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Víctor Martínez
- Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción, P.O. Box 2111, SL. San Lorenzo, Paraguay
| | - Cristina Parra
- Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción, P.O. Box 2111, SL. San Lorenzo, Paraguay
| | - María José Fernández-Nestosa
- Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción, P.O. Box 2111, SL. San Lorenzo, Paraguay
| | - Christian Schaerer
- Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción, P.O. Box 2111, SL. San Lorenzo, Paraguay
| | - María-Luisa Martínez-Robles
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Dora B Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Andrzej Stasiak
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jorge B Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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7
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Vetcher AA, McEwen AE, Abujarour R, Hanke A, Levene SD. Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity. Biophys Chem 2010; 148:104-11. [PMID: 20346570 PMCID: PMC2867096 DOI: 10.1016/j.bpc.2010.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/25/2010] [Accepted: 02/26/2010] [Indexed: 11/15/2022]
Abstract
Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, DeltaLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution.
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Affiliation(s)
- Alexandre A. Vetcher
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Abbye E. McEwen
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Ramzey Abujarour
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Andreas Hanke
- Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, TX 78520 USA
| | - Stephen D. Levene
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
- Department of Physics, University of Texas at Dallas, Richardson, TX 75083 USA
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8
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Stellwagen NC, Stellwagen E. Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A 2009; 1216:1917-29. [PMID: 19100556 PMCID: PMC2643323 DOI: 10.1016/j.chroma.2008.11.090] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/24/2008] [Accepted: 11/27/2008] [Indexed: 11/18/2022]
Abstract
DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.
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Affiliation(s)
- Nancy C Stellwagen
- Department of Biochemistry, University of Iowa, 4403 Bowen Science Building, Iowa City, IA 52242, USA.
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9
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Abstract
Agarose gel electrophoresis is by far the most widely used method for characterizing the topological state of DNA molecules. Although this technique has been used for more than 30 years, the physical mechanism underlying the resolution of topological states remains poorly understood. However, electrophoretic methods remain the most robust and precise techniques for determining the local unwinding of DNA induced by the binding of proteins and small-molecule ligands, analyzing conformational transitions in duplex DNA, measuring changes in helical repeat that accompany shifts in environmental conditions, and characterizing knotting and linking in duplex DNA.
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Affiliation(s)
- Stephen D Levene
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Dallas, TX, USA
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10
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Widgren S, Elvingson C. Computer simulation of DNA gel electrophoresis: influence of solid friction on linear and circular chains. MACROMOL THEOR SIMUL 2003. [DOI: 10.1002/mats.1996.040050602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stefan Widgren
- Department of Physical Chemistry, Chalmers University of Technology, S‐412 96 Göteborg, Sweden
| | - Christer Elvingson
- Department of Physical Chemistry, Chalmers University of Technology, S‐412 96 Göteborg, Sweden
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11
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D'Agostino L, Di Luccia A. Polyamines interact with DNA as molecular aggregates. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:4317-25. [PMID: 12199710 DOI: 10.1046/j.1432-1033.2002.03128.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
New compounds, named nuclear aggregates of polyamines, having a molecular mass of 8000, 4800 and < 1000 Da, were found in the nuclear extracts of several replicating cells. Their molecular structure is based on the formation of ionic bonds between polyamine ammonium and phosphate groups. The production of the 4800 Da compound, resulting from the aggregation of five or more < 1000 Da units, was increased in Caco-2 cells treated with the mitogen gastrin. Dissolving single polyamines in phosphate buffer resulted in the in vitro aggregation of polyamines with the formation of compounds with molecular masses identical to those of natural aggregates. After the interaction of the 4800 Da molecular aggregate with the genomic DNA at 37 degrees C, both the absorbance of DNA in phosphate buffer and the DNA mobility in agarose gel increased greatly. Furthermore, these compounds were able to protect the genomic DNA from digestion by DNase I, a phosphodiesterasic endonuclease. Our data indicate that the nuclear aggregate of polyamines interacts with DNA phosphate groups and influence, more efficaciously than single polyamines, both the conformation and the protection of the DNA.
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Affiliation(s)
- Luciano D'Agostino
- Department of Clinical and Experimental Medicine, Federico II University, Naples, Italy
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12
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Napoli A, Zivanovic Y, Bocs C, Buhler C, Rossi M, Forterre P, Ciaramella M. DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus. Nucleic Acids Res 2002; 30:2656-62. [PMID: 12060682 PMCID: PMC117289 DOI: 10.1093/nar/gkf377] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Members of the Sso7d/Sac7d family are small, abundant, non-specific DNA-binding proteins of the hyperthermophilic Archaea SULFOLOBUS: Crystal structures of these proteins in complex with oligonucleotides showed that they induce changes in the helical twist and marked DNA bending. On this basis they have been suggested to play a role in organising chromatin structures in these prokaryotes, which lack histones. We report functional in vitro assays to investigate the effects of the observed Sso7d-induced structural modifications on DNA geometry and topology. We show that binding of multiple Sso7d molecules to short DNA fragments induces significant curvature and reduces the stiffness of the complex. Sso7d induces negative supercoiling of DNA molecules of any topology (relaxed, positively or negatively supercoiled) and in physiological conditions of temperature and template topology. Binding of Sso7d induces compaction of positively supercoiled and relaxed DNA molecules, but not of negatively supercoiled ones. Finally, Sso7d inhibits the positive supercoiling activity of the thermophile-specific enzyme reverse gyrase. The proposed biological relevance of these observations is that these proteins might model the behaviour of DNA in constrained chromatin environments.
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Affiliation(s)
- Alessandra Napoli
- Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
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13
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Serban D, Benevides JM, Thomas GJ. DNA secondary structure and Raman markers of supercoiling in Escherichia coli plasmid pUC19. Biochemistry 2002; 41:847-53. [PMID: 11790106 DOI: 10.1021/bi011004z] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Negative supercoiling in the 2686 bp Escherichia coli plasmid pUC19 is comparable in linking number (Lk(0) = 258) and superhelical density (sigma = -0.05) to the moderate supercoiling exhibited by many eukaryotic chromosomal DNAs in vivo. Supercoiled and relaxed forms of purified pUC19 in aqueous solution (0.1 M NaCl, pH 8.3, 20 degrees C) have been investigated by Raman spectroscopy to assess changes in B-DNA secondary structure induced by superhelical stress and to identify putative Raman markers of DNA supercoiling. We find that supercoiling leads to small but significant changes to the B-form Raman signature of linear DNA. Spectral band shifts in the 780-850 cm(-1) interval are interpreted as resulting from a small net change in the average phosphodiester torsions alpha (O3'-P->-O5'-C5') and zeta (C3'-O3'->-P-O5') from the gauche(-)/gauche(-) range to the gauche(-)/trans range with supercoiling. The magnitude of the spectral intensity change implies that approximately 5% of the nucleotide moieties are affected. Supercoiling also introduces small redistributions of Raman intensity within the 1460-1490 and 1660-1670 cm(-1) intervals, consistent with small structural perturbations. Importantly, no Raman markers of Watson-Crick base pairing, base stacking, or C2'-endo/anti deoxynucleoside conformations are perturbed significantly by supercoiling of pUC19, indicating that the B-DNA structure is largely conserved under moderate superhelical stress. Peak and trough features at 814 and 783 cm(-1), and at 1462 and 1489 cm(-1), respectively, in the Raman difference spectrum between superhelical and relaxed DNA are proposed as markers of moderate negative supercoiling. We also show that in Tris-buffered solutions the Raman signature of supercoiled DNA can be obscured by Raman bands of Tris counterions. The subtle structural perturbations to B-DNA induced by moderate supercoiling are consistent with proposed mechanisms of transcriptional activation.
