Magnetic tweezers: A sensitive tool to study DNA and chromatin at the single-molecule level

Biochemistry and Cell Biology

Volumn 81, Issue 3, 2003, Pages 151-159

  Zlatanova, Jordanka ^a   Leuba, Sanford H ^b  

^a POLYTECHNIC UNIVERSITY   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Chromatin; Force; Magnetic tweezers; Single molecules; Topoisomerases

Indexed keywords

COMPLEXATION; DNA; MOLECULAR BIOLOGY; TORSIONAL STRESS;

MAGNETIC TWEEZERS;

BIOCHEMISTRY;

DNA; DNA TOPOISOMERASE;

CHROMATIN STRUCTURE; CHROMOSOME ANALYSIS; CONFERENCE PAPER; DNA DETERMINATION; DNA STRUCTURE; ENZYME ACTIVITY; FORCE; MAGNETISM; MOLECULAR BIOLOGY; NONHUMAN; PROTEIN FUNCTION;

BIOPHYSICS; CHROMATIN; DNA; DNA TOPOISOMERASES, TYPE I; MAGNETICS; MODELS, MOLECULAR; TIME FACTORS;

EID: 0041886795     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o03-048     Document Type: Conference Paper

References (48)

1. Allemand, J.F., Bensimon, D., Lavery, R., and Croquette, V. 1998. Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc. Natl. Acad. Sci. U.S.A. 95: 14 152-14 157.
2. Bennink, M.L., Pope, L.H., Leuba, S.H., de Grooth, B.G., and Greve, J. 2001. Single chromatin fibre assembly using optical tweezers. Single Mol. 2: 91-97.
3. Bockelmann, U., Thomen, P., Essevaz-Roulet, B., Viasnoff, V., and Heslot, F. 2002. Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J. 82: 1537-1553.
4. Bustamante, C., Macosko, J.C., and Wuite, G.J. 2000a. Grabbing the cat by the tail: manipulating molecules one by one. Nat. Rev. Mol. Cell Biol. 1: 130-136.
5. Bustamante, C., Smith, S.B., Liphardt, J., and Smith, D. 2000b. Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol. 10: 279-285.
6. Champoux, J.J. 2001. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70: 369-413.
7. Champoux, J.J. 2002. Type IA DNA topoisomerases: strictly one step at a time. Proc. Natl. Acad. Sci. U.S.A. 99: 11 998-12 000.
8. Clausen-Schaumann, H., Rief, M., Tolksdorf, C., and Gaub, H.E. 2000a. Mechanical stability of single DNA molecules. Biophys. J. 78: 1997-2007.
9. Clausen-Schaumann, H., Seitz, M., Krautbauer, R., and Gaub, H.E. 2000b. Force spectroscopy with single bio-molecules. Curr. Opin. Chem. Biol. 4: 524-530.
10. Cluzel, P., Lebrun, A., Heller, C., Lavery, R., Viovy, J.L., Chatenay, D., and Caron, F. 1996. DNA: an extensible molecule. Science (Washington, D.C.), 271: 792-794.
11. Crick, F.H.C., and Hughes, A.F.W. 1949. The physical properties of cytoplasm: a study by means of the magnetic particle method. Exp. Cell Res. 1: 36-80.
12. Crisona, N.J., Strick, T.R., Bensimon, D., Croquette, V., and Cozzarelli, N.R. 2000. Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev. 14: 2881-2892.
13. Dekker, N.H., Rybenkov, V.V., Duguet, M., Crisona, N.J., Cozzarelli, N.R., Bensimon, D., and Croquette, V. 2002. The mechanism of type IA topoisomerases. Proc. Natl. Acad. Sci. U.S.A. 99: 12 126-12 131.
14. Doublie, S., Tabor, S., Long, A.M., Richardson, C.C., and Ellenberger, T. 1998. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature (London), 391: 251-258.
15. Essevaz-Roulet, B., Bockelmann, U., and Heslot, F. 1997. Mechanical separation of the complementary strands of DNA. Proc. Natl. Acad. Sci. U.S.A. 94: 11 935-11 940.
16. Goel, A., Frank-Kamenetskii, M.D., Ellenberger, T., and Herschbach, D. 2001. Tuning DNA "strings": Modulation the rate of DNA replication with mechanical tension. Proc. Natl. Acad. Sci. U.S.A. 98: 8485-8489.
17. Gosse, C., and Croquette, V. 2002. Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys. J. 82: 3314-3329.
18. Hagerman, P.J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17: 265-268.
19. Harada, Y., Ohara, O., Takatsuki, A., Itoh, H., Shimamoto, N., and Kinosita, K., Jr. 2001. Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature (London), 409: 113-115.
20. Israelachvili, J.N. 1992. Intermolecular and surface forces. Academic Press, New York.
21. Kirkegaard, K., and Wang, J.C. 1985. Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. J. Mol. Biol. 185: 625-637.
