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Single-Molecule Manipulation Using Optical Traps

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Abstract

One of the most sensitive tools for manipulating single molecules and measuring their properties is the optical trap, also known as optical tweezers. Consisting essentially of a strongly focused light beam, optical traps were first developed and demonstrated in the 1970s and 1980s by Arthur Ashkin and colleagues (Ashkin et al. 1986). These early pioneers showed that micron-sized dielectric particles could be held and manipulated in solution by using optical forces to create a stable, three-dimensional potential well. Since then, optical trapping instrumentation has been refined and developed such that piconewton forces are now routinely applied, while at the same time measuring the resultant displacements to nanometre or even angström resolution. As a result of these advances, optical traps have been applied widely, from cytometry to the study of mesoscopic colloids and polymers and of course the properties of single biological macromolecules. This chapter begins with a description of the theory and design of optical traps, followed by an illustrative discussion of applications to the study of structure formation and molecular motors, a description of typical “tricks of the trade” for using optical traps, and a brief look at techniques for extending the capabilities of traps.

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References

  • Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, et al. (2005). Direct observation of base-pair stepping by RNA polymerase. Nature 438:460–465.

    Article  ADS  Google Scholar 

  • Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S (1986). Observation of a single-beam gradient force optical trap for dielectric particles. Optics Lett 11:288–290.

    Article  ADS  Google Scholar 

  • Bell GI (1978). Models for specific adhesion of cells to cells. Science 200:618–627.

    Article  ADS  Google Scholar 

  • Berg-Sørensen K, Flyvbjerg H (2004). Power spectrum analysis for optical tweezers. Rev Sci Instrum 75:594–612.

    Article  ADS  Google Scholar 

  • Best RB, Paci E, Hummer G, Dudko O (2008). Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. J Phys Chem B 112: 5968–5976.

    Article  Google Scholar 

  • Block SM (1998). Constructing optical tweezers. In: Spector DL, Goldman RD, Leinwand LA (eds.), Cells: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google Scholar 

  • Block SM, Asbury CL, Shaevitz JW, Lang MJ (2003). Probing the kinesin reaction cycle with a 2D optical force clamp. Proc Natl Acad Sci USA 100:2351–2356.

    Article  ADS  Google Scholar 

  • Borgia A, Williams PM, Clarke J (2008). Single-molecule studies of protein folding. Annu Rev Biochem 77:6.1–6.25.

    Article  Google Scholar 

  • Brower-Towland BD, Smith CL, et al. (2002). Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci USA 99:1960–1965.

    Article  ADS  Google Scholar 

  • Bustamante C, Chemla YR, Forde NR, Izhaky D (2004). Mechanical processes in biochemistry. Annu Rev Biochem 73:705–748.

    Article  Google Scholar 

  • Carter AR, King GM, Ulrich TA, et al. (2007). Stabilization of an optical microscope to 0.1 nm in three dimensions. Appl Opt 46:421–427.

    Article  ADS  Google Scholar 

  • Carter BC, Vershinin M, Gross SP (2008). A comparison of step-detection methods: How well can you do? Biophys J 94:306–319.

    Article  Google Scholar 

  • Cecconi C, Shank EA, Bustamante C, Marqusee S (2005). Direct observation of the three-state folding of a single protein molecule. Science 309:2057–2059.

    Article  ADS  Google Scholar 

  • Collin D, Ritort F, Jarzynski C, et al. (2005). Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature 437:231–234.

    Article  ADS  Google Scholar 

  • Crooks GE (1999). Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys Rev E 60:2721–2726.

    Article  ADS  Google Scholar 

  • Dalal RV, Larson MH, Neuman KC, et al. (2006). Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. Mol Cell 23:231–239.

    Article  Google Scholar 

  • Dame RT, Noom MC, Wuite GJ (2006). Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444:387–390.

    Article  ADS  Google Scholar 

  • deCastro MJ, Fondecave RM, Clarke LA, et al. (2000). Working strokes by single molecules of the kinesin-related microtubule motor ncd. Nat Cell Biol 2:724–729.