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Affiliation(s)
- Doinita Serban
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110-2499, USA
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14
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Abstract
ySWI/SNF complex belongs to a family of enzymes that use the energy of ATP hydrolysis to remodel chromatin structure. Here we examine the role of DNA topology in the mechanism of ySWI/SNF remodeling. We find that the ability of ySWI/SNF to enhance accessibility of nucleosomal DNA is nearly eliminated when DNA topology is constrained in small circular nucleosomal arrays and that this inhibition can be alleviated by topoisomerases. Furthermore, we demonstrate that remodeling of these substrates does not require dramatic histone octamer movements or displacement. Our results suggest a model in which ySWI/SNF remodels nucleosomes by using the energy of ATP hydrolysis to drive local changes in DNA twist.
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Affiliation(s)
- I Gavin
- Program in Molecular Medicine, Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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15
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Morales V, Richard-Foy H. Role of histone N-terminal tails and their acetylation in nucleosome dynamics. Mol Cell Biol 2000; 20:7230-7. [PMID: 10982840 PMCID: PMC86277 DOI: 10.1128/mcb.20.19.7230-7237.2000] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histone N-terminal tails are central to the processes that modulate nucleosome structure and function. We have studied the contribution of core histone tails to the structure of a single nucleosome and to a histone (H3-H4)(2) tetrameric particle assembled on a topologically constrained DNA minicircle. The effect of histone tail cleavage and histone tail acetylation on the structure of the nucleoprotein particle was investigated by analyzing the DNA topoisomer equilibrium after relaxation of DNA torsional stress by topoisomerase I. Removal of the H3 and H4 N-terminal tails, as well as their acetylation, provoked a dramatic change in the linking-number difference of the (H3-H4)(2) tetrameric particle, with a release of up to 70% of the negative supercoiling previously constrained by this structure. The (H3-H4)(2) tetramers containing tailless or hyperacetylated histones showed a striking preference for relaxed DNA over negatively supercoiled DNA. This argues in favor of a change in tetramer structure that constrains less DNA and adopts a relaxed flat conformation instead of its left-handed conformation within the nucleosome. In contrast neither removal or hyperacetylation of H3 and H4 tails nor removal or hyperacetylation of H2A and H2B N-terminal tails affected the nucleosome structure. This indicates that the globular domain of H2A and H2B is sufficient to stabilize the tailless or the hyperacetylated (H3-H4)(2) tetramer in a left-handed superhelix conformation. These results suggest that the effect of histone tail acetylation that facilitates transcription may be mediated via transient formation of an (H3-H4)(2) tetrameric particle that could adopt an open structure only when H3 and/or H4 tails are hyperacetylated.
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Affiliation(s)
- V Morales
- Laboratoire de Biologie Moléculaire Eucaryote, Institut de Biologie Cellulaire et de Génétique du Centre National de la Recherche Scientifique, 31062 Toulouse, France
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Sivolob A, Prunell A. Nucleosome dynamics V. Ethidium bromide versus histone tails in modulating ethidium bromide-driven tetrasome chiral transition. A fluorescence study of tetrasomes on DNA minicircles. J Mol Biol 2000; 295:41-53. [PMID: 10623507 DOI: 10.1006/jmbi.1999.3301] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protein and DNA contributions in the chiral transition of DNA minicircle-reconstituted tetrasomes (the particles made of DNA wrapped around the histone (H3-H4)(2) tetramer) to a right-handed conformation have been investigated in a recent article from this laboratory. As the evidence for a protein contribution, a sterical hindrance introduced at the H3/H3 interface of the two constituent H3-H4 dimers by oxidation of H3 cysteine 110 blocked the tetramer in a half-left-handed or semi-right-handed conformation, depending on the SH-reagent used. The DNA contributed at the level of the dyad region, which appeared to act through its sequence-dependent deformability in modulating both the loop threshold positive constraint required to trigger the transition, and the tetrasome lateral opening. This opening, which electron microscopic visualizations directly showed to be associated with the transition, is expected to help remove the clash between the entering and exiting DNAs. In this work, the transition mechanism was further investigated by applying a positive constraint in the loop through ethidium bromide (EtBr) intercalation. This technique, including the determination of binding isotherms, has first been used with mononucleosomes on DNA minicircles, and has revealed that these particles could tolerate large positive supercoilings without disruption, owing to the loop ability to cross positively in a histone tail-dependent manner. The transition of 359 bp tetrasomes was found to go to completion in lower salt (10 mM), but not in higher salt (100 mM), whereas the transition of 256 bp tetrasomes was already hindered in lower salt. Histone acetylation relieved that lower salt hindrance but enhanced the higher salt hindrances. These data again pointed to the DNA in the dyad region as a regulator of the transition. The block was indeed expected to originate from a local EtBr intercalation in that DNA, which opposed its overtwisting during the transition. The occurrence of the block, or its relief, then depended on the outcome of the competition between the tails and EtBr for binding to that region, that is, on whether the tails could prevent EtBr intercalation before the ongoing transition hampered both bindings. Destabilization of the tails in the course of the transition is documented in an accompanying article through a relaxation study of a 351-366 bp tetrasome series.
