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Chapter F5 - Single-molecule manipulation

from Part F - Optical microscopy

Published online by Cambridge University Press:  05 November 2012

Igor N. Serdyuk ,
Nathan R. Zaccai  and
Joseph Zaccai
Igor N. Serdyuk
Affiliation:
Institute of Protein Research, Moscow
Nathan R. Zaccai
Affiliation:
University of Bristol
Joseph Zaccai
Affiliation:
Institut de Biologie Structurale, Grenoble
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Summary

Historical review and introduction to biological problems

1986

A. Ashkin and coworkers proposed the idea of an optical trap (tweezers). An optical trap can be produced with a highly focused laser light, and can be used to grab, move and apply measurable forces on micrometre-sized objects, such as dielectric microspheres. A microsphere that is chemically coupled to a molecule of interest provides a means of measuring the molecule's position and the force that it exerts.

1992

K. Bustamante and coworkers pioneered direct mechanical measurements of the elasticity of single DNA molecules using magnetic trapping. In 1994 S. Chu and coworkers studied the relaxation properties of single DNA molecules using optical trapping and G. Li and colleagues made a direct measurement of the force between complementary strands of DNA with atomic force microscopy. Mechanical properties of individual strands and doubled-stranded DNA have been determined. In 1997 G. Shivashankar and A. Libchaber developed a new technique for single DNA molecule grafting and manipulation using combined atomic force microscopy and an optical tweezer. These studies opened up new possibilities in biosensors and bioelectronic devices.

1993

K. Svoboda and coworkers applied optical trapping nanometry (optical tweezers in conjunction with nanometre-precision position detection schemes) to study a single kinesin molecule.

Type
Chapter
Information
Methods in Molecular Biophysics
Structure, Dynamics, Function
 , pp. 709 - 764
Publisher: Cambridge University Press
Print publication year: 2007

