Cozzarelli NR, Cost GJ, Nollmann M, Viard T, Stray JE: Giant proteins that move DNA: bullies of the genomic playground. Nat Rev Mol Cell Biol. 2006, 7 (8): 580-588. 10.1038/nrm1982
Article
CAS
PubMed
Google Scholar
Bohrmann B, Haider M, Kellenberger E: Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM. Ultramicroscopy. 1993, 49 (1-4): 235-251. 10.1016/0304-3991(93)90230-U
Article
CAS
PubMed
Google Scholar
Reich Z, Wachtel EJ, Minsky A: Liquid-crystalline mesophases of plasmid DNA in bacteria. Science. 1994, 264 (5164): 1460-1463. 10.1126/science.8197460
Article
CAS
PubMed
Google Scholar
Minsky A: Information content and complexity in the high-order organization of DNA. Annu Rev Biophys Biomol Struct. 2004, 33: 317-342. 10.1146/annurev.biophys.33.110502.133328
Article
CAS
PubMed
Google Scholar
Yan J, Magnasco MO, Marko JF: A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases. Nature. 1999, 401 (6756): 932-935. 10.1038/44872
Article
CAS
PubMed
Google Scholar
Shishido K, Komiyama N, Ikawa S: Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants. J Mol Biol. 1987, 195 (1): 215-218. 10.1016/0022-2836(87)90338-X
Article
CAS
PubMed
Google Scholar
Martin-Parras L, Lucas I, Martinez-Robles ML, Hernandez P, Krimer DB, Hyrien O, Schvartzman JB: Topological complexity of different populations of pBR322 as visualized by two-dimensional agarose gel electrophoresis. Nucleic Acids Res. 1998, 26 (14): 3424-3432. 10.1093/nar/26.14.3424
Article
PubMed Central
CAS
PubMed
Google Scholar
Deibler RW: The biological implications of DNA knots and the in vivo activity of topoisomerase IV. 2003, Houston: Baylor College of Medicine; PhD thesis
Google Scholar
Shishido K, Ishii S, Komiyama N: The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant. Nucleic Acids Res. 1989, 17 (23): 9749-9759. 10.1093/nar/17.23.9749
Article
PubMed Central
CAS
PubMed
Google Scholar
Ishii S, Murakami T, Shishido K: Gyrase inhibitors increase the content of knotted DNA species of plasmid pBR322 in Escherichia coli . J Bacteriol. 1991, 173 (17): 5551-5553.
PubMed Central
CAS
PubMed
Google Scholar
Sikorav JL, Jannink G: Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model. Biophys J. 1994, 66 (3 Pt 1): 827-837.
Article
PubMed Central
CAS
PubMed
Google Scholar
Arsuaga J, Vazquez M, Trigueros S, Sumners D W, Roca J: Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc Natl Acad Sci USA. 2002, 99 (8): 5373-5377. 10.1073/pnas.032095099
Article
PubMed Central
CAS
PubMed
Google Scholar
Baker TA, Sekimizu K, Funnell BE, Kornberg A: Extensive unwinding of the plasmid template during staged enzymatic initiation of DNA replication from the origin of the Escherichia coli chromosome. Cell. 1986, 45 (1): 53-64. 10.1016/0092-8674(86)90537-4
Article
CAS
PubMed
Google Scholar
Hatfield GW, Benham CJ: DNA topology-mediated control of global gene expression in Escherichia coli. Annu Rev Genet. 2002, 36: 175-203. 10.1146/annurev.genet.36.032902.111815
Article
CAS
PubMed
Google Scholar
Liu Y, Bondarenko V, Ninfa A, Studitsky VM: DNA supercoiling allows enhancer action over a large distance. Proc Natl Acad Sci USA. 2001, 98: 14883-14888. 10.1073/pnas.261477898
Article
PubMed Central
CAS
PubMed
Google Scholar
Steck TR, Franco RJ, Wang JY, Drlica K: Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol Microbiol. 1993, 10 (3): 473-481. 10.1111/j.1365-2958.1993.tb00920.x
Article
CAS
PubMed
Google Scholar
Vologodskii AV, Cozzarelli NR: Monte Carlo analysis of the conformation of DNA catenanes. J Mol Biol. 1993, 232 (4): 1130-1140. 10.1006/jmbi.1993.1465
Article
CAS
PubMed
Google Scholar
Vologodskii AV, Levene SD, Klenin KV, Frank-Kamenetskii MD, Cozzarelli NR: Conformational and thermodynamic properties of supercoiled DNA. J Mol Biol. 1992, 227 (4): 1224-1243. 10.1016/0022-2836(92)90533-P
Article
CAS
PubMed
Google Scholar
Podtelezhnikov AA, Cozzarelli NR, Vologodskii AV: Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting. Proc Natl Acad Sci USA. 1999, 96 (23): 12974-12979. 10.1073/pnas.96.23.12974
Article
PubMed Central
CAS
PubMed
Google Scholar
Vologodskii AV, Marko JF: Extension of torsionally stressed DNA by external force. Biophys J. 1997, 73 (1): 123-132.
