Human topoisomerase II-DNA interaction study by using atomic force microscopy

FEBS Letters

Volumn 585, Issue 19, 2011, Pages 3139-3145

  Alonso Sarduy, Livan ^a   Roduit, Charles ^a   Dietler, Giovanni ^a   Kasas, Sandor ^a,b  

^a EPFL   (Switzerland)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

AFM; Binding geometry; DNA topology; Human topoisomerase II; Protein DNA interaction; Time lapse imaging

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA TOPOISOMERASE (ATP HYDROLYSING); DOUBLE STRANDED DNA;

ARTICLE; ATOMIC FORCE MICROSCOPY; CATALYSIS; CONTROLLED STUDY; DNA CROSS LINKING; DNA SUPERCOILING; ENZYME LOCALIZATION; HUMAN; HYDROLYSIS; IN VITRO STUDY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN FUNCTION;

DNA; DNA TOPOISOMERASES, TYPE II; HUMANS; MICROSCOPY, ATOMIC FORCE; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 80053275968     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.08.051     Document Type: Article

References (35)

1. J.C. Wang Cellular roles of DNA topoisomerases: a molecular perspective Nat. Rev. Mol. Cell Biol. 3 2002 430 440 (Pubitemid 34685700)
2. J.J. Champoux DNA topoisomerases: structure, function, and mechanism Annu. Rev. Biochem. 70 2001 369 413 (Pubitemid 32662215)
3. G. Capranico, and M. Binaschi DNA sequence selectivity of topoisomerases and topoisomerase poisons Biochim. Biophys. Acta 1400 1998 185 194 (Pubitemid 28475103)
4. R. Velez-Cruz, J.N. Riggins, J.S. Daniels, H. Cai, F.P. Guengerich, L.J. Marnett, and N. Osheroff Exocyclic DNA lesions stimulate DNA cleavage mediated by human topoisomerase II alpha in vitro and in cultured cells Biochemistry 44 2005 3972 3981 (Pubitemid 40358049)
5. N.J. Crisona, T.R. Strick, D. Bensimon, V. Croquette, and N.R. Cozzarelli Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements Genes Dev. 14 2000 2881 2892
6. A.K. McClendon, A.C. Rodriguez, and N. Osheroff Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks J. Biol. Chem. 280 2005 39337 39345 (Pubitemid 41713890)
7. K.C. Neuman, G. Charvin, D. Bensimon, and V. Croquette Mechanisms of chiral discrimination by topoisomerase IV Proc. Natl. Acad. Sci. USA 106 2009 6986 6991
8. V.V. Rybenkov, C. Ullsperger, A.V. Vologodskii, and N.R. Cozzarelli Simplification of DNA topology below equilibrium values by type II topoisomerases Science 277 1997 690 693 (Pubitemid 27373915)
9. G. Witz, and A. Stasiak DNA supercoiling and its role in DNA decatenation and unknotting Nucleic Acids Res. 38 2010 2119 2133
10. A.V. Vologodskii, W.T. Zhang, V.V. Rybenkov, A.A. Podtelezhnikov, D. Subramanian, J.D. Griffith, and N.R. Cozzarelli Mechanism of topology simplification by type II DNA topoisomerases Proc. Natl. Acad. Sci. USA 98 2001 3045 3049 (Pubitemid 32220796)
11. Y. Burnier, J. Dorier, and A. Stasiak DNA supercoiling inhibits DNA knotting Nucleic Acids Res. 36 2008 4956 4963
12. Z.R. Liu, J.K. Mann, E.L. Zechiedrich, and H.S. Chan Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases J. Mol. Biol. 361 2006 268 285 (Pubitemid 44092778)
13. G. Witz, G. Dietler, and A. Stasiak Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases Proc. Natl. Acad. Sci. USA 108 2011 3608 3611
14. J. Roca, J.M. Berger, and J.C. Wang On the Simultaneous Binding of Eukaryotic DNA Topoisomerase-Ii to a Pair of Double-Stranded DNA Helices J. Biol. Chem. 268 1993 14250 14255 (Pubitemid 23195549)