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References

Service, R. F. (1997). Chemists explore the power of one. Science, 276, 1027–1029.CrossRefGoogle Scholar
Mehta, A. D., Rief, M., Spudlich, J. A., Smith, D. A., and Simmons, R. M. (1999). Single-molecule biomechanics with optical methods. Science, 283, 1689–1695.CrossRefGoogle ScholarPubMed
Wang, M., (1999). Manipulation of single molecules in biology. Curr. Opini. Biotechnol., 10, 81–86.CrossRefGoogle ScholarPubMed
Ficher, T. E., Oberhauser, A. F., Carrion-Vazquez, M., Marszalek, P. E., and Fernandez, J. M. (1999). The study of protein mechanics with the atomic force microscope. TIBS, 24, 379–384.Google Scholar
Hegner, M. (2002). The light fantastic. Nature, 419, 125.CrossRefGoogle ScholarPubMed
Grier, D. (2003). A revolution in optical manipulation. Nature, 424, 810–816.CrossRefGoogle ScholarPubMed
Gross, S. D. (2003). Application of optical traps in vivo. Meth. Enzymol., 361, 162–174.CrossRefGoogle ScholarPubMed
Ishijima, A., and Yanagida, T. (2001). Single molecule nanobioscience. Trends Biochem. Sci., 26, 438–444.CrossRefGoogle ScholarPubMed
Finer, J. T., Simmons, R. M., and Spudlich, J. A. (1994). Single myosin molecule mechanics: piconewton forces and nanometer steps. Nature, 368, 113–119.CrossRefGoogle Scholar
Spudlich, J. A. (1994). How molecular motors work. Nature, 372, 515–518.CrossRefGoogle Scholar
Block, S. M. (1995). Nanometers and piconewtons: the macromolecular mechanics of kinesin. Trends Cell Biol., 5, 169–175.CrossRefGoogle Scholar
Kitamura, K., Tokunaga, M., Iwane, A. H., and Yanagida, T. (1999). A single myosin head moves along an actin filament with regular steps of 5.3 nanometers. Nature, 397, 129–134.CrossRefGoogle Scholar
Adachi, K., Ysuda, R., et al. (2000). Stepping rotation of F1-Atpase visualized through angle-resolved single-fluorophore imaging. PNAS, 97, 7243–7247.CrossRefGoogle ScholarPubMed
Oster, G., and Wang, H. (2003). Rotary protein motor. Trends Cell Biol., 13, 114–121.CrossRefGoogle Scholar
Vale, R. D. (1996). Switches, latches and amplifiers: Common themes of G proteins and molecular motors. J. Cell. Biol., 135, 291–302.CrossRefGoogle ScholarPubMed
Bustamante, C., Smith, S. B., Liphardt, J., and Smith, D. (2000). Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol., 10, 279–285.CrossRefGoogle ScholarPubMed
Strick, T., Allemand, J.-F., Croquete, V., and Bensimon, D. (2000). Twisting and stretching single DNA molecules. Prog. Biophys. Mol. Biol., 74, 115–140.CrossRefGoogle ScholarPubMed
Liphgardt, J., Onoa, B., Smith, S. B., Tinoco, I. Jr. and Bustamante, C. (2001). Reversible unfolding of single RNA molecules by mechanical force. Science, 292, 733–737.CrossRefGoogle Scholar
Brower-Toland, B. R., et al. (2002). Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl. Acad. Sci. USA, 99, 1960–1966.CrossRefGoogle ScholarPubMed
Vazques, M. C., Oberhauser, A. F., et al. (2000). Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. Prog. Biophys. Mol. Biol., 74, 63–91.Google Scholar
Fisher, T. E., Marszalek, P. E., and Fernandez, J. M. (2000). Stretching single molecules into novel conformations using the atomic force microscopy. Nature Struct. Biol., 7, 719–724.Google Scholar
Zlatanova, J., Lindsay, S. M., and Leuba, A. H. (2000). Single molecule force spectroscopy in biology using the atomic force microscope. Prog. Biophys. Mol. Biol., 74, 37–61.CrossRefGoogle ScholarPubMed
Rief, M., Oesterhelt, F., Heymann, B., and Gaub, H. E. (1997). Single molecule force spectroscopy on polysaccarides by atomic force microscopy. Science, 275, 1295–1297.CrossRefGoogle Scholar
Grandbois, M., Beyer, M., Rief, M., Clausen-Schaumann, H., and Caub, H. E. (1999). How strong is covalent bond? Science, 283, 1727–1730.CrossRefGoogle ScholarPubMed
Florin, E.-L., Moy, V. T., and Gaub, H. E. (1994). Adhesion forces between individual ligand-receptor pairs. Science, 264, 415–417.CrossRefGoogle ScholarPubMed
Gimzewski, J. K. and Joachim, C. (1999). Nanoscale science of single molecules using molecular probes. Science, 283, 1683–1688.CrossRefGoogle Scholar