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Affiliation(s)
- A Sivolob
- Institut Jacques Monod, Centre National de la Recherche Scientifique et Université Denis Diderot Paris 7, 2 place Jussieu, Paris Cédex 05, 75251, France
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17
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Hamiche A, Richard-Foy H. Characterization of specific nucleosomal states by use of selective substitution reagents in model octamer and tetramer structures. Methods 1999; 19:457-64. [PMID: 10579941 DOI: 10.1006/meth.1999.0882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Packaging of the DNA in nucleosomes restricts its access to regulatory factors and enzymatic complexes, making a local remodeling of the nucleosome structure a prerequisite to the establishment of protein-DNA interactions. The use of an experimental system in which one nucleosome is reconstituted on a topologically constrained DNA minicircle allows the visualization of different conformations of the nucleoprotein particle. The single cysteine located at position 110 of histone H3 can be titrated with thiol reagents, such as iodoacetamide (IAM), N-ethylmaleimide (NEM), and dithiobisnitrobenzoic acid (DTNB), in both histone octamers and histone (H3-H4)(2) tetramers. Treatment of histone H3 with IAM, NEM, and DTNB allows the trapping of different conformations of the (H3-H4)(2) tetramer within the nucleoprotein particle. When H3 cysteines are titrated within the histone octamer, IAM, NEM, and DTNB block the tetramer in the left-handed conformation, the conformation it adopts within the nucleosome. The left-handed conformation is initially dictated by H2A-H2B dimers and then frozen by the thiol reagents. When cysteines are titrated within the histone tetramer, the flexibility of the particle becomes apparent. NEM and IAM behave differently from DTNB. The first two reagents block the particle in its left-handed conformation while DTNB treatment favors the right-handed conformation. These thiol reagents that block the nucleoprotein particles in a given conformation should allow their structural analysis. They may also help the investigation of the role of the (H3-H4)(2) nucleoprotein particle structural transition in biological processes involving nucleosome dynamics, such as DNA transcription, replication, and repair.
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Affiliation(s)
- A Hamiche
- Institut de Biologie Moléculaire et de Génétique, Centre National de la Recherche Scientifique, 118 route de Narbonne, Toulouse Cedex, 31062, France
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18
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Alilat M, Sivolob A, Révet B, Prunell A. Nucleosome dynamics. Protein and DNA contributions in the chiral transition of the tetrasome, the histone (H3-H4)2 tetramer-DNA particle. J Mol Biol 1999; 291:815-41. [PMID: 10452891 DOI: 10.1006/jmbi.1999.2988] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our laboratory has previously reported the chiral transition of DNA minicircle-reconstituted tetrasomes (the particles made of DNA wrapped around the histone (H3-H4)2tetramer). This transition was induced by DNA positive torsional constraint, generated either by initial supercoiling of the loop or by its thermal fluctuations during topoisomerase relaxation. Taking into account the wrapping of the DNA around the histones into less than a turn, and its negative crossing at the entry-exit, the transition was proposed to involve a 360 degrees rotation of the loop around the particle dyad axis, and the formation of a positive crossing. The tetramer horseshoe-shaped conformation within the octamer further suggested that this process could be mediated by a reorientation of the two sector-like H3-H4 dimers about their H3/H3 interface, which would switch the overall handedness of the proteinaceous superhelix from left to right-handed. We now provide additional evidence for such a contribution of the protein by showing, through gel electrophoresis, topoisomerase relaxation and electron microscopy, that a sterical hindrance at the H3/H3 interface, introduced by covalent linking of bulky adducts through thiol oxidation of H3 cysteine 110, interferes with the transition. Such interference varies, depending on the particular SH-reagent used; but the most remarkable effect was obtained with 5, 5'-dithiobis (2-nitrobenzoic acid) (DTNB), which displaces the preferred conformation of the tetrasomes from left-handed to semi-right-handed, and at the same time preserves a significant degree of chiral flexibility. DNA contribution was evidenced by a specific fractionation of circular tetrasomes in gel electrophoresis which, together with a different positioning of control and DTNB tetrasomes on linear DNA, pointed to an interdependence between tetrasome conformation and positions. Moreover, linear tetrasomes fluctuate between crossed and uncrossed conformations in a salt-dependent equilibrium which appears to vary with their positions on the DNA. These data suggest a modulatable role of the DNA around the dyad in the transition, depending primarily on its sequence-dependent deformability. This role is played at both levels of H3-H4 dimer reorientation and lateral opening, a mechanism by which the particle may relieve the clash between its entering and exiting DNAs. These properties make the tetrasome an attractive potential intermediate in nucleosome dynamics in vivo, in particular duringX transcriptional activation and elongation.
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Affiliation(s)
- M Alilat
- Institut Jacques Monod, Centre National de la Recherche Scientifique, et Université Denis Diderot Paris 7, 2 place Jussieu, Paris, Cédex 05, 75251, France
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19
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Sivolob A, De Lucia F, Révet B, Prunell A. Nucleosome dynamics. II. High flexibility of nucleosome entering and exiting DNAs to positive crossing. An ethidium bromide fluorescence study of mononucleosomes on DNA minicircles. J Mol Biol 1999; 285:1081-99. [PMID: 9918718 DOI: 10.1006/jmbi.1998.2380] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
H2A-H2B exchange with the intranuclear histone pool upon chromatin transcription in vivo is generally viewed as being triggered by the DNA positive supercoiling wave pushed by the elongating polymerase. This notion was tested here by investigating a potential release of H2A-H2B by ethidium bromide-induced positive supercoiling in the loop of mononucleosomes reconstituted on DNA minicircles. The results of gel electrophoresis, fluorescence titration and electron microscopy showed that such a positive supercoiling was not able to release H2A-H2B, nor to unfold the nucleosome to any detectable extent. The reason appeared to be the ease with which the loop could undergo a positive crossing, a surprising observation in view of the DNA left-handed wrapping around the octamer. Moreover, the influence of histone acetylation suggested that such loop flexibility to positive crossing is mediated by histone N-terminal tails which, by interacting with entering and exiting DNAs, reduce their electrostatic repulsion. These conclusions are confirmed and extended in the accompanying article through relaxation with topoisomerase I.
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Affiliation(s)
- A Sivolob
- Institut Jacques Monod, Centre National de la Recherche Scientifique et Université Denis Diderot Paris 7, 2 place Jussieu, Paris Cédex 05, 75251, France
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20
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De Lucia F, Alilat M, Sivolob A, Prunell A. Nucleosome dynamics. III. Histone tail-dependent fluctuation of nucleosomes between open and closed DNA conformations. Implications for chromatin dynamics and the linking number paradox. A relaxation study of mononucleosomes on DNA minicircles. J Mol Biol 1999; 285:1101-19. [PMID: 9918719 DOI: 10.1006/jmbi.1998.2382] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mean linking number (<Lk>) of the topoisomer equilibrium distribution obtained upon relaxation of DNA minicircles with topoisomerase I did not increase linearly, but rather in a step wise fashion, with DNA size between 351 and 366 bp. As a consequence, the corresponding linking number difference (<DeltaLk>) did not remain equal to 0, but rather oscillated between +/-0.3 with the periodicity of the double helix. This oscillation, not observed with plasmid-size DNA, is an expected consequence of the stiffness of short DNA. When minicircles were reconstituted with a nucleosome, the associated <DeltaLkn> oscillated between approximately -1.4 +/-0. 2. This oscillation appears to result from the combined effects of DNA stiffness, and nucleosome ability to thermally fluctuate between three distinct DNA conformational states. Two of these states, a closed approximately 1.75-turn DNA conformation with negatively crossed entering and exiting DNAs, and an open approximately 1.4-turn conformation with uncrossed DNAs, are well known, whereas the third state, with a closed DNA conformation and DNAs tending to cross positively rather than negatively, is less familiar. Access to both closed "negative" and "positive" states appears to be mediated by histone N-terminal tails, as shown by specific alterations to the <DeltaLkn> oscillation caused by histone acetylation and phosphate ions, a potent tail destabilizator. These results extend previous observations of ethidium bromide fluorescence titration in the accompanying article, which have pointed to an histone tail-dependent flexibility of entering and exiting DNAs to positive crossing. They also show that DNA wrapping around the histones occurred without twist alteration compared to the DNA free in solution, and reveal an intriguing new facet of the "linking-number-paradox" problem: the possibility for linkers in chromatin to adopt different crossing status within an overall dynamic equilibrium which may be regulated by histone acetylation.