22. Ladoux, B., Quivy, J.P., Doyle, P., du Roure, O., Almouzni, G., and Viovy, J.L. 2000. Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy. Proc. Natl. Acad. Sci. U.S.A. 97: 14 251-14 256.
23. Lee, G.U., Chrisey, L.A., and Colton, R.J. 1994. Direct measurement of the forces between complementary strands of DNA. Science (Washington, D.C.), 266: 771-773.
24. Leger, J.F., Romano, G., Sarkar, A., Robert, J., Bourdieu, L., Chatenay, D., and Marko, J.F. 1999. Structural transitions of a twisted and stretched DNA molecule. Phys. Rev. Lett. 83: 1066-1069.
25. Leuba, S.H., and Zlatanova, J. (Editors). 2001. Biology at the single-molecule level. Pergamon, Amsterdam.
26. Leuba, S.H., Karymov, M.A., Tomschik, M., Ramjit, R., Smith, P., and Zlatanova, J. 2003. Assembly of single chromatin fibers depends on the tension in the DNA molecule: magnetic tweezers study. Proc. Natl. Acad. Sci. U.S.A. 100: 495-500.
27. Liu, D.J., and Day, L.A. 1994. Pf1 virus structure: helical coat protein and DNA with paraxial phosphates. Science (Washington, D.C.), 265: 671-674.
28. Maier, B., Bensimon, D., and Croquette, V. 2000. Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc. Natl. Acad. Sci. U.S.A. 97:12 002-12 007.
29. Noy, A., Vezenov, D.V., Kayyem, J.F., Meade, T.J., and Lieber, C.M. 1997. Stretching and breaking duplex DNA by chemical force microscopy. Chem. Biol. 4: 519-527.
30. Rief, M., Clausen-Schaumann, H., and Gaub, H.E. 1999. Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6: 346-349.
31. Smith, S.B., Finzi, L., and Bustamante, C. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science (Washington, D.C.), 258: 1122-1126.
32. smith, S.B., Cui, Y., and Bustamante, C. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science (Washington, D.C.), 271: 795-799.
33. Strick, T.R., Allemand, J.F., Bensimon, D., Bensimon, A., and Croquette, V. 1996. The elasticity of a single supercoiled DNA molecule. Science (Washington, D.C.), 271: 1835-1837.
34. Strick, T.R., Allemand, J.F., Bensimon, D., and Croquette, V. 1998a. Behavior of supercoiled DNA. Biophys. J. 74: 2016-2028.
35. Strick, T.R., Croquette, V., and Bensimon, D. 1998b. Homologous pairing in stretched supercoiled DNA. Proc. Natl. Acad. Sci. U.S.A. 95: 10 579-10 583.
36. Strick, T., Allemand, J., Croquette, V., and Bensimon, D. 2000a. Twisting and stretching single DNA molecules. Prog. Biophys. Mol. Biol. 74: 115-140.
37. Strick, T.R., Croquette, V., and Bensimon, D. 2000b. Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature (London), 404: 901-904.
38. Strick, T.R., Allemand, J.-F., Croquette, V., and Bensimon, D. 2001. The manipulation of single biomolecules. Physics Today, 54: 46.
39. Wang, J.C. 1996. DNA topoisomerases. Annu. Rev. Biochem. 65: 635-692.
40. Widom, J. 1999. In Methods Mol. Biol. Vol. 119. Edited by P.B. Becker. Humana Press, Totowa, N.J. pp. 61-77.
41. Williams, M.C., and Rouzina, I. 2002. Force spectroscopy of single DNA and RNA molecules. Curr. Opin. Struct. Biol. 12: 330-336.
42. Wuite, G.J., Smith, S.B., Young, M., Keller, D., and Bustamante, C. 2000. Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature (London), 404: 103-106.
43. Yager, T.D., and van Holde, K.E. 1984. Dynamics and equilibria of nucleosomes at elevated ionic strength. J. Biol. Chem. 259: 4212-4222.
44. Yagi, K. 1960. The mechanical and colloidal properties of amoeba protoplasm and their relations to the mechanism of amoeboid movement. Comp. Biochem. Physiol. 3: 73-91.
45. Ziemann, F., Radler, J., and Sackmann, E. 1994. Local measurements of viscoelastic moduli of entangled actin networks using an oscillating magnetic bead micro-rheometer. Biophys. J. 66: 2210-2216.
46. Zlatanova, J., and Leuba, S.H. 2002. Stretching and imaging single DNA molecules and chromatin. J. Muscle Res. Cell Motil. 23: 377-395.
47. Zlatanova, J., and Leuba, S.H. 2003. Chromatin fibers, one-at-a-time. J. Mol. Biol. In press.
48. Zlatanova, J.S., and van Holde, K.E. 1992. Chromatin loops and transcriptional regulation. Crit. Rev. Eukaryot. Gene Expr. 2: 211-224.