    Article  Google Scholar 

  • Dessinges MN, Maier B, Zhang Y, et al. (2002). Stretching single stranded DNA, a model polyelectrolyte. Phys Rev Lett 89:248102.

    Article  ADS  Google Scholar 

  • Dietz H, Berkemeier F, Bertz M, Reif M (2006). Anisotropic deformation response of single protein molecules. Proc Natl Acad Sci USA 103:12724–12728.

    Article  ADS  Google Scholar 

  • Dudko O, Hummer G, Szabo A (2006). Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett 96:108101.

    Article  ADS  Google Scholar 

  • Dumont S, Cheng W, Serebov V, et al. (2006). RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature 439:105–108.

    Article  ADS  Google Scholar 

  • Enger J, Goksor M, Ramser K, et al. (2004). Optical tweezers applied to a microfluidic system. Lab Chip 4:196–200.

    Article  Google Scholar 

  • Evans E, Ritchie K (1997). Dynamic strength of molecular adhesion bonds. Biophys J 72:1541–1555.

    Article  Google Scholar 

  • Finer JT, Simmons RM, Spudich JA (1994). Single myosin mechanics: picoNewton forces and nanometre steps. Nature 368: 113–119.

    Article  ADS  Google Scholar 

  • Fordyce PM, Valentine MT, Block SM (2007). Advances in surface-based assays for single molecules. In: Selvin P, Ha T (eds.), Single-molecule techniques: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 431--460.

    Google Scholar 

  • Gilbert SP and Mackey AT (2000). Kinetics: A tool to study molecular motors. Methods 22:337–354.

    Article  Google Scholar 

  • Gore J, Ritort F, Bustamante C (2003). Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc Natl Acad Sci USA 100:12564–12569.

    Article  MathSciNet  ADS  MATH  Google Scholar 

  • Greenleaf WJ, Woodside MT, Abbondanzieri EA, Block SM (2005). Passive all-optical force clamp for high-resolution laser trapping. Phys Rev Lett 95:208102.

    Article  ADS  Google Scholar 

  • Greenleaf WJ, Woodside MT, Block SM (2007). High-resolution, single-molecule measurements of biomolecular motion. Annu Rev Biophys Biomol Struct 36:171–190.

    Article  Google Scholar 

  • Greenleaf WJ, Frieda KL, Foster DNA, et al. (2008). Direct observation of hierarchical folding in single riboswitch aptamers. Science 319:630–633.

    Article  Google Scholar 

  • Grier DG, Roichman Y (2006). Holographic optical trapping. Appl Opt 45:880–887.

    Article  ADS  Google Scholar 

  • Harada Y, Asakura T (1996). Radiation forces on a dielectric sphere in the Rayleigh scattering regime. Opt Commun 124:529–541.

    Article  ADS  Google Scholar 

  • Herbert KM, La Porta A, Wong BJ, et al. (2006). Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell 125:1084–1094.

    Article  Google Scholar 

  • Herbert KM, Greenleaf WJ, Block SM (2008). Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem 77:149–176.

    Article  Google Scholar 

  • Hermanson GT (1996). Bioconjugate techniques. Academic Press, San Diego, CA.

    Google Scholar 

  • Hohng S, Zhou R, Nahas MK, et al. (2007). Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction. Science 318:279–283.

    Article  ADS  Google Scholar 

  • Hummer G, Szabo A (2005). Free energy surfaces from single-molecule force spectroscopy. Acc Chem Res 38: 504–513.

    Article  Google Scholar 

  • Hyeon C, Thirumalai D (2008). Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J Am Chem Soc 130:1538–1539.

    Article  Google Scholar 

  • Ishijima A, Kojima H, Funatsu T, et al. (1998). Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin. Cell 92:161–171.

    Article  Google Scholar 

  • Jarzynski C (1997). Non-equilibrium equality for free energy differences. Phys Rev Lett 78:2690–2693.

    Article  ADS  Google Scholar 

  • Kawaguchi K, Ishiwata S (2001). Nucleotide-dependent single- to double-headed binding of kinesin. Science 291:667–669.

