Skip to main content
×
Home
    • Aa
    • Aa
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 163
  • Cited by
    This article has been cited by the following publications. This list is generated based on data provided by CrossRef.

    Abu Saleh, Md. Solayman, Md. Hoque, Mohammad Mazharol Khan, Mohammad A. K. Sarwar, Mohammed G. and Halim, Mohammad A. 2016. Inhibition of DNA Topoisomerase Type IIα(TOP2A) by Mitoxantrone and Its Halogenated Derivatives: A Combined Density Functional and Molecular Docking Study. BioMed Research International, Vol. 2016, p. 1.


    Bacher, Felix Dömötör, Orsolya Enyedy, Éva A. Filipović, Lana Radulović, Siniša Smith, Gregory S. and Arion, Vladimir B. 2016. Complex formation reactions of gallium(III) and iron(III/II) with l-proline-thiosemicarbazone hybrids: A comparative study. Inorganica Chimica Acta,


    Bai, Yang Li, Liang-Dong Li, Jun and Lu, Xin 2016. Targeting of topoisomerases for prognosis and drug resistance in ovarian cancer. Journal of Ovarian Research, Vol. 9, Issue. 1,


    Basu, Aakash Parente, Angelica C. and Bryant, Zev 2016. Structural Dynamics and Mechanochemical Coupling in DNA Gyrase. Journal of Molecular Biology, Vol. 428, Issue. 9, p. 1833.


    Coelho, João Ferreira, Fernando Martins, Carlos and Leitão, Alexandre 2016. Functional characterization and inhibition of the type II DNA topoisomerase coded by African swine fever virus. Virology, Vol. 493, p. 209.


    Dahmane, Narimane Gadelle, Danièle Delmas, Stéphane Criscuolo, Alexis Eberhard, Stephan Desnoues, Nicole Collin, Sylvie Zhang, Hongliang Pommier, Yves Forterre, Patrick and Sezonov, Guennadi 2016. topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB. Nucleic Acids Research, Vol. 44, Issue. 6, p. 2795.


    Finzi, Laura and Dunlap, David 2016. Supercoiling biases the formation of loops involved in gene regulation. Biophysical Reviews,


    Gupta, Manish Nayyar, Nishtha Chawla, Meenakshi Sitaraman, Ramakrishnan Bhatnagar, Rakesh and Banerjee, Nirupama 2016. The Chromosomal parDE2 Toxin–Antitoxin System of Mycobacterium tuberculosis H37Rv: Genetic and Functional Characterization. Frontiers in Microbiology, Vol. 7,


    Ivenso, Ikenna D. and Lillian, Todd D. 2016. Simulation of DNA Supercoil Relaxation. Biophysical Journal, Vol. 110, Issue. 10, p. 2176.


    Naeem, Abdul Badshah, Syed Muska, Mairman Ahmad, Nasir and Khan, Khalid 2016. The Current Case of Quinolones: Synthetic Approaches and Antibacterial Activity. Molecules, Vol. 21, Issue. 4, p. 268.


    Narsimhan, Vivek Renner, C. Benjamin and Doyle, Patrick S. 2016. Translocation dynamics of knotted polymers under a constant or periodic external field. Soft Matter, Vol. 12, Issue. 22, p. 5041.


    Ogawa, Taisaku Sutoh, Kazuo Kikuchi, Akihiko and Kinosita, Kazuhiko 2016. Torsional stress in DNA limits collaboration among reverse gyrase molecules. FEBS Journal, Vol. 283, Issue. 8, p. 1372.


    Pochukalina, Galina N. Ilicheva, Nadya V. Podgornaya, Olga I. and Voronin, Alexey P. 2016. Nucleolus-like body of mouse oocytes contains lamin A and B and TRF2 but not actin and topo II. Molecular Cytogenetics, Vol. 9, Issue. 1,


    Rajan, Rakhi Osterman, Amy and Mondragón, Alfonso 2016. Methanopyrus kandleritopoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site. Nucleic Acids Research, Vol. 44, Issue. 7, p. 3464.


    Rawdon, Eric J. Dorier, Julien Racko, Dusan Millett, Kenneth C. and Stasiak, Andrzej 2016. How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation. Nucleic Acids Research, Vol. 44, Issue. 10, p. 4528.


    Savage, Victoria J. Charrier, Cédric Salisbury, Anne-Marie Moyo, Emmanuel Forward, Henry Chaffer-Malam, Nathan Metzger, Richard Huxley, Anthony Kirk, Ralph Uosis-Martin, Mario Noonan, Gary Mohmed, Sarfraz Best, Stuart A. Ratcliffe, Andrew J. and Stokes, Neil R. 2016. Biological profiling of novel tricyclic inhibitors of bacterial DNA gyrase and topoisomerase IV. Journal of Antimicrobial Chemotherapy, Vol. 71, Issue. 7, p. 1905.


    Schmidt, Michael A. Goodwin, Thomas J. and Pelligra, Ralph 2016. Incorporation of omics analyses into artificial gravity research for space exploration countermeasure development. Metabolomics, Vol. 12, Issue. 2,


    Seol, Yeonee and Neuman, Keir C. 2016. The dynamic interplay between DNA topoisomerases and DNA topology. Biophysical Reviews,


    Tse-Dinh, Yuk-Ching 2016. Targeting bacterial topoisomerases: how to counter mechanisms of resistance. Future Medicinal Chemistry, Vol. 8, Issue. 10, p. 1085.


    Veselkov, Dennis A. Laponogov, Ivan Pan, Xiao-Su Selvarajah, Jogitha Skamrova, Galyna B. Branstrom, Arthur Narasimhan, Jana Prasad, Josyula V. N. Vara Fisher, L. Mark and Sanderson, Mark R. 2016. Structure of a quinolone-stabilized cleavage complex of topoisomerase IV fromKlebsiella pneumoniaeand comparison with a relatedStreptococcus pneumoniaecomplex. Acta Crystallographica Section D Structural Biology, Vol. 72, Issue. 4, p. 488.


    ×

DNA topoisomerases: harnessing and constraining energy to govern chromosome topology

  • Allyn J. Schoeffler (a1) and James M. Berger (a1)
  • DOI: http://dx.doi.org/10.1017/S003358350800468X
  • Published online: 01 August 2008
Abstract
Abstract

DNA topoisomerases are a diverse set of essential enzymes responsible for maintaining chromosomes in an appropriate topological state. Although they vary considerably in structure and mechanism, the partnership between topoisomerases and DNA has engendered commonalities in how these enzymes engage nucleic acid substrates and control DNA strand manipulations. All topoisomerases can harness the free energy stored in supercoiled DNA to drive their reactions; some further use the energy of ATP to alter the topology of DNA away from an enzyme-free equilibrium ground state. In the cell, topoisomerases regulate DNA supercoiling and unlink tangled nucleic acid strands to actively maintain chromosomes in a topological state commensurate with particular replicative and transcriptional needs. To carry out these reactions, topoisomerases rely on dynamic macromolecular contacts that alternate between associated and dissociated states throughout the catalytic cycle. In this review, we describe how structural and biochemical studies have furthered our understanding of DNA topoisomerases, with an emphasis on how these complex molecular machines use interfacial interactions to harness and constrain the energy required to manage DNA topology.