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Affiliation(s)
- F De Lucia
- Institut Jacques Monod, Centre National de la Recherche Scientifique et Université Denis Diderot Paris 7, 2 place Jussieu, Paris Cedex 05, 75251, France
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21
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Åkerman B. Ring−Polymer Dynamics in Gels: Supercoiled and Relaxed Circular DNA in Polyacrylamide. J Phys Chem B 1998. [DOI: 10.1021/jp981905q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Björn Åkerman
- Department of Physical Chemistry, Chalmers University of Technology, S-412 96 Göteborg, Sweden
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22
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Hamiche A, Richard-Foy H. The switch in the helical handedness of the histone (H3-H4)2 tetramer within a nucleoprotein particle requires a reorientation of the H3-H3 interface. J Biol Chem 1998; 273:9261-9. [PMID: 9535919 DOI: 10.1074/jbc.273.15.9261] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has recently been proposed that the histone (H3-H4)2 tetramer undergoes structural changes, which allow the particle to accommodate both negatively and positively constrained DNA. To investigate this process, we modified histone H3 at the H3-H3 interface, within the histone (H2A-H2B-H3-H4)2 octamer or the histone (H3-H4)2 tetramer, by forming adducts on the single cysteine of duck histone H3. We used three sulfhydryl reagents, iodoacetamide, N-ethylmaleimide, and 5,5'-dithiobis(2-nitrobenzoic acid). Torsionally constrained DNA was assembled on the modified histones. The H3 adducts, which have no effect on the structure of the nucleosome, dramatically affected the structural transitions that the (H3-H4)2 tetrameric nucleoprotein particle can undergo. Iodoacetamide and N-ethylmaleimide treatment prevented the assembly of positively constrained DNA on the tetrameric particle, whereas 5, 5'-dithiobis(2-nitrobenzoic acid) treatment strongly favored it. Determination of DNA topoisomer equilibrium after relaxation of the tetrameric nucleoprotein particles with topoisomerase I demonstrated that the structural transition occurs without histone dissociation. Incorporation of H2A-H2B dimers into the tetrameric particle containing modified or unmodified cysteines allowed nucleosomes to reform and blocked the structural transition of the particle. We demonstrate the importance of the histone H3-H3 contact region in the conformational changes of the histone tetramer nucleoprotein particle and the role of H2A-H2B in preventing a structural transition of the nucleosome.
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Affiliation(s)
- A Hamiche
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, 118 route de Narbonne, 31062 Toulouse Cedex, France
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23
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Abstract
A purine repressor (PurR) mediates adenine nucleotide-dependent regulation of transcription initiation of the Bacillus subtilis pur operon. This repressor has been purified for the first time, and binding to control site DNA was characterized. PurR binds in vitro to four operons. Apparent Kd values for binding were 7 nM for the pur operon, 8 nM for purA, 13 nM for purR, and 44 nM for the pyr operon. In each case, DNase I footprints exhibited a pattern of protected and hypersensitive sites that extended over more than 60 bp. A GAAC-N24-GTTC sequence in the pur operon was necessary but not sufficient for the PurR-DNA interaction. However, this motif, which is conserved in the four binding sites, was not required for binding of PurR to purA. Thus, the common DNA recognition element for binding of PurR to the four operons is not known. Multiple PurR-pur operon DNA complexes having a binding stoichiometry that was either approximately two or six repressor molecules per DNA fragment were detected. The results of a torsional constraint experiment suggest that control site DNA forms one right-handed turn around PurR.
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Affiliation(s)
- B S Shin
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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24
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Hamiche A, Carot V, Alilat M, De Lucia F, O'Donohue MF, Revet B, Prunell A. Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: Potential flipping of the protein from a left- to a right-handed superhelical form. Proc Natl Acad Sci U S A 1996; 93:7588-93. [PMID: 8755519 PMCID: PMC38790 DOI: 10.1073/pnas.93.15.7588] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have studied the ability of the histone (H3-H4)2 tetramer, the central part of the nucleosome of eukaryotic chromatin, to form particles on DNA minicircles of negative and positive superhelicities, and the effect of relaxing these particles with topoisomerase I. The results show that even modest positive torsional stress from the DNA, and in particular that generated by DNA thermal fluctuations, can trigger a major, reversible change in the conformation of the particle. Neither a large excess of naked DNA, nor a crosslink between the two H3s prevented the transition from one form to the other. This suggested that during the transition, the histones neither dissociated from the DNA nor were even significantly reshuffled. Moreover, the particles reconstituted on negatively and positively supercoiled minicircles look similar under electron microscopy. These data agree best with a transition involving a switch of the wrapped DNA from a left- to a right-handed superhelix. It is further proposed, based on the left-handed overall superhelical conformation of the tetramer within the octamer [Arents, G., Burlingame, R. W., Wang, B. C., Love, W. E. & Moudrianakis, E. N. (1991) Proc. Natl.Acad. Sci. USA 88, 10148-10152] that this change in DNA topology is mediated by a similar change in the topology of the tetramer itself, which may occur through a rotation (or a localized deformation) of the two H3-H4 dimers about their H3-H3 interface. Potential implications of this model for nucleosome dynamics in vivo are discussed.