Article
PubMed Central
CAS
PubMed
Google Scholar
Deibler RW, Rahmati S, Zechiedrich EL: Topoisomerase IV, alone, unknots DNA in E. coli. Genes Dev. 2001, 15: 748-761. 10.1101/gad.872301
Article
PubMed Central
CAS
PubMed
Google Scholar
Adams DE, Shekhtman EM, Zechiedrich EL, Schmid MB, Cozzarelli NR: The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell. 1992, 71 (2): 277-288. 10.1016/0092-8674(92)90356-H
Article
CAS
PubMed
Google Scholar
Zechiedrich EL, Cozzarelli NR: Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev. 1995, 9 (22): 2859-2869. 10.1101/gad.9.22.2859
Article
CAS
PubMed
Google Scholar
Zechiedrich EL, Khodursky AB, Bachellier S, Schneider R, Chen D, Lilley DM, Cozzarelli NR: Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J Biol Chem. 2000, 275 (11): 8103-8113. 10.1074/jbc.275.11.8103
Article
CAS
PubMed
Google Scholar
Merickel SK, Johnson RC: Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro. Mol Microbiol. 2004, 51 (4): 1143-1154. 10.1046/j.1365-2958.2003.03890.x
Article
CAS
PubMed
Google Scholar
Heichman KA, Moskowitz IPG, Johnson RC: Configuration of DNA strands and mechanism of strand exchange in the Hin invertasome as revealed by analysis of recombinant knots. Genes Dev. 1991, 5 (9): 1622-1634. 10.1101/gad.5.9.1622
Article
CAS
PubMed
Google Scholar
Rochman M, Aviv M, Glaser G, Muskhelishvili G: Promoter protection by a transcription factor acting as a local topological homeostat. EMBO Rep. 2002, 3: 355-360. 10.1093/embo-reports/kvf067
Article
PubMed Central
CAS
PubMed
Google Scholar
Hardy CD, Cozzarelli NR: A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure. Mol Microbiol. 2005, 57 (6): 1636-1652. 10.1111/j.1365-2958.2005.04799.x
Article
CAS
PubMed
Google Scholar
Postow L, Hardy CD, Arsuaga J, Cozzarelli NR: Topological domain structure of the Escherichia coli chromosome. Genes Dev. 2004, 18 (14): 1766-1779. 10.1101/gad.1207504
Article
PubMed Central
CAS
PubMed
Google Scholar
Glasgow AC, Bruist MF, Simon MI: DNA-binding properties of the Hin recombinase. J Biol Chem. 1989, 264 (17): 10072-10082.
CAS
PubMed
Google Scholar
Johnson RC, Bruist MF: Intermediates in Hin-mediated DNA inversion: a role for Fis and the recombinational enhancer in the strand exchange reaction. Embo J. 1989, 8 (5): 1581-1590.
PubMed Central
CAS
PubMed
Google Scholar
Lee SY, Lee HJ, Lee H, Kim S, Cho EH, Lim HM: In vivo assay of protein-protein interactions in Hin-mediated DNA inversion. J Bacteriol. 1998, 180 (22): 5954-5960.