Service, R. F. (1997). Chemists explore the power of one. Science, 276, 1027–1029.CrossRefGoogle Scholar
Mehta, A. D., Rief, M., Spudlich, J. A., Smith, D. A., and Simmons, R. M. (1999). Single-molecule biomechanics with optical methods. Science, 283, 1689–1695.CrossRefGoogle ScholarPubMed
Wang, M., (1999). Manipulation of single molecules in biology. Curr. Opini. Biotechnol., 10, 81–86.CrossRefGoogle ScholarPubMed
Ficher, T. E., Oberhauser, A. F., Carrion-Vazquez, M., Marszalek, P. E., and Fernandez, J. M. (1999). The study of protein mechanics with the atomic force microscope. TIBS, 24, 379–384.Google Scholar
Hegner, M. (2002). The light fantastic. Nature, 419, 125.CrossRefGoogle ScholarPubMed
Grier, D. (2003). A revolution in optical manipulation. Nature, 424, 810–816.CrossRefGoogle ScholarPubMed
Gross, S. D. (2003). Application of optical traps in vivo. Meth. Enzymol., 361, 162–174.CrossRefGoogle ScholarPubMed
Ishijima, A., and Yanagida, T. (2001). Single molecule nanobioscience. Trends Biochem. Sci., 26, 438–444.CrossRefGoogle ScholarPubMed
Finer, J. T., Simmons, R. M., and Spudlich, J. A. (1994). Single myosin molecule mechanics: piconewton forces and nanometer steps. Nature, 368, 113–119.CrossRefGoogle Scholar
Spudlich, J. A. (1994). How molecular motors work. Nature, 372, 515–518.CrossRefGoogle Scholar
Block, S. M. (1995). Nanometers and piconewtons: the macromolecular mechanics of kinesin. Trends Cell Biol., 5, 169–175.CrossRefGoogle Scholar
Kitamura, K., Tokunaga, M., Iwane, A. H., and Yanagida, T. (1999). A single myosin head moves along an actin filament with regular steps of 5.3 nanometers. Nature, 397, 129–134.CrossRefGoogle Scholar
Adachi, K., Ysuda, R., et al. (2000). Stepping rotation of F1-Atpase visualized through angle-resolved single-fluorophore imaging. PNAS, 97, 7243–7247.CrossRefGoogle ScholarPubMed
Oster, G., and Wang, H. (2003). Rotary protein motor. Trends Cell Biol., 13, 114–121.CrossRefGoogle Scholar
Vale, R. D. (1996). Switches, latches and amplifiers: Common themes of G proteins and molecular motors. J. Cell. Biol., 135, 291–302.CrossRefGoogle ScholarPubMed
Bustamante, C., Smith, S. B., Liphardt, J., and Smith, D. (2000). Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol., 10, 279–285.CrossRefGoogle ScholarPubMed
Strick, T., Allemand, J.-F., Croquete, V., and Bensimon, D. (2000). Twisting and stretching single DNA molecules. Prog. Biophys. Mol. Biol., 74, 115–140.CrossRefGoogle ScholarPubMed
Liphgardt, J., Onoa, B., Smith, S. B., Tinoco, I. Jr. and Bustamante, C. (2001). Reversible unfolding of single RNA molecules by mechanical force. Science, 292, 733–737.CrossRefGoogle Scholar
Brower-Toland, B. R., et al. (2002). Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl. Acad. Sci. USA, 99, 1960–1966.CrossRefGoogle ScholarPubMed
Vazques, M. C., Oberhauser, A. F., et al. (2000). Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. Prog. Biophys. Mol. Biol., 74, 63–91.Google Scholar
Fisher, T. E., Marszalek, P. E., and Fernandez, J. M. (2000). Stretching single molecules into novel conformations using the atomic force microscopy. Nature Struct. Biol., 7, 719–724.Google Scholar
Zlatanova, J., Lindsay, S. M., and Leuba, A. H. (2000). Single molecule force spectroscopy in biology using the atomic force microscope. Prog. Biophys. Mol. Biol., 74, 37–61.CrossRefGoogle ScholarPubMed
Rief, M., Oesterhelt, F., Heymann, B., and Gaub, H. E. (1997). Single molecule force spectroscopy on polysaccarides by atomic force microscopy. Science, 275, 1295–1297.CrossRefGoogle Scholar
Grandbois, M., Beyer, M., Rief, M., Clausen-Schaumann, H., and Caub, H. E. (1999). How strong is covalent bond? Science, 283, 1727–1730.CrossRefGoogle ScholarPubMed
Florin, E.-L., Moy, V. T., and Gaub, H. E. (1994). Adhesion forces between individual ligand-receptor pairs. Science, 264, 415–417.CrossRefGoogle ScholarPubMed
Gimzewski, J. K. and Joachim, C. (1999). Nanoscale science of single molecules using molecular probes. Science, 283, 1683–1688.CrossRefGoogle Scholar

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