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Affiliation(s)
- A Hamiche
- Institut Jaccques Monod, Centre Nationale la Recherche Scientifique et Université Denis Diderot Paris 7, France
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25
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Wheeler DL, Chrambach A. Computer simulation of the directional displacement of rod-shaped, arc-shaped, and circular objects in an array of obstacles, representing a simple model for the gel electrophoresis of small DNA. Biopolymers 1995; 35:179-85. [PMID: 7696563 DOI: 10.1002/bip.360350206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The gel electrophoresis of DNA of identical length but various static conformations was simulated using a two-dimensional model of the movement of rod-shaped, arc-shaped, and circular objects through random arrays of disk-shaped obstacles. At low obstacle density, the displacement rate of these objects decreases from the rod-shaped to the circular to the arc-shaped objects. At high obstacle densities, the displacement rate of circular objects approaches zero. The alignment of the arc-shaped objects along the axis of the directional movement of the objects were retarded in their movement by collisions with the obstacles; the number of collisions of the former, in view of their greater ability to align, was less than that of the latter. Circular objects were exclusively retarded by collisions, while the arc-shaped objects exhibited an additional retarding mechanism, viz. the suspension ("hanging") on the obstacles. When the rigid objects were made flexible, their displacement increased. The increase was most pronounced with the circular objects, allowing them to penetrate at obstacle densities from which the rigid objects were excluded.
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Affiliation(s)
- D L Wheeler
- Section on Macromolecular Analysis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-0001
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26
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Mojica FJ, Charbonnier F, Juez G, Rodríguez-Valera F, Forterre P. Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J Bacteriol 1994; 176:4966-73. [PMID: 8051009 PMCID: PMC196334 DOI: 10.1128/jb.176.16.4966-4973.1994] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We report here the effect of environmental parameters, salinity, temperature, and an intercalating drug on plasmid topology in the halophilic archaeon Haloferax volcanii. We first studied the topological state of the plasmid pHV11 in media of different salt compositions and concentrations. The superhelical density of plasmid PHV11 varies in a way that depends on the kind of salt and on the concentrations of individual salts. With respect to growth temperature, the plasmid linking number increased at higher temperature in a linear way, contrary to what has been reported for Escherichia coli, in which the plasmid linking number decreased at higher temperature. These results suggest that some of the mechanisms that control DNA supercoiling in halophilic Archaea may be different from those described for E. coli. However, homeostatic control of DNA supercoiling seems to occur in haloarchaea, as in Bacteria, since we found that relaxation of DNA by chloroquine triggers an increase in negative supercoiling.
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Affiliation(s)
- F J Mojica
- Departamento de Genética y Microbiología, Universidad de Alicante, Spain
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27
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Culard F, Spotheim-Maurizot M, Sabattier R, Charlier M. Radiosensitivity of DNA minicircles. Int J Radiat Biol 1994; 65:651-6. [PMID: 7912714 DOI: 10.1080/09553009414550761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA minicircles of 207 bp were constructed by the ligation of linear restriction fragments in the presence of various concentrations of ethidium bromide. Three topoisomers characterized by linking numbers (Lk) of 20, 19 and 18, and with helical repeats of 10.35, 10.9 and 11.5 bp/turn respectively, were obtained. They are called, respectively, relaxed minicircle or topoisomer 0, topoisomer -1 and topoisomer -2. Owing to the limited flexibility of such small circles, the stress created by the lack of 1 or 2 turns cannot be eliminated by a spatial circle-axis writhing (supercoiling) of the circular molecules. These two undertwisted, stressed topoisomers have to adopt a flat, non-crossed shape, similar to that of the relaxed minicircle. The three minicircles were irradiated with gamma-rays or fast neutrons. The same yields of single-strand breaks, double-strand breaks and alkali-induced single-strand breaks were observed for the three topoisomers showing that their base and sugar moieties are attacked equally by gamma photon- or fast neutron-induced radicals. We conclude that untwisting of a B helix does not modify the radiosensitivity of DNA.
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Affiliation(s)
- F Culard
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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28
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Abstract
The instability of cell cultures containing plasmid vectors is a major problem in the commercial exploitation of molecular cloning techniques. Plasmid stability is influenced by the nature of the host cell, the type of plasmid and/or environmental conditions. Plasmid encoded properties may confer a selective advantage on the host cell but can be an energy drain due to replication and expression. Stability of recombinant cultures ultimately may be determined by the cost to benefit ratio of plasmid carriage. The relative competition between plasmid containing and plasmid-free or indigenous populations can determine the degree of dominance of recombinant cultures. The use of inocula in biotechnological processes in which dynamic environmental conditions dominate may also result in instabilities resulting from the characteristics of the ecosystem. In such dynamic conditions plasmid stability is just one contribution to culture stability. Strategies to enhance plasmid stability, within such environments, based on manipulation of physiological state of host cells, must consider the responsiveness or plasticity of both cells and populations. The robustness of cells or the responses to stresses or transient environmental conditions can influence the levels of instability detected; for example, instability or mutation in the host genome may lead to enhanced plasmid stability. Competition among subpopulations arising from unstable copy number control may determine the levels of recombinant cells in open versus closed fermenter systems. Thus the ecological competence (ability to survive and compete) of recombinant cells in dynamic or transient environments is fundamental to the understanding of the ultimate dominance or survival of such recombinant cultures and may form the basis of a strategy to enhance or control stability either in fermenter systems or dynamic process environments. The creation of microniches in time and/or space can enhance plasmid stability. Transient operation based on defined environmental stresses or perturbations in fermenter systems or in heterogeneous or dynamic environments found in gel immobilized cultures have resulted in enhanced stability. Spatial organization resulting from immobilization has the additional advantage of regulated cell protection within defined microenvironments and controlled release, depending on the nature of the gel, from these microenvironments or microcosms. This regulation of ecological competence allied to the advantages of microbial cell growth in gel microenvironments combined with the spatial organization (or juxtapositioning of cells, selective agents, nutrients, protectants, etc.) possible through immobilization technology offers new strategies to enhance plasmid and culture stability.
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Affiliation(s)
- A J McLoughlin
- Department of Industrial Microbiology, University College Dublin, Ireland
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29
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Meury J, Kohiyama M. Potassium ions and changes in bacterial DNA supercoiling under osmotic stress. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05559.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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30
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Hamiche A, Prunell A. Chromatin reconstitution on small DNA rings. V. DNA thermal flexibility of single nucleosomes. J Mol Biol 1992; 228:327-37. [PMID: 1453443 DOI: 10.1016/0022-2836(92)90821-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The thermal flexibility of DNA minicircles reconstituted with single nucleosomes was measured relative to the naked minicircles. The measurement used a new method based on the electrophoretic properties of these molecules, whose mobility strongly depended on the DNA writhe, either of the whole minicircle, when naked, or of the extranucleosomal loop, when reconstituted. The experiment was as follows. The DNA length was first increased by one base-pair (bp), and the correlative shift in mobility resulting from the altered DNA writhe was recorded. Second, the gel temperature was increased so that the former mobility was restored. Under these conditions, the untwisting of the thermally flexible DNA due to the temperature shift exactly compensates for the increase in the DNA mean twist number resulting from the one bp addition. The relative thermal flexibility was then calculated as the ratio between the increases in temperature measured for the naked and the reconstituted DNAs, respectively. The figure, 0.69 (+/- 0.07), was used to derive the length of DNA in interaction with the histones, 109 (+/- 25) bp. Such length was in good agreement with the mean value of 115 bp we have previously obtained from the distribution of the angles between DNAs at the entrance and exit of similar nucleosomes measured from high resolution electron microscopy. This consistency further reinforces our previous conclusion that minicircle-reconstituted nucleosomes, with 1.3(109/83) to 1.4(115/83) turns of superhelical DNA, show no crossing of entering and exiting DNAs when the loop is in its most probable configuration, and therefore, that these nucleosomes behave topologically as "single-turn" particles. The present data are also within the range of values, 50 to 100 bp of thermally rigid DNA per nucleosome, obtained by others for yeast plasmid chromatin, suggesting that the "single-turn" particle notion may be extended to this particular case of naturally-occurring H1-free chromatin. However, these data are quite different from the 230 bp figure derived from thermal measurements of reconstituted H1-free minichromosomes. It is proposed that nucleosome interactions occurring in this chromatin, but not in yeast chromatin, may be partly responsible for the discrepancy.