15. A.H. Corbett, E.L. Zechiedrich, and N. Osheroff A Role for the Passage Helix in the DNA Cleavage Reaction of Eukaryotic Topoisomerase-Ii - a 2-Site Model for Enzyme-Mediated DNA Cleavage J. Biol. Chem. 267 1992 683 686
16. G. Binnig, C.F. Quate, and C. Gerber Atomic force microscope Phys. Rev. Lett. 56 1986 930 933
17. P.K. Hansma Tapping mode atomic-force microscopy in liquids Appl. Phys. Lett. 64 1994 1738 1740
18. S. Kasas Escherichia coli RNA polymerase activity observed using atomic force microscopy Biochemistry 36 1997 461 468 (Pubitemid 27056993)
19. D.J. Muller, and Y.F. Dufrene Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology Nat. Nanotechnol. 3 2008 261 269 (Pubitemid 351668045)
20. M. Yaneva, T. Kowalewski, and M.R. Lieber Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies EMBO J. 16 1997 5098 5112 (Pubitemid 27348418)
21. S. Trigueros, J. Arsuaga, M.E. Vazquez, D.W. Sumners, and J. Roca Novel display of knotted DNA molecules by two-dimensional gel electrophoresis Nucleic Acids Res. 29 2001 E67-7
22. P. Zhang Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA Protein Expr. Purif. 69 2010 226 234
23. S. Kasas, L. Alonso, P. Jacquet, J. Adamcik, C. Haeberli, and G. Dietler Microcontroller-driven fluid-injection system for atomic force microscopy Rev. Sci. Instrum. 81 2010 013704
24. E.L. Zechiedrich, and N. Osheroff Eukaryotic topoisomerases recognize nucleic-acid topology by preferentially interacting with DNA crossovers EMBO J. 9 1990 4555 4562 (Pubitemid 120026015)
25. N. Osheroff, and E.L. Zechiedrich Calcium-promoted DNA cleavage by eukaryotic topoisomerase II: trapping the covalent enzyme-DNA complex in an active form Biochemistry 26 1987 4303 4309
26. M.D. Stone, Z. Bryant, N.J. Crisona, S.B. Smith, A. Vologodskii, C. Bustamante, and N.R. Cozzarelli Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases Proc. Natl. Acad. Sci. USA 100 2003 8654 8659 (Pubitemid 36899153)
27. O. Pietrement Reversible binding of DNA on NiCl2-treated mica by varying the ionic strength Langmuir 19 2003 2536 2539
28. J.M. Berger, S.J. Gamblin, S.C. Harrison, and J.C. Wang Structure and mechanism of DNA topoisomerase II Nature 379 1996 225 232 (Pubitemid 26025206)
29. H. Wei, A.J. Ruthenburg, S.K. Bechis, and G.L. Verdine Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase J. Biol. Chem. 280 2005 37041 37047 (Pubitemid 41587788)
30. L. Brino, A. Urzhumtsev, M. Mousli, C. Bronner, A. Mitschler, P. Oudet, and D. Moras Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center J. Biol. Chem. 275 2000 9468 9475 (Pubitemid 30185175)
31. P. Schultz, S. Olland, P. Oudet, and R. Hancock Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy Proc. Natl. Acad. Sci. USA 93 1996 5936 5940 (Pubitemid 26190780)
32. S.R. Nettikadan, C.S. Furbee, M.T. Muller, and K. Takeyasu Molecular structure of human topoisomerase II alpha revealed by atomic force microscopy J. Electron Microsc. 47 1998 671 674 (Pubitemid 29042902)
33. T. Ando, T. Uchihashi, N. Kodera, A. Miyagi, R. Nakakita, H. Yamashita, and M. Sakashita High-speed atomic force microscopy for studying the dynamic behavior of protein molecules at work Jpn. J. Appl. Phys. 1-Reg. Pap. Brief Commun. Rev. Pap. 45 2006 1897 1903
34. G.E. Fantner, P. Hegarty, J.H. Kindt, G. Schitter, G.A.G. Cidade, and P.K. Hansma Data acquisition system for high speed atomic force microscopy Rev. Scient. Instrum. 76 2005 026118
35. M.B. Viani Probing protein-protein interactions in real time Nat. Struct. Biol. 7 2000 644 647 (Pubitemid 30636674)