Direct observation of strand passage by dna-topoisomerase and its limited processivity

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Yogo, Katsunori ^a   Ogawa, Taisaku ^a   Hayashi, Masahito ^b   Harada, Yoshie ^c   Nishizaka, Takayuki ^d   Kinosita, Kazuhiko ^a  

^a WASEDA UNIVERSITY   (Japan)

^b KANAGAWA ACADEMY OF SCIENCE AND TECHNOLOGY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d GAKUSHUIN UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA; DNA BINDING PROTEIN; DNA TOPOISOMERASE II ALPHA; TUMOR ANTIGEN;

ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DNA BINDING; DNA STRAND; DNA STRAND BREAKAGE; ENZYME ANALYSIS; HUMAN; NUCLEIC ACID TRANSPORT; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN PROCESSING; BINDING SITE; CHEMISTRY; METABOLISM;

ANTIGENS, NEOPLASM; BINDING SITES; DNA; DNA TOPOISOMERASES, TYPE II; DNA-BINDING PROTEINS; HUMANS;

EID: 84859503433     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034920     Document Type: Article

References (24)

1. Liu LF, Liu CC, Alberts BM, (1979) T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication. Nature 281: 456-461.
2. Brown PO, Cozzarelli NR, (1979) A sign inversion mechanism for enzymatic supercoiling of DNA. Science 206: 1081-1083.
3. Mizuuchi K, Fisher LM, O'Dea MH, Gellert M, (1980) DNA gyrase action involves the introduction of transient double-strand breaks into DNA. Proc Natl Acad Sci U S A 77: 1847-1851.
4. Wang JC, (1998) Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Q Rev Biophys 31: 107-144.
5. Schoeffler AJ, Berger JM, (2008) DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys 41: 41-101.
6. Strick TR, Croquette V, Bensimon D, (2000) Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404: 901-904.
7. Charvin G, Bensimon D, Croquette V, (2003) Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases. Proc Natl Acad Sci U S A 100: 9820-9825.
8. Stone MD, Bryant Z, Crisona NJ, Smith SB, Vologodskii A, et al. (2003) Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci U S A 100: 8654-8659.
9. Nöllmann M, Stone MD, Bryant Z, Gore J, Crisona NJ, et al. (2007) Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol 14: 264-271.
10. Renodon-Cornière A, Jensen LH, Nitiss JL, Jensen PB, Sehested M, (2002) Interaction of human DNA topoisomerase IIα with DNA: Quantification by surface plasmon resonance. Biochemistry 41: 13395-13402.
11. Mueller-Planitz F, Herschlag D, (2008) Coupling between ATP binding and DNA cleavage by DNA Topoisomerase II: A unifying kinetic and structural mechanism. J Biol Chem 283: 17463-17476.
12. Smiley RD, Collins TRL, Hammes GG, Hsieh TS, (2007) Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II. Proc Natl Acad Sci U S A 104: 4840-4845.
13. McClendon AK, Rodriguez AC, Osheroff N, (2005) Human topoisomerase IIα rapidly relaxes positively supercoiled DNA. Implications for enzyme action ahead of replication forks. J Biol Chem 280: 39337-39345.
14. Zechiedrich EL, Osheroff N, (1990) Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. EMBO J 9: 4555-4562.
15. Koster DA, Wiggins CH, Dekker NH, (2006) Multiple events on single molecules: Unbiased estimation in single-molecule biophysics. Proc Natl Acad Sci U S A 103: 1750-1755.
16. Tanabe K, Ikegami Y, Ishida R, Andoh T, (1991) Inhibition of topoisomerase II by antitumor agents bis(2,6-dioxopiperazine) derivatives. Cancer Res 51: 4903-4908.
17. Bromberg KD, Burgin AB, Osheroff N, (2003) A two-drug model for etoposide action against human topoisomerase IIα. J Biol Chem 278: 7406-7412.
18. Harada Y, Ohara O, Takatsuki A, Itoh H, Shimamoto N, et al. (2001) Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409: 113-115.
19. Hayashi M, Harada Y, (2007) Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide. Nucleic Acids Res 35: e125.
20. Arai Y, Yasuda R, Akashi K, Harada Y, Miyata H, et al. (1999) Tying a molecular knot with optical tweezers. Nature 399: 446-448.
21. Yasuda R, Noji H, Yoshida M, Kinosita K Jr, Itoh H, (2001) Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase. Nature 410: 898-904.
22. Marko JF, (1997) Supercoiled and braided DNA under tension. Phys Rev E 55: 1758-1772.
23. Bustamante C, Marko JF, Siggia ED, Smith SB, (1994) Entropic elasticity of λ-phage DNA. Science 265: 1599-1600.
24. Strick TR, Allemand J-F, Bensimon D, Croquette V, (1998) Behavior of supercolied DNA. Biophys J 74: 2016-2028.