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Affiliation(s)
- A Hamiche
- Centre National de la Recherche Scientifique, Paris, France
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31
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Duband-Goulet I, Carot V, Ulyanov AV, Douc-Rasy S, Prunell A. Chromatin reconstitution on small DNA rings. IV. DNA supercoiling and nucleosome sequence preference. J Mol Biol 1992; 224:981-1001. [PMID: 1314907 DOI: 10.1016/0022-2836(92)90464-u] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleosome formation on inverted repeats or on some alternations of purines and pyrimidines can be inhibited in vitro by DNA supercoiling through their supercoiling-induced structural transitions to cruciforms or Z-form DNA, respectively. We report here, as a result of study of single nucleosome reconstitutions on a DNA minicircle, that a physiological level of DNA supercoiling can also enhance nucleosome sequence preference. The 357 base-pair minicircle was composed of a promoter of phage SP6 RNA polymerase joined to a 256 base-pair fragment containing a sea urchin 5 S RNA gene. Nucleosome formation on the promoter was found to be enhanced on a topoisomer with in vivo superhelix density when compared to topoisomers of lower or higher superhelical densities, to the nicked circle, or to the linear DNA. In contrast, nucleosomes at other positions appeared to be insensitive to supercoiling. This observation relied on a novel procedure for the investigation of nucleosome positioning. The reconstituted circular chromatin was first linearized using a restriction endonuclease, and the linear chromatin so obtained was electrophoresed as nucleoprotein in a polyacrylamide gel. The gel showed well-fractionated bands whose mobilities were a V-like function of nucleosome positions, with the nucleosome near the middle migrating less. This behavior is similar to that previously observed for complexes of sequence-specific DNA-bending proteins with circularly permuted DNA fragments, and presumably reflects the change in the direction of the DNA axis between the entrance and the exit of the particle. Possible mechanisms for such supercoiling-induced modulation of nucleosome formation are discussed in the light of the supercoiling-dependent susceptibility to cleavage of the naked minicircle with S1 and Bal31 nucleases; and a comparison between DNase I cleavage patterns of the modulated nucleosome and of another, non-modulated, overlapping nucleosome.
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Affiliation(s)
- I Duband-Goulet
- Institut Jaques Monod, Centre National de la Recherche Scientifique and Université, Paris, France
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32
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Garner MM, Chrambach A. Resolution of circular, nicked circular and linear DNA, 4.4 kb in length, by electrophoresis in polyacrylamide solutions. Electrophoresis 1992; 13:176-8. [PMID: 1592050 DOI: 10.1002/elps.1150130136] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Circular DNA of more than 1,400 bp in size is known not to migrate into polyacrylamide gels. The migration of supercoiled plasmid pBR322 DNA (4,363 by) into uncrosslinked polyacrylamide (Mw 5 x 10(6)) solutions and its separation, on the basis of conformation, from its nicked form is demonstrated in this study. Migration of the supercoiled, nicked circular and linear forms of the plasmid DNA is retarded in proportion to the concentration of uncrosslinked polyacrylamide, the degree of retardation being highest for the nicked circular form. Decreasing the level of supercoiling of the covalently closed circular form by decreasing the concentration of the intercalating dye (ethidium homodimer) shows that the degree of retardation decreases in proportion to the superhelix density.
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Affiliation(s)
- M M Garner
- Section on Macromolecular Analysis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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33
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Nordén B, Elvingson C, Jonsson M, Akerman B. Microscopic behaviour of DNA during electrophoresis: electrophoretic orientation. Q Rev Biophys 1991; 24:103-64. [PMID: 1924681 DOI: 10.1017/s0033583500003395] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study of the behaviour of DNA when subjected to electric fields poses several intriguing problems of fundamental physico-chemical importance. Electric field (Kerr effect) orientation of DNA in free solution as well as migration of DNA in gel electrophoresis are two well-established, but so far rather separate, research fields. Whereas the first one has been generally concerned with basic structural and dynamical properties of DNA (Charney, 1988), the second is closely related to techniques of molecular biology (for a review on DNA electrophoresis, see stellwagen 1987).
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Affiliation(s)
- B Nordén
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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34
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Gaillard C, Strauss F. Sequence-specific single-strand-binding protein for the simian virus 40 early promoter stimulates transcription in vitro. J Mol Biol 1990; 215:245-55. [PMID: 2170663 DOI: 10.1016/s0022-2836(05)80343-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have detected, in nuclear extracts of non-infected cultured monkey cells, a protein (protein H16) that binds a specific single-stranded DNA sequence in the early promoter of simian virus 40 (SV40). This protein does not bind double-stranded DNA, nor RNA. In the present paper, the DNA-binding properties of protein H16 and its effects on transcription by RNA polymerase II in vitro have been investigated. The protein binds only to the late strand of the early promoter, within the region of the 21 base-pair repeats, and shows no affinity for any other SV40 sequence. The high percentage of cytosine residues in the late strand in this region appears to be important for recognition by the protein. Protein H16 does not bind the control region of SV40 in negatively supercoiled DNA circles. When bound to the late strand, the protein is displaced from its binding site by reassociation of the early strand with the late strand. Its binding to DNA is not sensitive to methylation of the dinucleotide CG in its binding site. The protein has been purified to near homogeneity by preparative gel retardation, and has an apparent molecular weight of 70,000. Purified protein H16 stimulates transcription by purified RNA polymerase II in vitro. The possible role of sequence-specific single-strand-binding proteins in transcription is discussed.