Copyright
Corresponding author
*Author for correspondence: Dr J. M. Berger, Department of Molecular and Cell Biology, California Institute for Quantitative Biology, University of California-Berkeley, Stanley Hall 3220, Berkeley, CA 94720-3220, USA.  Tel.: 510-643-9483; Fax: 510-666-2768; Email: jmberger@berkeley.edu
Linked references
Hide All

This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

G. Aburashidova , S. Radulescu , O. Sandoval , S. Zahariev , M. B. Danailov , A. Demidovich , L. Santamaria , G. Biamonti , S. Riva & A. Falaschi (2007). Functional interactions of DNA topoisomerases with a human replication origin. EMBO Journal 26, 9981009.

D. E. Adams , E. M. Shekhtman , E. L. Zechiedrich , M. B. Schmid & N. R. Cozzarelli (1992). The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell 71, 277288.

J. A. Ali , A. P. Jackson , A. J. Howells & A. Maxwell (1993). The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs. Biochemistry 32, 27172724.

J. A. Ali , G. Orphanides & A. Maxwell (1995). Nucleotide binding to the 43-kilodalton N-terminal fragment of the DNA gyrase B protein. Biochemistry 34, 98019808.

T. Andoh & R. Ishida (1998). Catalytic inhibitors of DNA topoisomerase II. Biochimica et Biophysica Acta 1400, 155171.

L. Aravind , D. D. Leipe & E. V. Koonin (1998). Toprim – a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Research 26, 42054213.

H. Atomi , R. Matsumi & T. Imanaka (2004). Reverse gyrase is not a prerequisite for hyperthermophilic life. Journal of Bacteriology 186, 48294833.

S. Bahng , E. Mossessova , P. Nurse & K. J. Marians (2000). Mutational analysis of Escherichia coli topoisomerase IV: III. Identification of a region of parE involved in covalent catalysis. Journal of Biological Chemistry 275, 41124117.

C. L. Baird , T. T. Harkins , S. K. Morris & J. E. Lindsley (1999). Topoisomerase II drives DNA transport by hydrolyzing one ATP. Proceedings of the National Academy of Sciences USA 96, 1368513690.

N. A. Baker , D. Sept , S. Joseph , M. J. Holst & J. A. McCammon (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences USA 98, 1003710041.

M. I. Baldi , P. Benedetti , E. Mattoccia & G. P. Toccini-Valentini (1980). In vitro catenation and decatenation of DNA and a novel eukaryotic ATP dependent topoisomerase. Cell 20, 461467.

A. D. Bates & A. Maxwell (2007). Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry 46, 79297941.

S. Bellon , J. D. Parsons , Y. Wei , K. Hayakawa , L. L. Swenson , P. S. Charifson , J. A. Lippke , R. Aldape & C. H. Gross (2004). Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potentcy against topoisomerase IV and DNA gyrase. Antimicrobial Agents and Chemotherapy 48, 18561864.

G. I. Belova , R. Prasad , S. A. Kozyavkin , J. A. Lake , S. H. Wilson & A. I. Slesarev (2001). A type IB topoisomerase with DNA repair activities. Proceedings of the National Academy of Sciences USA 98, 60156020.

D. Benarroch , J. M. Claverie , D. Raoult & S. Shuman (2006). Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria. Journal of Virology 80, 314321.

J. M. Berger , S. J. Gamblin , S. C. Harrison & J. C. Wang (1996). Structure and mechanism of DNA topoisomerase II. Nature 379, 225232.

A. Bergerat , B. De Massy , D. Gadelle , P. C. Varoutas , A. Nicolas & P. Forterre (1997). An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386, 414417.

L. Bjergbaek , S. Jensen , O. Westergaard & A. H. Andersen (1999). Using a biochemical approach to identify the primary dimerization regions in human DNA topoisomerase IIalpha. Journal of Biological Chemistry 274, 2652926536.

L. Bjergbaek , P. Kingma , I. S. Nielsen , Y. Wang , O. Westergaard , N. Osheroff & A. H. Andersen (2000). Communication between the ATPase and cleavage/religation domains of human topoisomerase IIalpha. Journal of Biological Chemistry 275, 1304113048.

T. C. Boles , J. H. White & N. R. Cozzarelli (1990). Structure of plectonemically supercoiled DNA. Journal of Molecular Biology 213, 931951.

C. Breuer , N. J. Stacey , C. E. West , Y. Zhao , J. Chory , H. Tsukaya , Y. Azumi , A. Maxwell , K. Roberts & K. Sugimoto-Shirasu (2007). BIN4, a novel component of the plant DNA topoisomerase VI complex, is required for endoreplication in Arabidopsis. The Plant Cell 19, 36553668.

L. Brino , A. Urzhumtsev , M. Mousli , C. Bronner , A. Mitschler , P. Oudet & D. Moras (2000). Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. Journal of Biological Chemistry 275, 94689475.

C. Brochier-Armanet & P. Forterre (2007). Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2, 8393.

P. O. Brown & N. R. Cozzarelli (1979). A sign inversion mechanism for enzymatic supercoiling of DNA. Science 206, 10811083.

P. O. Brown & N. R. Cozzarelli (1981). Catenation and knotting of duplex DNA by type I topoisomerases: a mechanistic parallel with type 2 topoisomerases. Proceedings of the National Academy of Sciences USA 78, 843847.

P. O. Brown , C. L. Peebles & N. R. Cozzarelli (1979). A topoisomerase from Escherichia coli related to DNA gyrase. Proceedings of the National Academy of Sciences USA 76, 61106114.

G. R. Buck & E. L. Zechiedrich (2004). DNA disentangling by type-2 topoisomerases. Journal of Molecular Biology 340, 933939.

C. Buhler , J. H. Lebbink , C. Bocs , R. Ladenstein & P. Forterre (2001). DNA topoisomerase VI generates ATP-dependent double-strand breaks with two-nucleotide overhangs. Journal of Biological Chemistry 276, 3721537222.

D. A. Burden & N. Osheroff (1998). Mechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme. Biochimica et Biophysica Acta 1400, 139154.

Y. Burnier , C. Weber , A. Flammini & A. Stasiak (2007). Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases. Nucleic Acids Research 35, 52235231.

J. Cairns (1963). The bacterial chromosome and its manner of replication as seen by autoradiography. Journal of Molecular Biology 6, 208213.