PubMed Central
CAS
PubMed
Google Scholar
Tam CK, Hackett J, Morris C: Rate of inversion of the Salmonella enterica shufflon regulates expression of invertible DNA. Infect Immun. 2005, 73 (9): 5568-5577. 10.1128/IAI.73.9.5568-5577.2005
Article
PubMed Central
CAS
PubMed
Google Scholar
Eisenstadt E, Carlton BC, Brown BJ: Gene Mutation. Methods for General and Molecular Bacteriology. Edited by: Gerhardt P, Murray RGE, Wood WA, Krieg NR. 1994, 304-Washington, D.C.: American Society for Microbiology
Google Scholar
Portugal J, Rodriguez-Campos A: T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Res. 1996, 24 (24): 4890-4894. 10.1093/nar/24.24.4890
Article
PubMed Central
CAS
PubMed
Google Scholar
Saitta AM, Soper PD, Wasserman E, Klein ML: Influence of a knot on the strength of a polymer strand. Nature. 1999, 399 (6731): 46-48. 10.1038/19935
Article
CAS
PubMed
Google Scholar
Arai Y, Yasuda R, Akashi K, Harada Y, Miyata H, Kinosita KJ, Itoh H: Tying a molecular knot with optical tweezers. Nature. 1999, 399 (6735): 446-448. 10.1038/20894
Article
CAS
PubMed
Google Scholar
Pieranski P, Kasas S, Dietler G, Dubochet J, Stasiak A: Localization of breakage points in knotted strings. New Journal of Physics. 2001, 3: 10-10.1088/1367-2630/3/1/310.
Article
Google Scholar
Uehara H, Kimura H, Aoyama A, Yamanobe T, Komoto T: Effects of knot characteristics on tensile breaking of a polymeric monofilament. New Journal of Physics. 2007, 9: 65-10.1088/1367-2630/9/3/065.
Article
Google Scholar
Lee CL, Ow DS, Oh SK: Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. J Microbiol Methods. 2006, 65 (2): 258-267. 10.1016/j.mimet.2005.07.019
Article
CAS
PubMed
Google Scholar
Lee C, Kim J, Shin SG, Hwang S: Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli . J Biotechnol. 2006, 123 (3): 273-280. 10.1016/j.jbiotec.2005.11.014
Article
CAS
PubMed
Google Scholar
Noack D, Roth M, Geuther R, Muller G, Undisz K, Hoffmeier C, Gaspar S: Maintenance and genetic stability of vector plasmids pBR322 and pBR325 in Escherichia coli K12 strains grown in a chemostat. Mol Gen Genet. 1981, 184 (1): 121-124. 10.1007/BF00271207
Article
CAS
PubMed
Google Scholar
Sundin O, Varshavsky A: Arrest of segregation leads to accumulation of highly intertwined catenated dimers: dissection of final stages of SV40 DNA replication. Cell. 1981, 25 (3): 659-669. 10.1016/0092-8674(81)90173-2
Article
CAS
PubMed
Google Scholar
Katritch V, Olson WK, Vologodskii AV, Dubochet J, Stasiak A: Tightness of random knotting. Phys Rev E. 2000, 61 (5 Pt B): 5545-5549. 10.1103/PhysRevE.61.5545.
Article
CAS
Google Scholar
Metzler R, Hanke A, Dommersnes PG, Kantor Y, Kardar M: Equilibrium shapes of flat knots. Phys Rev Lett. 2002, 88 (18): 188101- 10.1103/PhysRevLett.88.188101
Article
PubMed
Google Scholar
Wuite GJ, Smith SB, Young M, Keller D, Bustamante C: Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature. 2000, 404 (6773): 103-106. 10.1038/35003614
Article
CAS
PubMed
Google Scholar
Maier B, Bensimon D, Croquette V: Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc Natl Acad Sci USA. 2000, 97 (22): 12002-12007. 10.1073/pnas.97.22.12002
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM: Force and velocity measured for single molecules of RNA polymerase. Science. 1998, 282 (5390): 902-907. 10.1126/science.282.5390.902
Article
CAS
PubMed
Google Scholar
Davenport RJ, Wuite GJ, Landick R, Bustamante C: Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science. 2000, 287 (5462): 2497-2500. 10.1126/science.287.5462.2497
Article
CAS
PubMed
Google Scholar
Bao XR, Lee HJ, Quake SR: Behavior of complex knots in single DNA molecules. Phys Rev Lett. 2003, 91 (26 Pt 1): 265506- 10.1103/PhysRevLett.91.265506
Article
PubMed
Google Scholar
Beaber JW, Hochhut B, Waldor MK: SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature. 2004, 427 (6969): 72-74. 10.1038/nature02241
Article
CAS
PubMed
Google Scholar
Friedberg EC, Walker GC, Siede W: DNA repair and mutagenesis. 1995, edn. Washington: ASM Press
Google Scholar
Rosche WA, Foster PL: Determining mutation rates in bacterial populations. Methods. 2000, 20 (1): 4-17. 10.1006/meth.1999.0901
Article
PubMed Central
CAS
PubMed
Google Scholar
Levine C, Hiasa H, Marians KJ: DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim Biophys Acta. 1998, 1400 (1-3): 29-43.
