Single-molecule measurements of DNA topology and topoisomerases

Journal of Biological Chemistry

Volumn 285, Issue 25, 2010, Pages 18967-18971

  Neuman, Keir C ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL INTERACTIONS; DNA MOLECULES; DNA TOPOLOGY; GENOMIC DNA; MECHANICAL STRESS; PRECISE CONTROL; SINGLE MOLECULE MEASUREMENTS; SINGLE-MOLECULE; SINGLE-MOLECULE TECHNIQUE; TOPOISOMERASES; TOPOLOGICAL PROPERTIES;

DNA; GENES; MECHANICAL PROPERTIES; MOLECULES; STRESSES;

TOPOLOGY;

DNA TOPOISOMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING);

ANALYTICAL EQUIPMENT; DNA BINDING; DNA DETERMINATION; DNA STRAND; DNA STRUCTURE; DNA SUPERCOILING; ENZYME ACTIVITY; MAGNETIC TWEEZERS; MOLECULAR MECHANICS; OPTICAL TWEEZERS; PRIORITY JOURNAL; SHORT SURVEY; TORQUE;

BIOPHYSICS; CHROMATIN; DNA; DNA GYRASE; DNA TOPOISOMERASES; DNA TOPOISOMERASES, TYPE I; DNA, BACTERIAL; DNA, SUPERHELICAL; DNA-DIRECTED RNA POLYMERASES; HUMANS; NUCLEIC ACID CONFORMATION; OPTICAL TWEEZERS; PLASMIDS; TIME FACTORS;

EID: 77953523095     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.R109.092437     Document Type: Short Survey

References (44)