J. F. Carey , S. J. Schultz , L. Sisson , T. G. Fazzio & J. J. Champoux (2003). DNA relaxation by human topoisomerase I occurs in the closed clamp conformation of the protein. Proceedings of the National Academy of Sciences USA 100, 56405645.

P. R. Caron , P. Watt & J. C. Wang (1994). The C-terminal domain of Saccharomyces cerevisiae DNA topoisomerase II. Molecular and Cellular Biology 14, 31973207.

A. J. Carpenter & A. C. Porter (2004). Construction, characterization, and complementation of a conditional-lethal DNA topoisomerase IIalpha mutant human cell line. Molecular Biology of the Cell 15, 57005711.

J. J. Champoux (2001). DNA topoisomerases: structure, function, and mechanism. Annual Review of Biochemistry 70, 369413.

S. Chang , T. Hu & T. S. Hsieh (1998). Analysis of a core domain in Drosophila DNA topoisomerase II. Targeting of an antitumor agent ICRF-159. Journal of Biological Chemistry 273, 1982219828.

A. Changela , R. J. Digate & A. Mondragon (2001). Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature 411, 10771081.

A. Changela , R. J. Digate & A. Mondragon (2007). Structural studies of E. coli topoisomerase–IIIDNA complexes reveal a novel type IA topoisomerase–DNA conformational intermediate. Journal of Molecular Biology 368, 105118.

G. Charvin , T. R. Strick , D. Bensimon & V. Croquette (2005a). Topoisomerase IV bends and overtwists DNA upon binding. Biophysics Journal 89, 384392.

G. Charvin , T. R. Strick , D. Bensimon & V. Croquette (2005b). Tracking topoisomerase activity at the single-molecule level. Annual Review of Biophysics and Biomolecular Structure 34, 201219.

S. J. Chen & J. C. Wang (1998). Identification of active site residues in Escherichia coli DNA topoisomerase I. Journal of Biological Chemistry 273, 60506056.

C. Cheng , P. Kussie , N. Pavletich & S. Shuman (1998). Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell 92, 841850.

G. Chillemi , A. Bruselles , P. Fiorani , S. Bueno & A. Desideri (2007). The open state of human topoisomerase I as probed by molecular dynamics simulation. Nucleic Acids Research 35, 30323038.

G. Chillemi , P. Fiorani , S. Castelli , A. Bruselles , P. Benedetti & A. Desideri (2005). Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study. Nucleic Acids Research 33, 33393350.

G. Chillemi , M. Redinbo , A. Bruselles & A. Desideri (2004). Role of the linker domain and the 203–214 N-terminal residues in the human topoisomerase I DNA complex dynamics. Biophysics Journal 87, 40874097.

J. E. Chrencik , B. L. Staker , A. B. Burgin , P. Pourquier , Y. Pommier , L. Stewart & M. R. Redinbo (2004). Mechanisms of camptothecin resistance by human topoisomerase I mutations. Journal of Molecular Biology 339, 773784.

S. Classen , S. Olland & J. M. Berger (2003). Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proceedings of the National Academy of Sciences USA 100, 1062910634.

K. D. Corbett & J. M. Berger (2003a). Emerging roles for plant topoisomerase VI. Chemistry and Biology 10, 107111.

K. D. Corbett & J. M. Berger (2003b). Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution. EMBO Journal 22, 151163.

K. D. Corbett & J. M. Berger (2004). Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annual Review of Biophysics and Biomolecular Structure 33, 95118.

K. D. Corbett & J. M. Berger (2005). Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure 13, 873882.

K. D. Corbett , A. J. Schoeffler , N. D. Thomsen & J. M. Berger (2005). The structural basis for substrate specificity in DNA topoisomerase IV. Journal of Molecular Biology 351, 545561.

K. D. Corbett , R. K. Shultzaberger & J. M. Berger (2004). The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proceedings of the National Academy of Sciences USA 101, 72937298.

L. Costenaro , J. G. Grossmann , C. Ebel & A. Maxwell (2005). Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit. Structure 13, 287296.

N. L. Craig & H. A. Nash (1984). E. coli integration host factor binds to specific sites in DNA. Cell 39, 707716.

F. H. Crick (1976). Linking numbers and nucleosomes. Proceedings of the National Academy of Sciences USA 73, 26392643.

N. J. Crisona , T. R. Strick , D. Bensimon , V. Croquette & N. R. Cozzarelli (2000). Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes and Development 14, 28812892.

S. E. Critchlow , M. H. O'Dea , A. J. Howells , M. Couturier , M. Gellert & A. Maxwell (1997). The interaction of the F plasmid killer protein, CcdB, with DNA gyrase: induction of DNA cleavage and blocking of transcription. Journal of Molecular Biology 273, 826839.

G. E. Crooks , G. Hon , J.-M. Chandonia & S. WebLogo Brenner . (2004). WebLogo: a sequence logo generator. Genome Research 14(6): 11881990.

M. H. Dao-Thi , L. Van Melderen , E. De Genst , H. Afif , L. Buts , L. Wyns & R. Loris (2005). Molecular basis of gyrase poisoning by the addiction toxin CcdB. Journal of Molecular Biology 348, 10911102.

D. R. Davies , A. Mushtaq , H. Interthal , J. J. Champoux & W. G. Hol (2006). The structure of the transition state of the heterodimeric topoisomerase I of Leishmania donovani as a vanadate complex with nicked DNA. Journal of Molecular Biology 357, 12021210.

A. C. Declais , J. Marsault , F. Confalonieri , C. B. De La Tour & M. Duguet (2000). Reverse gyrase, the two domains intimately cooperate to promote positive supercoiling. Journal of Biological Chemistry 275, 1949819504.

R. W. Deibler , J. K. Mann , D. W. L. Sumners & E. L. Zechiedrich (2007). Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Molecular Biology 8, 4457.

N. H. Dekker , V. V. Rybenkov , M. Duguet , N. J. Crisona , N. R. Cozzarelli , D. Bensimon & V. Croquette (2002). The mechanism of type IA topoisomerases. Proceedings of the National Academy of Sciences USA 99, 1212612131.

R. E. Depew & J. C. Wang (1975). Conformational fluctuations of DNA helix. Proceedings of the National Academy of Sciences USA, 72 42754279.

J. S. Dickey & N. Osheroff (2005). Impact of the C-terminal domain of topoisomerase II-alpha on the DNA cleavage activity of the human enzyme. Biochemistry 44, 1154611554.

P. L. Domanico & Y. C. Tse-Dinh (1991). Mechanistic studies on E. coli DNA topoisomerase I: divalent ion effects. Journal of Inorganic Biochemistry 42, 8796.

K. C. Dong & J. M. Berger (2007). Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 450, 12011205.

F. H. Drake , G. A. Hofmann , H. F. Bartus , M. R. Mattern , S. T. Crooke & C. K. Mirabelli (1989). Biochemical and pharmacological properties of p170 and p180 forms of topoisomerase II. Biochemistry 28, 81548160.