Article
CAS
PubMed
Google Scholar
Kato J-I, Nishimura Y, Imamura R, Niki H, Hiraga S, Susuki H: New topoisomerase essential for chromosome segregation in Escherichia coli . Cell. 1990, 63 (2): 393-404. 10.1016/0092-8674(90)90172-B
Article
CAS
PubMed
Google Scholar
Zechiedrich EL, Khodursky AB, Cozzarelli NR: Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes Dev. 1997, 11 (19): 2580-2592.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grompone G, Bidnenko V, Ehrlich SD, Michel B: PriA is essential for viability of the Escherichia coli topoisomerase IV parE10(Ts) mutant. J Bacteriol. 2004, 186 (4): 1197-1199. 10.1128/JB.186.4.1197-1199.2004
Article
PubMed Central
CAS
PubMed
Google Scholar
Heller RC, Marians KJ: Replication fork reactivation downstream of a blocked nascent leading strand. Nature. 2006, 439 (7076): 557-562. 10.1038/nature04329
Article
CAS
PubMed
Google Scholar
Posfai G, Plunkett G, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR: Emergent properties of reduced-genome Escherichia coli . Science. 2006, 312 (5776): 1044-1046. 10.1126/science.1126439
Article
CAS
PubMed
Google Scholar
Haniford DB: Transpososome dynamics and regulation in Tn 10 transposition. Crit Rev Biochem Mol Biol. 2006, 41 (6): 407-424. 10.1080/10409230600987415
Article
CAS
PubMed
Google Scholar
Hastings PJ, Slack A, Petrosino JF, Rosenberg SM: Adaptive amplification and point mutation are independent mechanisms: evidence for various stress-inducible mutation mechanisms. PLoS Biol. 2004, 2 (12): e399- 10.1371/journal.pbio.0020399
Article
PubMed Central
CAS
PubMed
Google Scholar
Hersh MN, Ponder RG, Hastings PJ, Rosenberg SM: Adaptive mutation and amplification in Escherichia coli : two pathways of genome adaptation under stress. Res Microbiol. 2004, 155 (5): 352-359. 10.1016/j.resmic.2004.01.020
Article
CAS
PubMed
Google Scholar
Foster PL: Stress responses and genetic variation in bacteria. Mutat Res. 2005, 569 (1-2): 3-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chao L, McBroom SM: Evolution of transposable elements: an IS10 insertion increases fitness in Escherichia coli. Mol Biol Evol. 1985, 2 (5): 359-369.
CAS
PubMed
Google Scholar
Chao L, Vargas C, Spear BB, Cox EC: Transposable elements as mutator genes in evolution. Nature. 1983, 303 (5918): 633-635. 10.1038/303633a0
Article
CAS
PubMed
Google Scholar
Kato J-I, Nishimura Y, Yamada M, Suzuki H, Hirota Y: Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli. J Bacteriol. 1988, 170 (9): 3967-3977.
PubMed Central
CAS
PubMed
Google Scholar
Hughes KT, Gaines PC, Karlinsey JE, Vinayak R, Simon MI: Sequence-specific interaction of the Salmonella Hin recombinase in both major and minor grooves of DNA. Embo J. 1992, 11 (7): 2695-2705.
PubMed Central
CAS
PubMed
Google Scholar
Crisona NJ, Kanaar R, Gonzalez TN, Zechiedrich EL, Klippel A, Cozzarelli NR: Processive recombination by wild-type gin and an enhancer-independent mutant. Insight into the mechanisms of recombination selectivity and strand exchange. J Mol Biol. 1994, 243 (3): 437-457. 10.1006/jmbi.1994.1671
Article
CAS
PubMed
Google Scholar
Plasterk RHA, Brinkman A, van de Putte P: DNA inversions in the chromosome of Escherichia coli and in bacteriophage Mu: relationship to other site-specific recombination systems. Proc Natl Acad Sci USA. 1983, 80 (17): 5355-5358. 10.1073/pnas.80.17.5355
Article
PubMed Central
CAS
PubMed
Google Scholar
Bauer AW, Kirby WMM, Sherris JC, Turck M: Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol. 1966, 45: 493-496.
CAS
PubMed
Google Scholar
Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: a laboratory manual. 1989, Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2
Google Scholar
Barzilai R: SV40 DNA: quantitative conversion of closed circular to open circular form by an ethidium bromide-restricted endonuclease. J Mol Biol. 1973, 74 (4): 739-742. 10.1016/0022-2836(73)90062-4
Article
CAS
PubMed
Google Scholar