    Article  ADS  Google Scholar 

  • Kimura Y, Bianco PR (2006). Single molecule studies of DNA binding proteins using optical tweezers. Analyst 131:868–874.

    Article  ADS  Google Scholar 

  • Koch SJ, Shundrovsky A, Jantzen BC, Wang MD (2002). Probing protein–DNA interactions by unzipping a single DNA double helix. Biophys J 83:1098–1105.

    Article  Google Scholar 

  • Lang MJ, Fordyce PM, Engh AM, et al. (2004). Simultaneous, coincident optical trapping and single molecule fluorescence. Nat Methods 1:133–139.

    Article  Google Scholar 

  • Lang MJ, Asbury CL, Shaevitz, JW, Block SM (2002). An automated two-dimensional optical force clamp for single molecule studies. Biophys J 83:491–501.

    Article  Google Scholar 

  • La Porta A, Wang MD (2004). Optical torque wrench: Angular trapping, rotation and torque detection using quartz microparticles. Phys Rev Lett 92: 190801.

    Article  Google Scholar 

  • Larson MH, Greenleaf WJ, Landick R, Block SM (2008). Applied force reveals mechanistic and energetic details of transcription termination. Cell 132:971–982.

    Article  Google Scholar 

  • Li PTX, Collin D, Smith SB, et al. (2006). Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J 90:250–260.

    Article  Google Scholar 

  • Lister I, Schmitz S, Walker M, et al. (2004). A monomeric myosin VI with a large working stroke. EMBO J 23: 1729–1738.

    Article  Google Scholar 

  • Mañosas M, Collin D, Ritort F (2006). Force-dependent fragility in RNA hairpins. Phys Rev Lett 96:218301.

    Article  ADS  Google Scholar 

  • Mañosas M, Wen JD, Li PTX, et al. (2007). Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Biophys J 92:3010–3021.

    Article  Google Scholar 

  • Marko JF, Siggia ED (1995). Stretching DNA. Macromolecules 28:8759–8770.

    Article  ADS  Google Scholar 

  • Moffitt JR, Chemla YR, Izhaky D, Bustamante C (2006). Differential detection of dual traps improves the spatial resolution of optical tweezers. Proc Natl Acad Sci USA 103:9006–9011.

    Article  ADS  Google Scholar 

  • Moffitt JR, Chemla YR, Smith SB, Bustamante C (2008). Recent advances in optical tweezers. Annu Rev Biochem. 77:19.1–19.24.

    Article  Google Scholar 

  • Molloy JE, Burns JE, Kendrick-Jones J, et al. (1995). Movement and force produced by a single myosin head. Nature 378:209–212.

    Article  ADS  Google Scholar 

  • Nambiar R, Gajraj A, Meiner JC (2004). All-optical constant-force laser tweezers. Biophys J 87:1972–1980.

    Article  Google Scholar 

  • Neuman KC, Chadd EH, Liou GF, et al. (1999). Characterization of photodamage to Escherichia coli in optical traps. Biophys J 77:2656–2863.

    Article  Google Scholar 

  • Neuman KC, Block SM (2004). Optical trapping. Rev Sci Instrum 75:2787–2809.

    Article  ADS  Google Scholar 

  • Neuman KC, Abbondanzieri EA, Block SM (2005). Measurement of the effective focal shift in an optical trap. Opt Lett 30:1318–1320.

    Article  ADS  Google Scholar 

  • Neuman KC, Nagy A (2008). Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5:491–505.

    Article  Google Scholar 

  • Nishizaka T, Miyata H, Yoshikawa H, et al. (1995). Unbinding force of a single motor molecule of muscle using optical tweezers. Nature 337:251–254.

    Article  ADS  Google Scholar 

  • Nugent-Glandorf L, Perkins TT (2004). Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection. Opt Lett 29:2611–2613.

    Article  ADS  Google Scholar 

  • Rasnik I, McKinney SA, Ha T (2006). Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Methods 3: 891–893.

    Article  Google Scholar 

  • Rock RS, Rief M, Mehta AD, Spudich JA (2000). In vitro assays of processive myosin motors. Methods 22:373–381.