K. Drlica (1992). Control of bacterial DNA supercoiling. Molecular Microbiology 6, 425433.

M. Duguet , M. C. Serre & C. Bouthier De La Tour (2006). A universal type IA topoisomerase fold. Journal of Molecular Biology 359, 805812.

R. Dutta & M. Inouye (2000). GHKL, an emergent ATPase/kinase superfamily. Trends in Biochemical Sciences 25, 2428.

O. Espeli , C. Lee & K. J. Marians (2003). A physical and functional interaction between Escherichia coli FtsK and topoisomerase IV. Journal of Biological Chemistry 278, 4463944644.

P. Fiorani , A. Bruselles , M. Falconi , G. Chillemi , A. Desideri & P. Benedetti (2003). Single mutation in the linker domain confers protein flexibility and camptothecin resistance to human topoisomerase I. Journal of Biological Chemistry 278, 4326843275.

P. Forterre , A. Bergerat & P. Lopez-Garcia (1996). The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea. FEMS Microbiology Reviews 18, 237248.

P. Forterre , S. Gribaldo , D. Gadelle & M. C. Serre (2007). Origin and evolution of DNA topoisomerases. Biochimie 89, 427446.

R. F. Frohlich , F. F. Andersen , O. Westergaard , A. H. Andersen & B. R. Knudsen (2004). Regions within the N-terminal domain of human topoisomerase I exert important functions during strand rotation and DNA binding. Journal of Molecular Biology 336, 93103.

R. F. Frohlich , C. Veigaard , F. F. Andersen , A. K. McClendon , A. C. Gentry , A. H. Andersen , N. Osheroff , T. Stevnsner & B. R. Knudsen (2007). Tryptophane-205 of human topoisomerase I is essential for camptothecin inhibition of negative but not positive supercoil removal. Nucleic Acids Research 35, 51706180.

D. Gadelle , J. Filee , C. Buhler & P. Forterre (2003). Phylogenomics of type II DNA topoisomerases. BioEssays 25, 232242.

K. S. Gajiwala & S. K. Burley (2000). Winged helix proteins. Current Opinion in Structural Biology 10, 110116.

M. Gellert , K. Mizuuchi , M. H. O'Dea & H. A. Nash (1976). DNA gyrase: an enzyme that introduces superhelical turns in DNA. Proceedings of the National Academy of Sciences USA 73, 38723876.

J. Gore , Z. Bryant , M. D. Stone , M. Nollmann , N. R. Cozzarelli & C. Bustamante (2006). Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 439, 100104.

T. Gottler & D. Klostermeier (2007). Dissection of the nucleotide cycle of B. subtilis DNA gyrase and its modulation by DNA. Journal of Molecular Biology 367, 13921404.

M. Graille , L. Cladiere , D. Durand , F. Lecointe , D. Gadelle , S. Quevillon-Cheruel , P. Vachette , P. Forterre & H. van Tilbeurgh (2008). Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms. Structure 16, 360370.

N. V. Grishin (2000a). C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily. Journal of Molecular Biology 299, 11651177.

N. V. Grishin (2000b). Two tricks in one bundle: helix–turn–helix gains enzymatic activity. Nucleic Acids Research 28, 22292233.

P. Grue , A. Grasser , M. Sehested , P. B. Jensen , A. Uhse , T. STraub , W. Ness & F. Boege (1998). Essential mitotic functions of DNA topoisomerase IIalpha are not adopted by topoisomerase IIbeta in human H69 cells. Journal of Biological Chemistry 273, 3366033666.

R. Hanai & J. C. Wang (1994). Protein footprinting by the combined use of reversible and irreversible lysine modifications. Proceedings of the National Academy of Sciences USA 91, 1190411908.

G. Hansen , A. Harrenga , B. Wieland , D. Schomburg & P. Reinemer (2006). Crystal structure of full length topoisomerase I from Thermotoga maritima. Journal of Molecular Biology 358, 13281340.

I. Har-Vardi , R. Mali , M. Breietman , Y. Sonin , S. Albotiano , E. Levitas , G. Potashnik & E. Priel (2007). DNA topoisomerases I and II in human mature sperm cells: characterization and unique properties. Human Reproduction 22, 21832189.

T. T. Harkins , T. J. Lewis & J. E. Lindsley (1998). Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP. Biochemistry 37, 72997312.

F. G. Harmon , R. J. Digate & S. C. Kowalczykowsji (1999). RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination. Molecular Cell 3, 611620.

S. C. Harrison & A. K. Aggarwal (1990). DNA recognition by proteins with the helix–turn–helix motif. Annual Review of Biochemistry 59, 933969.

F. Hartung & H. Puchta (2001). Molecular characterization of homologues of both subunits A (SPO11) and B of the archaebacterial topoisomerase 6 in plants. Gene 271, 8186.

M. M. Heck & W. C. Earnshaw (1986). Topoisomerase II: a specific marker for cell proliferation. Journal of Cell Biology 103, 25692581.

J. G. Heddle , S. Mitelheiser , A. Maxwell & N. H. Thomson (2004). Nucleotide binding to DNA gyrase causes loss of DNA wrap. Journal of Molecular Biology 337, 597610.

S. S. Hegde , M. W. Vetting , S. L. Roderick , L. A. Mitchenall , A. Maxwell , H. E. Takiff & J. S. Blanchard (2005). A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA. Science 308, 14801483.

V. F. Holmes & N. R. Cozzarelli (2000). Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling. Proceedings of the National Academy of Sciences USA 97, 13221324.

D. C. Hooper & E. Rubinstein (2003). Quinolone Antimicrobial Agents, 3rd edn. Washington, DC: ASM Press.

M. T. Howard , M. P. Lee , T. S. Hsieh & J. D. Griffith (1991). Drosophila topoisomerase II–DNA interactions are affected by DNA structure. Journal of Molecular Biology 217, 5362.

T. Hsieh & D. Brutlag (1980). ATP-dependent DNA topoisomerase from D. melanogaster reversibly catenates duplex DNA rings. Cell 21, 115125.

T. J. Hsieh , L. Farh , W. M. Huang & N. L. Chan (2004). Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis. Journal of Biological Chemistry 279, 5558755593.

T. S. Hsieh & C. Capp (2005). Nucleotide- and stoichiometry-dependent DNA supercoiling by reverse gyrase. Journal of Biological Chemistry 280, 2046720475.

T. S. Hsieh & J. L. Plank (2006). Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate. Journal of Biological Chemistry 281, 56405647.