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35
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Zivanovic Y, Duband-Goulet I, Schultz P, Stofer E, Oudet P, Prunell A. Chromatin reconstitution on small DNA rings. III. Histone H5 dependence of DNA supercoiling in the nucleosome. J Mol Biol 1990; 214:479-95. [PMID: 2166168 DOI: 10.1016/0022-2836(90)90195-r] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mononucleosomes were reconstituted on small DNA rings in the presence of histone H5 and relaxed to an equilibrium using calf thymus topoisomerase I. DNA products, when compared to the equilibria observed with the same minicircles in the absence of histones, showed that a linking number reduction of 1.6 to 1.7 was associated with this reconstitution, in contrast with the 1.1 to 1.2 figure reported in our recent study of the H5-free nucleosome. Gel electrophoretic properties and electron microscopic visualization of the nucleosomes suggest a correlation between this increase and a further wrapping of the DNA around the histone core from less than 1.5 turns of the superhelix in the absence of H5, to close to two turns in its presence. Implications for DNA topology in chromatin are discussed.
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Affiliation(s)
- Y Zivanovic
- Centre National de la Recherche Scientifique, Paris, F|rance
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36
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Gilson E, Perrin D, Hofnung M. DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization. Nucleic Acids Res 1990; 18:3941-52. [PMID: 2197600 PMCID: PMC331097 DOI: 10.1093/nar/18.13.3941] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to the DNA polymerase I (Pol I). This constitutes the first indication for a specific interaction between Pol I and a duplex DNA. This interaction requires the presence of PU. It was confirmed and analyzed by native gel electrophoresis and DNase I footprinting experiments. The other activity contained at least five polypeptides. Its binding to PU DNA sequences was confirmed by native gel electrophoresis. Implications for the possible origin and functions of PU are discussed.
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Affiliation(s)
- E Gilson
- Unité de Programmation Moléculaire et Toxicologie Génétique, CNRS UA271 INSERM U163, Institut Pasteur, Paris, France
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37
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Eismann ER, Müller-Hill B. lac repressor forms stable loops in vitro with supercoiled wild-type lac DNA containing all three natural lac operators. J Mol Biol 1990; 213:763-75. [PMID: 2359123 DOI: 10.1016/s0022-2836(05)80262-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have analyzed protein-DNA complexes formed between lac repressor and linear or differently supercoiled lac DNA (802 or 816 base-pairs in length), which carry all three natural lac operators (O1, O2 and O3) in their wild-type sequence context and spacing and compared them with constructs that contain specifically mutated "pseudo-operators" O2 or O3. We used gel retardation assays to identify the nature of the complexes according to their characteristic electrophoretic mobility and dissociation rate measurements to determine their stability. With linear DNA we found only indirect evidence for loop formation between O1 and O2. In covalently closed DNA minicircles the formation of a loop between O1 and O2 could be demonstrated by the observation that O1-O2 containing DNA with low negative supercoiling (sigma = -0.013 and less) is constricted by binding of lac repressor, resulting in an increased electrophoretic mobility. At elevated negative supercoiling (sigma = -0.025, -0.037, -0.05) O1-O2 containing DNA complexed with lac repressor migrates significantly slower than the corresponding O1-DNA, indicating loop formation. The dissociation of lac repressor-operator complexes is decreased with increasing negative supercoiling for all tested operator combinations of O1, O2 and O3. However, in the presence of at least two natural lac operators on the same DNA minicircle the enhancement of stability is particularly large. This indicates that a DNA loop is formed between these two lac operators, O1 and O2 as well as O1 and O3, since negative supercoiling is known specifically to promote the formation of looped structures. Additionally, we observe a dependence of dissociation rate on the spatial alignment of the operators as a result of changing helical periodicity in differently supercoiled DNA and consider this to be further evidence for loop formation between O1 and O2 as well as O1 and O3.
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Affiliation(s)
- E R Eismann
- Institut für Genetik, Universität zu Köln, F.R.G
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38
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Douc-Rasy S, Kolb A, Prunell A. Protein-induced unwinding of DNA: measurement by gel electrophoresis of complexes with DNA minicircles. Application to restriction endonuclease EcoRI, catabolite gene activator protein and lac repressor. Nucleic Acids Res 1989; 17:5173-89. [PMID: 2548154 PMCID: PMC318104 DOI: 10.1093/nar/17.13.5173] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An electrophoretic procedure for the measurement of the helix unwinding induced by a sequence-specific protein is described. The method, which was applied here to EcoR I, CAP and lac repressor, involved the migration of the complexes with positively and negatively supercoiled DNA minicircles carrying a single protein binding site. Mobility shifts of complexes relative to naked DNAs appeared to be a result of i) the unwinding; of ii) an increase in the molecular frictional coefficient, which led to a retardation; of iii) bending, in the particular case of CAP, which induced an acceleration; and of iv) looping, in the case of lac repressor, which also resulted in an acceleration. Under conditions where the migration of the naked topoisomers was V-like (topoisomer mobility showed the same linear increase with both negative and positive supercoilings; Zivanovic et al. (1986) J. Mol. Biol., 192, 645-660), the protein unwinding contribution to mobility was assumed to be identical to that experimentally observed in the case of a thermal unwinding: all negatively supercoiled topoisomers were retarded and all positively supercoiled topoisomers were accelerated to the same extent. In contrast, the mobility contribution of the frictional term, as well as those of bending and looping, appeared to vary strongly with the magnitude of the supercoiling, but only weakly with its polarity. As a consequence, these latter contributions may approximately cancel when one is measuring the difference between the shifts observed for two comigrating, negatively and positively supercoiled, topoisomers, allowing the unwinding to be calculated. While estimates obtained for EcoR I, 23 +/- 3 degrees, and CAP, about 29 degrees, were in good agreement with previous measurements using topoisomerase I, the value found for lac repressor, 13 to 16 degrees, was significantly smaller.
