Abstract
The past few years have seen the application of single-molecule force spectroscopy techniques to the study of topoisomerases. Magnetic tweezers are particularly suited to the study of topoisomerases due to their unique ability to exert precise and straightforward control of the supercoiled state of DNA. Here, we illustrate in a stepwise fashion how the dynamic properties of type IB topoisomerases can be monitored using this technique.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Wang, J. C. (1996) DNA topoisomerases. Annu Rev Biochem 65, 635–692.
Champoux, J. J. (2001) DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem 70, 369–413.
Wang, J. C. (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 3, 430–440.
Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A. and Croquette, V. (1996) The elasticity of a single supercoiled DNA molecule. Science 271, 1835–1837.
Strick, T. R., Croquette, V. and Bensimon, D. (2000) Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404, 901–904.
Koster, D. A., Croquette, V., Dekker, C., Shuman, S. and Dekker, N. H. (2005) Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434, 671–674.
Taneja, B., Schnurr, B., Slesarev, A., Marko, J. F. and Mondragon, A. (2007) Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proc Natl Acad Sci USA 104, 14670–14675.
Koster, D. A., Palle, K., Bot, E. S., Bjornsti, M. A. and Dekker, N. H. (2007) Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature 448, 213–217.
Neuman, K. C., Lionnet, T. and Allemand, J. F. (2007) Single-molecule micromanipulation techniques. Ann Rev Mater Res 37, 33–67.
Forth, S., Deufel, C., Sheinin, M. Y., Daniels, B., Sethna, J. P. and Wang, M. D. (2008) Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules. Phys Rev Lett 100, 4.
Strick, T., Dessinges, M.-N., Charvin, G., Dekker, N. H., Allemand, J.-F., Bensimon, D. and Croquette, V. (2003) Stretching of macromolecules and proteins. Rep Prog Phys 66, 1–45.
Bryant, Z., Stone, M. D., Gore, J., Smith, S. B., Cozzarelli, N. R. and Bustamante, C. (2003) Structural transitions and elasticity from torque measurements on DNA. Nature 424, 338–341.
Strick, T., Allemand, J., Croquette, V. and Bensimon, D. (2000) Twisting and stretching single DNA molecules. Prog Biophys Mol Biol 74, 115–140.
Strick, T. R., Dessinges, M. N., Charvin, G., Dekker, N. H., Allemand, J. F., Bensimon, D. and Croquette, V. (2003) Stretching of macromolecules and proteins. Rep Prog Phys 66, 1–45.
Gosse, C. and Croquette, V. (2002) Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys J 82, 3314–3329.
Cheezum, M. K., Walker, W. F. and Guilford, W. H. (2001) Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys J 81, 2378–2388.
Gelles, J., Schnapp, B. J. and Sheetz, M. P. (1988) Tracking kinesin-driven movements with nanometre-scale precision. Nature 331, 450–453.
Ribeck, N. and Saleh, O. A. (2008) Multiplexed single-molecule measurements with magnetic tweezers. Rev Sci Instrum 79, 094301.
Abels, J. A., Moreno-Herrero, F., van der Heijden, T., Dekker, C. and Dekker, N. H. (2005) Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J 88, 2737–2744.
Fulconis, R., Mine, J., Bancaud, A., Dutreix, M. and Viovy, J. L. (2006) Mechanism of RecA-mediated homologous recombination revisited by single molecule nanomanipulation. Embo J 25, 4293–4304.
Kruithof, M., Chien, F., de Jager, M. and van Noort, J. (2008) Subpiconewton dynamic force spectroscopy using magnetic tweezers. Biophys J 94, 2343–2348.
Skinner, G. M., Baumann, C. G., Quinn, D. M., Molloy, J. E. and Hoggett, J. G. (2004) Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle. J Biol Chem 279, 3239–3244.
Revyakin, A., Ebright, R. H. and Strick, T. R. (2005) Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments. Nat Methods 2, 127–138.
Koster, D. A., Wiggins, C. H. and Dekker, N. H. (2006) Multiple events on single molecules: unbiased estimation in single-molecule biophysics. Proc Natl Acad Sci USA 103, 1750–1755.
Bouchiat, C., Wang, M. D., Allemand, J., Strick, T., Block, S. M. and Croquette, V. (1999) Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys J 76, 409–413.
Kerssemakers, J. W., Munteanu, E. L., Laan, L., Noetzel, T. L., Janson, M. E. and Dogterom, M. (2006) Assembly dynamics of microtubules at molecular resolution. Nature 442, 709–712.
Koster, D. A., Czerwinski, F., Halby, L., Crut, A., Vekhoff, P., Palle, K., Arimondo, P. B. and Dekker, N. H. (2008) Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence. Nucleic Acids Res 36, 2301–2310.
Acknowledgments
We thank the many members of our laboratory who have contributed to the research effort on topoisomerases over the last few years, in particular Jacob W. J. Kerssemakers and Jaap Beekman for technical support. We are grateful to the laboratories of Stewart Shuman (Sloan Kettering Institute, New York, USA) and Mary-Ann Bjornsti (St. Jude Children’s Research Hospital, Memphis, USA) for fruitful collaborations on topoisomerase research. Funding is acknowledged from the Dutch Foundation for Research on Matter (FOM), the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) via its Vidi program (JL, IDV, and NHD), Nanoned (NHD and IDV), the Human Frontiers Science Program (DAK), the European Science Foundation via a EURYI grant (NHD), and Delft University of Technology (NHD).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Lipfert, J., Koster, D.A., Vilfan, I.D., Hage, S., Dekker, N.H. (2009). Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases. In: Clarke, D. (eds) DNA Topoisomerases. Methods in Molecular Biology™, vol 582. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-340-4_7
Download citation
DOI: https://doi.org/10.1007/978-1-60761-340-4_7
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-339-8
Online ISBN: 978-1-60761-340-4
eBook Packages: Springer Protocols