W. M. Huang (1996). Bacterial diversity based on type II DNA topoisomerase genes. Annual Review of Genetics, 30 79107.

Y. Y. Huang , J. Y. Deng , J. Gu , Z. P. Zhang , A. Maxwell , L. J. Bi , Y. Y. Chen , Y. F. Zhou , Z. N. Yu & X. E. Zhang (2006). The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA). Nucleic Acids Research 34, 56505659.

H. Interthal , P. M. Quigley , W. G. Hol & J. J. Champoux (2004). The role of lysine 532 in the catalytic mechanism of human topoisomerase I. Journal of Biological Chemistry 279, 29842992.

R. J. Isaacs , S. L. Davies , M. I. Sandri , C. Redwood , N. J. Wells & I. D. Hickson (1998). Physiological regulation of eukaryotic topoisomerase II. Biochimica et Biophysica Acta 1400, 121137.

K. Iwabata , A. Koshiyama , T. Yamaguchi , H. Sugawara , F. N. Hamada , S. H. Namekawa , S. Ishii , T. Ishizaki , H. Chiku , T. Nara & K. Sakaguchi (2005). DNA topoisomerase II interacts with Lim15/Dmc1 in meiosis. Nucleic Acids Research 33, 58095818.

L. M. Iyer , D. D. Leipe , E. V. Koonin & L. Aravind (2004). Evolutionary history and higher order classification of AAA+ ATPases. Journal of Structural Biology 146, 1131.

P. Jain & V. Nagaraja (2002). An orphan gyrB in the Mycobacterium smegmatis genome uncovered by comparative genomics. Journal of Genetics 81, 105110.

P. Jain & V. Nagaraja (2005). An atypical type II topoisomerase from Mycobacterium smegmatis with positive supercoiling activity. Molecular Microbiology 58, 13921405.

B. G. Ju , V. V. Lunyak , V. Perissi , I. Garcia-Bassets , D. W. Rose , C. K. Glass & M. G. Rosenfeld (2006). A topoisomerase II beta-mediated dsDNA break required for regulated transcription. Science 312, 17981802.

S. P. Jungblut & D. Klostermeier (2007). Adenosine 5′-O-(3-thio)triphosphate (ATPgammaS) promotes positive supercoiling of DNA by T. maritima reverse gyrase. Journal of Molecular Biology 371, 197209.

M. Kampmann & D. Stock (2004). Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Research 32, 35373545.

S. C. Kampranis , A. D. Bates & A. Maxwell (1999). A model for the mechanism of strand passage by DNA gyrase. Proceedings of the National Academy of Sciences USA 96, 84148419.

S. C. Kampranis & A. Maxwell (1996). Conversion of DNA gyrase into a conventional type II topoisomerase. Proceedings of the National Academy of Sciences USA 93, 1441614421.

J. Kato , Y. Nishimura , R. Imamura , H. Niki , S. Hiraga & H. Suzuki (1990). New topoisomerase essential for chromosome segregation in E. coli. Cell 63, 393404.

K. Katoh , K. Misawa , K. Kuma & T. Miyata (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30, 30593066.

S. Keeney , C. N. Giroux & N. Kleckner (1997). Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88, 375384.

A. Kikuchi & K. Asai (1984). Reverse gyrase – a topoisomerase which introduces positive superhelical turns into DNA. Nature 309, 677681.

K. Kirkegaard & J. C. Wang (1985). Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. Journal of Molecular Biology 185, 625637.

D. A. Koster , V. Croquette , C. Dekker , S. Shuman & N. H. Dekker (2005). Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434, 671674.

D. A. Koster , K. Palle , E. S. Bot , M. A. Bjornsti & N. H. Dekker (2007). Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature 448, 213217.

S. A. Kozyavkin , A. V. Pushkin , F. A. Eiserling , K. O. Stetter , J. A. Lake & A. I. Slesarev (1995). DNA enzymology above 100 degrees C. Topoisomerase V unlinks circular DNA at 80–122 degrees C. Journal of Biological Chemistry 270, 1359313595.

V. M. Kramlinger & H. Hiasa (2006). The ‘GyrA-box’ is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction. Journal of Biological Chemistry 281, 37383742.

B. O. Krogh , C. D. Claeboe , S. M. Hecht & S. Shuman (2001). Effect of 2′–5′ phosphodiesters on DNA transesterification by vaccinia topoisomerase. Journal of Biological Chemistry 276, 2090720912.

B. O. Krogh & S. Shuman (2000). Catalytic mechanism of DNA topoisomerase IB. Molecular Cell 5, 10351041.

B. O. Krogh & S. Shuman (2002a). A poxvirus-like type IB topoisomerase family in bacteria. Proceedings of the National Academy of Sciences USA 99, 18531858.

B. O. Krogh & S. Shuman (2002b). Proton relay mechanism of general acid catalysis by DNA topoisomerase IB. Journal of Biological Chemistry 277, 57115714.

E. U. Kurz , K. B. Leader , D. J. Kroll , M. Clark & F. Gieseler (2000). Modulation of human DNA topoisomerase IIalpha function by interaction with 14-3-3epsilon. Journal of Biological Chemistry 275, 1394813954.

V. Lamour , L. Hoermann , J. M. Jeltsch , P. Oudet & D. Moras (2002). An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. Journal of Biological Chemistry 277, 1894718953.

I. Laponogov , D. A. Veselkov , M. K. Sohi , X. Pan , A. Achari , C. Yang , J. D. Ferrara , L. M. Fisher & M. R. Sanderson (2007). Breakage–reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target. PLoS One 2(3), e301.

O. V. Lavrukhin , J. M. Fortune , T. G. Wood , D. E. Burbank , J. L. van Etten , N. Osheroff & R. S. Lloyd (2000). Topoisomerase II from Chlorella virus PBCV-1. Journal of Biological Chemistry 275, 69156921.

C. Levine , H. Hiasa & K. J. Marians (1998). DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochimica et Biophysica Acta 1400, 2943.

Z. Li , H. Hiasa & R. Digate (2006). Characterization of a unique type IA topoisomerase in Bacillus cereus. Molecular Microbiology 60, 140151.

Z. Li , A. Mondragon , H. Hiasa , K. J. Marians & R. J. Digate (2000). Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates. Molecular Microbiology 35, 888895.

C. D. Lima , J. C. Wang & A. Mondragon (1994). Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature 367, 138146.

R. M. Linka , A. C. Porter , A. Volkov , C. Mielke , F. Boege & M. O. Christensen (2007). C-terminal regions of topoisomerase IIalpha and IIbeta determine isoform-specific functioning of the enzymes in vivo. Nucleic Acids Research 35, 38103822.

L. F. Liu , C. C. Liu & B. M. Alberts (1979). T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication. Nature 281, 456461.

L. F. Liu & J. C. Wang (1978). DNA–DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell 15, 979984.

L. F. Liu & J. C. Wang (1987). Supercoiling of the DNA template during transcription. Proceedings of the National Academy of Sciences USA 84, 70247027.