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Affiliation(s)
- S Douc-Rasy
- Centre National de la Recherche Scientifique, Université Paris VII, Institut Jacques Monod, France
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39
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Zivanovic Y, Goulet I, Revet B, Le Bret M, Prunell A. Chromatin reconstitution on small DNA rings. II. DNA supercoiling on the nucleosome. J Mol Biol 1988; 200:267-90. [PMID: 2836595 DOI: 10.1016/0022-2836(88)90239-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA supercoiling on the nucleosome was investigated by relaxing with topoisomerase I mono- and dinucleosomes reconstituted on small DNA rings. Besides 359 base-pair (bp) rings whose linking differences were integers, two additional series of rings with fractional differences, 341 and 354 bp in size, were used. Mononucleosomes reconstituted on 359 bp rings were found to relax into a single mononucleosome form. In contrast, 341 and 354 bp mononucleosomes relaxed into a mixture of two forms, corresponding to two adjacent topoisomers. The observation that the ratio between these two forms was, within each ring series, virtually independent of the initial linking number of the topoisomer used for the reconstitution suggested that each partition reflected an equilibrium. Comparison with the equilibria observed for the same rings in the absence of histones showed that the formation of a single nucleosome is associated with a linking number change of -1.1(+/-0.1) turn. Dinucleosomes, in contrast, were not relaxed to completion and do not reach equilibria. The corresponding linking number change per nucleosome was, however, estimated to be similar to the above figure, in agreement with previous data from the literature obtained with circular chromatins containing larger numbers of nucleosomes. DNA structure in mononucleosomes was subsequently investigated by means of high-resolution electron microscopy and gel electrophoresis. It was found that the above linking number reduction could be ascribed to a particle with a large open extranucleosomal DNA loop and with no more than 1.5 turns of a superhelix around the histone core. A theoretical model of a nucleosome on a small ring was constructed in which one part of the DNA was wrapped around a cylinder and the other part was free to vary both in torsion and flexion. The linking number reduction predicted was found to be most consistent with experimental data when the twist of the DNA in the superhelix was between 10.5 and 10.65 pb per turn, suggesting that wrapping on the nucleosome does not alter the twist of the DNA significantly. A lower estimate of the linking number reduction associated with a two-turn nucleosome was also derived, based on an analysis of recent data obtained upon treatment of reconstituted minichromosomes with gyrase. The value, 1.6 turns, set a lower limit of 10.44 bp per turn for the twist of nucleosomal DNA, in agreement with the above estimate.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- Y Zivanovic
- Centre National de la Recherche Scientifique, Université Paris VII, Institut Jacques Monod, Paris, France
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40
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Abstract
Chromatin was reconstituted using the four core histones on 359 base-pair nicked and closed rings by salt dialysis and/or at physiological ionic strength by means of polyglutamic acid. The products, which consisted of mono- and dinucleosomes, were characterized by gel electrophoresis, sedimentation in sucrose gradients and high-resolution electron microscopy. The results were as follows. (1) The efficiency of the reconstitution was found first to increase with the negative linking difference of the closed rings relative to their relaxed configuration to reach a maximum for -2 turns, and then to decrease for the largest difference of -3 turns. Discrepancies between topoisomers were also observed with regard to differential formation of mono- and dinucleosomes. Topoisomer -1 reconstituted monomers easily but reconstituted dimers with difficulty, whilst this discrimination was virtually absent in the case of topoisomers -2 and -3. Moreover, mononucleosomes on the nicked ring were, with respect to their electrophoretic mobility, similar to mononucleosomes formed on topoisomer -1 but not to those on the other topoisomers, whose mobilities were greater. These features were interpreted in terms of the linking number change associated with the formation of a nucleosome monomer and dimer, approximately -1 and -2 turns, respectively. (2) Two dinucleosome subtypes were found to form in a sequential manner. Their different electrophoretic mobilities and sedimentation coefficients suggested that the early subtype is lighter, probably because of an incomplete histone complement in the second nucleosome of that subtype as a result of an impaired co-operativity in octamer assembly due to the small ring size. (3) An electron microscopic examination of the chromatin reconstituted on topoisomer -2 revealed that both mono- and dinucleosomes adopt two different, salt-dependent, morphologies each: in type I, entering and exiting DNAs do not cross, whilst they do in type II. Type I configuration is favoured in lower salt, whereas type II is favoured in higher salt. Such behaviour explains why nucleosomes in dimers were found to be always diametrically opposed on the rings rather than sometimes apposed, as would have been expected from a random deposition of the histone cores.
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Affiliation(s)
- I Goulet
- Centre National de la Recherche Scientifique, Université Paris VII, Institut Jacques Monod, France
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41
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Nordheim A, Meese K. Topoisomer gel retardation: detection of anti-Z-DNA antibodies bound to Z-DNA within supercoiled DNA minicircles. Nucleic Acids Res 1988; 16:21-37. [PMID: 3340525 PMCID: PMC334610 DOI: 10.1093/nar/16.1.21] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Small DNA fragments of approximately 350 bp in length, either with or without d(CG)n tracts, are ligated into underwound DNA minicircles to generate topoisomeric rings with different topological linking numbers, Lk. These minicircles, differing by an Lk of one, can be separated by acrylamide gel electrophoresis. Furthermore, electrophoresis can be used to reveal DNA double helix conformational changes that are induced by supercoiling, such as left-handed Z-DNA. When anti-Z-DNA antibodies are added to such minicircles, their binding leads to a selective retardation of the electrophoretic migration of the Z-DNA containing circles. This effect is not seen with relaxed minicircles and those with insufficient torsional stress to induce a conformational transition. Thus the technique of 'topoisomer gel retardation' presents a very sensitive assay for the identification of proteins that selectively bind to DNA conformations stabilized by negative DNA supercoiling.
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Affiliation(s)
- A Nordheim
- Zentrum für Molekulare Biologie (ZMBH), Universität Heidelberg, FRG
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42
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Benham CJ. The influence of tertiary structural restraints on conformational transitions in superhelical DNA. Nucleic Acids Res 1987; 15:9985-95. [PMID: 3320960 PMCID: PMC306545 DOI: 10.1093/nar/15.23.9985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transitions are shown to occur at equilibrium at less extreme superhelicities in DNA whose tertiary structure is restrained than in unrestrained molecules where the residual linking difference alpha res (that part of the superhelical deformation which is not absorbed by transitions) may be freely partitioned between twisting and bending. In the extreme case of a rigidly held tertiary structure, this analysis predicts that the B-Z transition will occur at roughly half the superhelix density needed to drive the same transition in solution, other factors remaining fixed. This suggests that superhelical transitions may occur at more moderate superhelical deformations in vivo than in solution. The influence on transition behavior of the tertiary structural restraints imposed by gel conditions also are discussed.
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Affiliation(s)
- C J Benham
- Mathematics Department, University of Kentucky, Lexington 40506
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43
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Goulet I, Zivanovic Y, Prunell A. Helical repeat of DNA in solution. The V curve method. Nucleic Acids Res 1987; 15:2803-21. [PMID: 3562239 PMCID: PMC340700 DOI: 10.1093/nar/15.7.2803] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The V-like dependence of the electrophoretic mobility of small DNA rings on their topological constraint, which has been documented in a recent paper [Zivanovic et al. (1986), J. Mol. Biol., 192, 645-660], has been explored as a tool to measure the helical twist of the torsionally unstressed duplex. The method was applied to single mixed sequence fragments approximately 350 to 1400 base pairs in length, providing estimates of their average helical periodicity. It was also used to compare two DNA fragments, and to evaluate the helical repeat of poly(dA.dT).poly(dA.dT) and poly(dA).poly(dT) inserts, and the helix unwindings associated with dA and dC methylations by dam and Hhal methylases, respectively. Data were found to be highly reproducible and helical repeat estimates were in good agreement with those obtained from previous techniques.
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