1. Watson, J. D., and Crick, F. H. (1953) Nature 171, 737-738
2. Watson, J. D., and Crick, F. H. (1953) Nature 171, 964-967
3. Meselson, M., and Stahl, F. W. (1958) Proc. Natl. Acad. Sci. U.S.A. 44, 671-682
4. Wang, J. C. (1971) J. Mol. Biol. 55, 523-533
5. Wang, J. C. (1998) Q. Rev. Biophys. 31, 107-144
6. Vinograd, J., Lebowitz, J., Radloff, R., Watson, R., and Laipis, P. (1965) Proc. Natl. Acad. Sci. U.S.A. 53, 1104-1111
7. Wang, J. C. (2002) Nat. Rev. Mol. Cell Biol. 3, 430-440
8. Travers, A., and Muskhelishvili, G. (2005) Nat. Rev. Microbiol. 3, 157-169
9. Champoux, J. J. (2001) Annu. Rev. Biochem. 70, 369-413
10. Drlica, K., and Malik, M. (2003) Curr. Top. Med. Chem. 3, 249-282
11. Li, T. K., and Liu, L. F. (2001) Annu. Rev. Pharmacol. Toxicol. 41, 53-77
12. Espeli, O., and Marians, K. J. (2004) Mol. Microbiol. 52, 925-931
13. Neuman, K. C., Lionnet, T., and Allemand, J. F. (2007) Annu. Rev. Mater. Res. 37, 33-67
14. Bates, A. D., and Maxwell, A. (2005) DNA Topology, 2nd Ed., Oxford University Press, New York
15. White, J. H. (1969) Am. J. Math. 91, 693-728
16. Neuman, K. C., and Nagy, A. (2008) Nat. Methods 5, 491-505
17. Charvin, G., Allemand, J. F., Strick, T. R., Bensimon, D., and Croquette, V. (2004) Contemp. Phys. 45, 383-403
18. Lionnet, T., Allemand, J.-F., Revyakin, A., Strick, T. R., Saleh, O. A., Bensimon, D., and Croquette, V. (2008) in Single-Molecule Techniques: A Laboratory Manual (Selvin, P. R., and Ha, T. eds) pp. 347-369, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
19. La Porta, A., and Wang, M. D. (2004) Phys. Rev. Lett 92, 190801-1-190801-4
20. Deufel, C., Forth, S., Simmons, C. R., Dejgosha, S., and Wang, M. D. (2007) Nat. Methods 4, 223-225
21. Bryant, Z., Stone, M. D., Gore, J., Smith, S. B., Cozzarelli, N. R., and Bustamante, C. (2003) Nature 424, 338-341
22. Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A., and Croquette, V. (1996) Science 271, 1835-1837
23. Allemand, J. F., Bensimon, D., Lavery, R., and Croquette, V. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 14152-14157
24. Forth, S., Deufel, C., Sheinin, M. Y., Daniels, B., Sethna, J. P., and Wang, M. D. (2008) Phys. Rev. Lett. 100, 148301-1-148301-4
25. Marko, J. F. (2007) Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 76, 021926-1-021926-4
26. Charvin, G., Strick, T. R., Bensimon, D., and Croquette, V. (2005) Annu. Rev. Biophys. Biomol. Struct. 34, 201-219
27. Strick, T. R., Croquette, V., and Bensimon, D. (2000) Nature 404, 901-904
28. Brown, P. O., and Cozzarelli, N. R. (1979) Science 206, 1081-1083
29. Roca, J., Berger, J. M., Harrison, S. C., and Wang, J. C. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 4057-4062
30. Crisona, N. J., Strick, T. R., Bensimon, D., Croquette, V., and Cozzarelli, N. R. (2000) Genes Dev. 14, 2881-2892
31. Stone, M. D., Bryant, Z., Crisona, N. J., Smith, S. B., Vologodskii, A., Bustamante, C., and Cozzarelli, N. R. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 8654-8659
32. Charvin, G., Bensimon, D., and Croquette, V. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 9820-9825
33. Charvin, G., Vologodskii, A., Bensimon, D., and Croquette, V. (2005) Biophys. J. 88, 4124-4136
34. Neuman, K. C., Charvin, G., Bensimon, D., and Croquette, V. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 6986-6991
35. Gore, J., Bryant, Z., Stone, M. D., Nöllmann, M., Cozzarelli, N. R., and Bustamante, C. (2006) Nature 439, 100-104
36. Nöllmann, M., Stone, M. D., Bryant, Z., Gore, J., Crisona, N. J., Hong, S. C., Mitelheiser, S., Maxwell, A., Bustamante, C., and Cozzarelli, N. R. (2007) Nat. Struct. Mol. Biol. 14, 264-271
37. Koster, D. A., Croquette, V., Dekker, C., Shuman, S., and Dekker, N. H. (2005) Nature 434, 671-674
38. Koster, D. A., Palle, K., Bot, E. S., Bjornsti, M. A., and Dekker, N. H. (2007) Nature 448, 213-217
39. Revyakin, A., Ebright, R. H., and Strick, T. R. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 4776-4780
40. Revyakin, A., Liu, C., Ebright, R. H., and Strick, T. R. (2006) Science 314, 1139-1143
41. Seidel, R., van Noort, J., van der Scheer, C., Bloom, J. G., Dekker, N. H., Dutta, C. F., Blundell, A., Robinson, T., Firman, K., and Dekker, C. (2004) Nat. Struct. Mol. Biol. 11, 838-843
42. Saleh, O. A., Pérals, C., Barre, F. X., and Allemand, J. F. (2004) EMBO J. 23, 2430-2439
43. Lia, G., Praly, E., Ferreira, H., Stockdale, C., Tse-Dinh, Y. C., Dunlap, D., Croquette, V., Bensimon, D., and Owen-Hughes, T. (2006) Mol. Cell 21, 417-425
44. Bancaud, A., Conde e Silva, N., Barbi, M., Wagner, G., Allemand, J. F., Mozziconacci, J., Lavelle, C., Croquette, V., Victor, J. M., Prunell, A., and Viovy, J. L. (2006) Nat. Struct. Mol. Biol. 13, 444-450