C. R. Lopez , S. Yang , R. W. Deibler , S. A. Ray , J. M. Pennington , R. J. Digate , P. J. Hastings , S. M. Rosenberg & E. L. Zechiedrich (2005). A role for topoisomerase III in a recombination pathway alternative to RuvABC. Molecular Microbiology 58, 80101.

Z. Lou , K. Minter-Dykhouse & J. Chen (2005). BRCA1 participates in DNA decatenation. Nature Structural and Molecular Biology 12, 589593.

S. B. Malik , M. A. Ramesh , A. M. Hulstrand & J. M. J. Logsdon (2007). Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal and evolutionary history of gene duplication and lineage-specific loss. Molecular Biology and Evolution 24, 28272841.

Y. Mao , S. D. Desai & L. F. Liu (2000). SUMO-1 conjugation to human DNA topoisomerase II isoenzymes. Journal of Biological Chemistry 275, 2606626073.

A. Maxwell , L. Costenaro , S. Mitelheiser & A. D. Bates (2005). Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases. Biochemical Society Transactions, 33, 14601464.

A. Maxwell & D. M. Lawson (2003). The ATP-binding site of type II topoisomerases as a target for antibacterial drugs. Current Topics in Medicinal Chemistry 3, 283303.

A. K. McClendon , J. S. Dickey & N. Osheroff (2006). Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: bimodal recognition of DNA geometry by type II enzymes. Biochemistry 45, 1167411680.

A. K. McClendon & N. Osheroff (2006). The geometry of DNA supercoils modulates topoisomerase-mediated DNA cleavage and enzyme response to anticancer drugs. Biochemistry 45, 30403050.

A. K. McClendon , A. C. Rodriguez & N. Osheroff (2005). Human topoisomerase II-alpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks. Journal of Biological Chemistry 280, 3933739345.

D. B. McKay & T. A. Steitz (1981). Structure of catabolite gene activator protein at 2·9 Å resolution suggests binding to left-handed B-DNA. Nature 290, 744749.

Y. Miki , Z. T. Chang & T. Horiuchi (1984a). Control of cell division by sex factor F in Escherichia coli. II. Identification of genes for inhibitor protein and trigger protein on the 42·84–43·6 F segment. Journal of Molecular Biology 174, 627646.

S. E. Mirski , J. H. Gerlach , H. J. Cummings , R. Zirngibl , P. A. Greer & S. P. Cole (1997). Bipartite nuclear localization signals in the C terminus of human topoisomerase II alpha. Experimental Cell Research 237, 452455.

K. Mizuuchi , L. M. Fisher , M. H. O'Dea & M. Gellert (1980). DNA gyrase action involves the introduction of transient double-strand breaks into DNA. Proceedings of the National Academy of Sciences USA 77, 18471851.

A. Mondragon (2005). Unraveling the mechanistic details of topoisomerases. Structure 13, 502503.

A. Mondragon & R. Digate (1999). The structure of Escherichia coli DNA topoisomerase III. Structure 7, 13731383.

S. K. Morris , C. L. Baird & J. E. Lindsley (2000). Steady-state and rapid kinetic analysis of topoisomerase II trapped as the closed-clamp intermediate by ICRF-193. Journal of Biological Chemistry 275, 26132618.

A. Morrison & N. R. Cozzarelli (1979). Site-specific cleavage of DNA by E. coli DNA gyrase. Cell 17, 903906.

F. Mueller-Plantiz & D. Herschlag (2006). Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation. Journal of Biological Chemistry 281, 2339523404.

F. Mueller-Plantiz & D. Herschlag (2007). DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity. Nucleic Acids Research 35, 37643773.

M. Nadal (2007). Reverse gyrase: an insight into the role of DNA-topoisomerases. Biochimie 89, 447455.

A. Nakanishi , T. Oshida , T. Matsushita , S. Imajoh-Ohmi & T. Ohnuki (1998). Identification of DNA gyrase inhibitor (GyrI) in Escherichia coli. Journal of Biological Chemistry 273, 19331938.

M. D. Nichols , K. Deangelis , J. L. Keck & J. M. Berger (1999). Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. EMBO Journal 18, 61776188.

C. G. Noble & A. Maxwell (2002). The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. Journal of Molecular Biology 318, 361371.

M. Nollmann , N. J. Crisona & P. B. Arimondo (2007a). Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie 89, 490499.

M. Nollmann , M. D. Stone , Z. Bryant , J. Gore , N. J. Crisona , S. C. Hong , S. Mitelheiser , A. Maxwell , C. Bustamante & N. R. Cozzarelli (2007b). Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nature Structural and Molecular Biology 14, 264271.

S. Olland & J. C. Wang (1999). Catalysis of ATP hydrolysis by two NH(2)-terminal fragments of yeast DNA topoisomerase II. Journal of Biological Chemistry 274, 2168821694.

M. Oram , A. A. Travers , A. J. Howells , A. Maxwell & M. L. Pato (2006). Dissection of the bacteriophage Mu strong gyrase site (SGS): significance of the SGS right arm in Mu biology and DNA gyrase mechanism. Journal of Bacteriology 188, 619632.

G. Orphanides & A. Maxwell (1994). Evidence for a conformational change in the DNA gyrase–DNA complex from hydroxyl radical footprinting. Nucleic Acids Research 22, 15671575.

E. F. Pai , W. Kabsch , U. Krengel , K. C. Holmes , J. John & A. Wittinghofer (1989). Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature 341, 209214.

A. Patel , S. Shuman & A. Mondragon (2006). Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA. Journal of Biological Chemistry 281, 60306037.

H. Peng & K. J. Marians (1993a). Decatenation activity of topoisomerase IV during oriC and pBR322 DNA replication in vitro. Proceedings of the National Academy of Sciences USA 90, 85718575.

H. Peng & K. J. Marians (1995). The interaction of Escherichia coli topoisomerase IV with DNA. Journal of Biological Chemistry 270, 2528625290.

K. Perry , Y. Hwang , F. D. Bushman & G. D. Van Duyne (2006). Structural basis for specificity in the poxvirus topoisomerase. Molecular Cell 23, 343354.

K. Perry & A. Mondragon (2002). Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis. Journal of Biological Chemistry 277, 1323713245.

K. Perry & A. Mondragon (2003). Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure 11, 13491358.

B. J. Peter , C. Ullsperger , H. Hiasa , K. J. Marians & N. R. Cozzarelli (1998). The structure of supercoiled intermediates in DNA replication. Cell 94, 819827.

A. A. Podtelezhnikov , N. R. Cozzarelli & A. Vologodskii (1999). Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting. Proceedings of the National Academy of Sciences USA 96, 1297412979.

Y. Pommier (2006). Topoisomerase I inhibitors: camptothecins and beyond. Nature Reviews Cancer 6, 789802.

Y. Pommier & J. Cherfils (2005). Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. Trends in Pharmacological Sciences 26, 138145.

