Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 9, 2011, Pages 3608-3611

  Witz, Guillaume ^a,b   Dietler, Giovanni ^a   Stasiak, Andrzej ^b  

^a EPFL   (Switzerland)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Brownian dynamics; DNA configurations; DNA structure; DNA topology

Indexed keywords

CURVED DNA; DNA TOPOISOMERASE (ATP HYDROLYSING);

ARTICLE; DNA STRUCTURE; DNA SUPERCOILING; ELECTROPHORETIC MOBILITY; ENZYME SUBSTRATE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; SIMULATION;

BASE PAIRING; COMPUTER SIMULATION; DNA TOPOISOMERASES, TYPE II; DNA, SUPERHELICAL; ELECTROPHORESIS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION;

EID: 79952767999     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1016150108     Document Type: Article

References (33)

1. Krasnow MA, et al. (1983) Determination of the absolute handedness of knots and catenanes of DNA. Nature 304:559-560. (Pubitemid 13026960)
2. Schvartzman JB, Stasiak A (2004) A topological view of the replicon. EMBO Rep 5:256-261. (Pubitemid 38500104)
3. Sogo JM, et al. (1999) Formation of knots in partially replicated DNA molecules. J Mol Biol 286:637-643. (Pubitemid 29106205)
4. Deibler RW, Mann JK, Sumners DW, Zechiedrich L (2007) Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Mol Biol 8:44.
5. Portugal J, Rodriguez-Campos A (1996) T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Res 24:4890-4894. (Pubitemid 27007892)
6. Bates AD, Maxwell A (2007) Energy coupling in type II topoisomerases: Why do they hydrolyze ATP? Biochemistry 46:7929-7941.
7. Rybenkov VV, Ullsperger C, Vologodskii AV, Cozzarelli NR (1997) Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277:690-693. (Pubitemid 27373915)
8. Buck GR, Zechiedrich EL (2004) DNA disentangling by type-2 topoisomerases. J Mol Biol 340:933-939. (Pubitemid 38968692)
9. Liu ZR, Zechiedrich L, Chan HS (2010) Local site preference rationalizes disentangling by DNA topoisomerases. Phys Rev E 81:031902.
10. Yan J, Magnasco MO, Marko JF (1999) A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases. Nature 401:932-935.
11. Stuchinskaya T, et al. (2009) How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. J Mol Biol 385:1397-1408.
12. Marko JF (1999) Coupling of intramolecular and intermolecular linkage complexity of two DNAs. Phys Rev E 59:900-912.
13. Travers A, Muskhelishvili G (2007) A common topology for bacterial and eukaryotic transcription initiation? EMBO Rep 8:147-151.
14. Larson RG, Hua H, Smith DE, Chu S (1999) Brownian dynamics simulations of a DNA molecule in an extensional flow field. J Rheol 43:267-304. (Pubitemid 129582301)
15. Vologodskii A (2006) Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophys J 90:1594-1597.
16. Shaw SY, Wang JC (1997) Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments. Proc Natl Acad Sci USA 94:1692-1697. (Pubitemid 27113897)
17. Stasiak A, Katritch V, Bednar J, Michoud D, Dubochet J (1996) Electrophoretic mobility of DNA knots. Nature 384:122.
18. Vologodskii AV, et al. (1998) Sedimentation and electrophoretic migration of DNA knots and catenanes. J Mol Biol 278:1-3. (Pubitemid 28196146)
19. Marcone B, Orlandini E, Stella AL, Zonta F (2005) What is the length of a knot in a polymer? J Phys A: Math Gen 38:L15-L21.
20. Witz G, Stasiak A (2010) DNA supercoiling and its role in DNA decatenation and unknotting. Nucleic Acids Res 38:2119-2133.
21. Bliska JB, Cozzarelli NR (1987) Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J Mol Biol 194:205-218. (Pubitemid 17044517)
22. Katritch V, Olson WK, Vologodskii A, Dubochet J, Stasiak A (2000) Tightness of random knotting. Phys Rev E 61:5545-5549.
23. Marcone B, Orlandini E, Stella AL, Zonta F (2007) Size of knots in ring polymers. Phys Rev E 75:041105.
24. Dong KC, Berger JM (2007) Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 450:1201-1205.
25. Vologodskii AV, et al. (2001) Mechanism of topology simplification by type II DNA topoisomerases. Proc Natl Acad Sci USA 98:3045-3049. (Pubitemid 32220796)
26. Neuman KC, Charvin G, Bensimon D, Croquette V (2009) Mechanisms of chiral discrimination by topoisomerase IV. Proc Natl Acad Sci USA 106:6986-6991.
27. Ullsperger C, Cozzarelli NR (1996) Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli. J Biol Chem 271:31549-31555. (Pubitemid 26408614)
28. Ishii S, Murakami T, Shishido K (1991) Gyrase inhibitors increase the content of knotted DNA species of plasmid pBR322 in Escherichia coli. J Bacteriol 173:5551-5553.
29. Shishido K, Komiyama N, Ikawa S (1987) Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants. J Mol Biol 195:215-218.
30. Allison SA (1986) Brownian dynamics simulation of wormlike chains. Fluorescence depolarization and depolarized light scattering. Macromolecules 19:118-124.
31. Jian HM, Vologodskii AV, Schlick T (1997) Combined wormlike-chain and bead model for dynamic simulations of long linear DNA. J Comput Phys 136:168-179. (Pubitemid 127170097)
32. Klenin K, Merlitz H, Langowski J (1998) A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys J 74:780-788. (Pubitemid 28345273)
33. Stigter D (1977) Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers 16:1435-1448.