A. M. Pyle (2008). Translocation and unwinding mechanisms of RNA and DNA helicases. Annual Reviews in Biophysics 37, 317336.

D. E. Pulleyblank , M. Shure , D. Tang , J. Vinograd & H. P. Vosberg (1975). Action of nicking–closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proceedings of the National Academy of Sciences USA 72, 42804284.

Y. Qi , J. Pei & N. V. Grishin (2000). C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Proteins 47, 258264.

D. Raoult , S. Audic , C. Robert , C. Abergel , P. Renesto , H. Ogata , B. La Scola , M. Suzan & J. M. Claverie (2004). The 1·2-megabase genome sequence of Mimivirus. Science 306, 13441350.

M. R. Redinbo , J. J. Champoux & W. G. Hol (2000). Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA. Biochemistry 39, 68326840.

M. R. Redinbo , L. Stewart , J. J. Champoux & W. G. Hol (1999). Structural flexibility in human topoisomerase I revealed in multiple non-isomorphous crystal structures. Journal of Molecular Biology 292, 685696.

M. R. Redinbo , L. Stewart , P. Kuhn , J. J. Champoux & W. G. Hol (1998). Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279, 15041513.

R. J. Reece & A. Maxwell (1991). The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Research 19, 13991405.

D. Rhodes & A. Klug (1980). Helical periodicity of DNA determined by enzyme digestion. Nature 286, 573578.

P. A. Rice , S. Yang , K. Mizuuchi & H. A. Nash (1996). Crystal structure of an IHF–DNA complex: a protein-induced DNA U-turn. Cell 87, 12951306.

J. Roca , J. M. Berger , S. C. Harrison & J. C. Wang (1996). DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proceedings of the National Academy of Sciences USA 93, 40574062.

J. Roca , R. Ishida , J. M. Berger , T. Andoh & J. C. Wang (1994). Antitumor bisdioxopiperazines inhibit yeast DNA topoisomerase II by trapping the enzyme in the form of a closed protein clamp. Proceedings of the National Academy of Sciences USA 91, 17811785.

J. Roca & J. C. Wang (1992). The capture of a DNA double helix by an ATP-dependent protein clamp: a key state in DNA transport by type II DNA topoisomerases. Cell 71, 833840.

J. Roca & J. C. Wang (1994). DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism. Cell 77, 609616.

J. Roca & J. C. Wang (1996). The probabilities of supercoil removal and decatenation by yeast DNA topoisomerase II. Genes Cells 1, 1727.

A. C. Rodriguez (2002). Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional ‘latch’ in the mechanism of reverse gyrase. Journal of Biological Chemistry 277, 2986529873.

A. C. Rodriguez (2003). Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase. Biochemistry 42, 59936004.

A. C. Rodriguez & D. Stock (2002). Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO Journal 21, 418426.

A. J. Ruthenburg , D. M. Graybosch , J. C. Huetsch & G. L. Verdine (2005). A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. Journal of Biological Chemistry 280, 2617726184.

V. V. Rybenkov , C. Ullsperger , A. V. Vologodskii & N. R. Cozzarelli (1997). Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277, 690693.

L. Sari & I. Andricioaei (2005). Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Research 33, 66216634.

P. Schultz , S. Olland , P. Oudet & R. Hancock (1996). Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy. Proceedings of the National Academy of Sciences USA 93, 59365940.

S. Sengupta , M. Shah & V. Nagaraja (2006). Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding. Nucleic Acids Research 34, 55675576.

M. A. Singleton , M. S. Dillingham & D. B. Wigley (2007). Structure and mechanism of helicases and nucleic acid translocases. Annual Review of Biochemistry 76, 2350.

A. I. Slesarev , K. O. Stetter , J. A. Lake , M. Gellert , R. Krah & S. A. Kozyavkin (1993). DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote. Nature 364, 735737.

R. D. Smiley , T. R. L. Collins , G. G. Hammes & T.-S. Hsieh (2007). Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II. Proceedings of the National Academy of Sciences USA 104, 48404845.

A. B. Smith & A. Maxwell (2006). A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site. Nucleic Acids Research 34, 46674676.

K. S. Srivenugopal , D. Lockshon & D. R. Morris (1984). Escherichia coli DNA topoisomerase III: purification and characterization of a new type I enzyme. Biochemistry 23, 18991906.

B. L. Staker , K. Hjerrild , M. D. Feese , C. A. Behnke , A. B. Burgin Jr. & L. Stewart (2002). The mechanism of topoisomerase I poisoning by a camptothecin analog. Proceedings of the National Academy of Sciences USA 99, 1538715392.

G. L. Stetler , G. J. King & W. M. Huang (1979). T4 DNA-delay proteins requires for specific DNA replication form a complex that has ATP-dependent topoisomerase activity. Proceedings of the National Academy of Sciences USA 76, 37373741.

L. Stewart , G. C. Ireton & J. J. Champoux (1997). Reconstitution of human topoisomerase I by fragment complementation. Journal of Molecular Biology 269, 355372.

L. Stewart , G. C. Ireton & J. J. Champoux (1999). A functional linker in human topoisomerase I is required for maximum sensitivity to camptothecin in a DNA relaxation assay. Journal of Biological Chemistry 274, 3295032960.

L. Stewart , M. R. Redinbo , X. Qiu , W. G. Hol & J. J. Champoux (1998). A model for the mechanism of human topoisomerase I. Science 279, 15341541.

J. T. Stivers , T. K. Harris & A. S. Mildvan (1997). Vaccinia DNA topoisomerase I: evidence supporting a free rotation mechanism for DNA supercoil relaxation. Biochemistry 36, 52125222.

M. D. Stone , Z. Bryant , N. J. Crisona , S. B. Smith , A. Vologodskii , C. Bustamante & N. R. Cozzarelli (2003). Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proceedings of the National Academy of Sciences USA 100, 86548659.

R. M. Story & T. A. Steitz (1992). Structure of the recA protein–ADP complex. Nature 355, 374376.

K. Sugimoto-Shirasu , G. R. Roberts , N. J. Stacey , M. C. McCann & A. Maxwell (2005). RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth. Proceedings of the National Academy of Sciences USA 102, 1873618741.

A. Sugino , N. P. Higgins & N. R. Cozzarelli (1980). DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage. Nucleic Acids Research 8, 38653874.

B. Taneja , A. Patel , A. Slesarev & A. Mondragon (2006). Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO Journal 25, 398408.

B. Taneja , B. Schnurr , A. Slesarev , J. F. Marko & A. Mondragon (2007). Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proceedings of the National Academy of Sciences USA 104, 1467014675.

R. J. Thompson & G. Mosig (1985). An ATP-dependent supercoiling topoisomerase of Chlamydomonas reinhardtii affects accumulation of specific chloroplast transcripts. Nucleic Acids Research 13, 873891.

B. Thomsen , C. Bendixen , K. Lund , A. H. Anderson , B. S. Sorensen & O. Westergaard (1990). Characterization of the interaction between topoisomerase II and DNA by transcriptional footprinting. Journal of Molecular Biology 215, 237244.

L. Tian , C. D. Claeboe , S. M. Hecht & S. Shuman (2004). Remote phosphate contacts trigger assembly of the active site of DNA topoisomerase IB. Structure 12, 3140.

L. Tian , C. D. Claeboe , S. M. Hecht & S. Shuman (2005). Mechanistic plasticity of DNA topoisomerase IB: phosphate electrostatics dictate the need for a catalytic arginine. Structure 13, 513520.

A. P. Tingey & A. Maxwell (1996). Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase. Nucleic Acids Research 24, 48684873.

J. H. Tran & G. A. Jacoby (2002). Mechanism of plasmid-mediated quinolone resistance. Proceedings of the National Academy of Sciences USA 99, 56385642.

S. Trigueros , J. Salceda , I. Bermudez , X. Fernandez & J. Roca (2004). Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. Journal of Molecular Biology 335, 723731.

J. Vinograd , J. Lebowitz , R. Radloff , R. Watson & P. Laipis (1965). The twisted circular form of polynoma viral DNA. Proceedings of the National Academy of Sciences USA 53, 11041111.

A. V. Vologodskii & N. R. Cozzarelli (1994). Conformational and thermodynamic properties of supercoiled DNA. Annual Review of Biophysics and Biomolecular Structure 23, 609643.

A. V. Vologodskii , W. Zhang , V. V. Rybenkov , A. A. Podtelezhnikov , D. Subramanian , J. D. Griffith & N. R. Cozzarelli (2001). Mechanism of topology simplification by type II DNA topoisomerases. Proceedings of the National Academy of Sciences USA 98, 30453049.

J. W. Wallis , G. Chrebet , G. Brodsky , M. Rolfe & R. Rothstein (1989). A hyper-recombination mutation in S. cerevisiae identifies a novel eukaryotic topoisomerase. Cell 58, 409419.

J. C. Wang (1971). Interaction between DNA and an Escherichia coli protein omega. Journal of Molecular Biology 55, 523533.

J. C. Wang (1998). Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Quarterly Review of Biophysics 31, 107144.

J. C. Wang (2002). Cellular roles of DNA topoisomerases: a molecular perspective. Nature Reviews Molecular and Cellular Biology 3, 430440.

J. C. Wang (2007). Unlocking and opening a DNA gate. Proceedings of the National Academy of Sciences USA 104, 47734774.

S. C. Wang & L. Shapiro (2004). The topoisomerase IV ParC subunit colocalizes with the Caulobacter replisome and is required for polar localization of replication origins. Proceedings of the National Academy of Sciences USA 101, 92519256.

D. Ward & A. Newton (1997). Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Molecular Microbiology 26, 897910.

H. Wei , A. J. Ruthenburg , S. K. Bechis & G. L. Verdine (2005). Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. Journal of Biological Chemistry 280, 3704137047.

K. L. West , E. L. Meczes , R. Thorn , R. M. Turnbull , R. Marshall & C. A. Austin (2000). Mutagenesis of E477 or K505 in the B′ domain of human topoisomerase II beta increases the requirement for magnesium ions during strand passage. Biochemistry 39, 12231233.

J. H. White (1969). Self-linking and the Gauss integral in higher dimensions. American Journal of Mathematics 91, 693728.

D. B. Wigley , G. J. Davies , E. J. Dodson , A. Maxwell & G. Dodson (1991). Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351, 624629.

N. L. Williams & A. Maxwell (1999). Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking. Biochemistry 38, 1350213511.

M. H. Woo , C. Losasso , H. Guo , L. Pattarello , P. Benedetti & M. A. Bjornsti (2003). Locking the DNA topoisomerase I protein clamp inhibits DNA rotation and induces cell lethality. Proceedings of the National Academy of Sciences USA 100, 1376713772.

H. Y. Wu , S. H. Shyy , J. C. Wang & L. F. Liu (1988). Transcription generates positively and negatively supercoiled domains in the template. Cell 53, 433440.

L. Wu , C. Z. Bachrati , J. Ou , C. Xu , J. Yin , M. Chang , W. Wang , L. Li , G. W. Brown & I. D. Hickson (2006). BLAP75/RMI1 promotes the BLM-dependent dissolution of homologous recombination intermediates. Proceedings of the National Academy of Sciences USA 103, 40684073.

L. Wu , S. L. Davies , P. S. North , H. Goulaouic , J. F. Riou , H. Turley , K. C. Gatter & I. D. Hickson (2000). The Bloom's syndrome gene product interacts with topoisomerase III. Journal of Biological Chemistry 275, 96369644.

L. Yakovleva , S. Chen , S. M. Hecht & S. Shuman (2008). Chemical and traditional mutagenesis of vaccinia DNA topoisomerase provide insights to cleavage site recognition and transesterification chemistry. Journal of Biological Chemistry.

K. Yamane , M. Kawabata & T. Tsuruo (1997). A DNA-topoisomerase-II-binding protein with eight repeating regions similar to DNA-repair enzymes and to a cell-cycle regulator. European Journal of Biochemistry 250, 794799.

J. Yan , M. O. Magnasco & J. F. Marko (2001). Kinetic proofreading can explain the suppression of supercoiling of circular DNA molecules by type-II topoisomerases. Physical Review E, Statistical and Nonlinear Soft Matter Physics 63, 031909.

X. Yang , W. Li , E. D. Prescott , S. J. Burden & J. C. Wang (2000). DNA topoisomerase IIbeta and neural development. Science 287, 131134.

G. W. Yu , M. D. Allen , A. Andreeva , A. R. Fersht & M. Bycroft (2006). Solution structure of the C4 zinc finger domain of HDM2. Protein Science 15, 384389.

L. Yu , C. X. Zhu , Y. C. Tse-Dinh & S. W. Fesik (1995). Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I. Biochemistry 34, 76227628.

E. L. Zechiedrich , A. B. Khodursky , S. Bachellier , R. Schneider , D. Chen , D. M. Lilley & N. R. Cozzarelli (2000). Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. Journal of Biological Chemistry 275, 81038113.

E. L. Zechiedrich , A. B. Khodursky & N. R. Cozzarelli (1997). Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes and Development 11, 25802592.

C. X. Zhu , C. J. Roche , N. Papanicolaou , A. Dipietrantonio & Y. C. Tse-Dinh (1998). Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I. Journal of Biological Chemistry 273, 87838789.

C. X. Zhu & Y. C. Tse-Dinh (2000). The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. Journal of Biological Chemistry 275, 53185322.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×