    Article  Google Scholar 

  • Rohrbach A, Stelzer EHK (2001). Optical trapping of dielectric particles in arbitrary fields. J Opt Soc Am A 18: 839–853.

    Article  ADS  Google Scholar 

  • Schnitzer MJ, Visscher K, Block SM (2000). Mechanism of force production by single kinesin motors. Nat Cell Biol 2:718–723.

    Article  Google Scholar 

  • Seol Y, Li J, Nelson PC, et al. (2007). Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6–7 micron. Biophys J 93:4360–4373.

    Article  Google Scholar 

  • Shaevitz JW, Block SM, Schnitzer MJ (2005). Statistical kinetics of macromolecular dynamics. Biophys J. 89: 2275–2285.

    Article  Google Scholar 

  • Shaevitz JW, Abbondanzieri EA, Landick R, Block SM (2003). Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426:684–687.

    Article  ADS  Google Scholar 

  • Smith SB, Cui Y, Bustamante C (1996). Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science 271: 795–799.

    Article  ADS  Google Scholar 

  • Smith SB, Cui Y, Bustamante C (2003). Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol 361:134–162.

    Article  Google Scholar 

  • Svoboda K, Block SM (1994a). Biological applications of optical forces. Annu Rev Biophys Biomol Struct 23: 247–285.

    Article  Google Scholar 

  • Svoboda K, Block SM (1994b). Force and velocity measured for single kinesin molecules. Cell 77: 773–784.

    Article  Google Scholar 

  • Tolić-Nørrelykke SF, Schäffer E, Howard J, et al. (2006). Calibration of optical tweezers with positional detection in the back focal plane. Rev Sci Instrum 77:103101.

    Article  ADS  Google Scholar 

  • Trapagnier EH, Radenovic A, Sivak D, et al. (2007). Controlling DNA capture and propagation through artificial nanopores. Nano Lett 7:2824–2830.

    Article  ADS  Google Scholar 

  • Valentine MT, Fordyce PM, Krzysiak TC, et al. (2006). Individual dimers of the mitotic kinesin motor Eg5 step processively and support substantial loads in vitro. Nat Cell Biol 8:470–476.

    Article  Google Scholar 

  • Veigel C, Schmitz S, Wang F, Sellers JR (2005). Load-dependent kinetics of myosin-V can explain its high processivity. Nat Cell Biol 7:861–869.

    Article  Google Scholar 

  • Vilar JMG, Rubi JM (2008). Failure of the work-Hamiltonian connection for free-energy calculations. Phys Rev Lett 100:020601.

    Article  ADS  Google Scholar 

  • Visscher K, Gross SP, Block SM (1996). Construction of multiple-beam optical traps with nanometer-resolution position sensing. IEEE J Sel Top Quant Electr 2:1066–1076.

    Article  Google Scholar 

  • Visscher K, Block SM (1998). Versatile optical traps with feedback control. Methods Enzymol 298: 460–489.

    Article  Google Scholar 

  • Visscher K, Schnitzer MJ, Block SM (1999). Single kinesin molecules studied with a molecular force clamp. Nature 400:184–189.

    Article  ADS  Google Scholar 

  • Wang MD, Yin H, Landick R, et al. (1997). Stretching DNA with optical tweezers. Biophys J 72:1335–1346.

    Article  Google Scholar 

  • Williams PM, Fowler SB, Best RB, et al. (2003). Hidden complexity on the mechanical properties of titin. Nature 422:446–449.

    Article  ADS  Google Scholar 

  • Woodside MT, Behnke-Parks WM, Larizadeh K, et al. (2006a). Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci USA 103:6190–6195.

    Article  ADS  Google Scholar 

  • Woodside MT, Anthony PC, Behnke-Parks WM, et al. (2006b). Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science 314:1001–1004.

    Article  ADS  Google Scholar 

  • Woodside MT, García-García C, Block SM (2008). Folding and unfolding single RNA molecules under tension. Curr Opin Chem Biol, vol. 12, pp. 640--646.

    Google Scholar 

  • Wuite GJL, Smith SB, Young M, et al. (2000). Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404:103–106.

    Article  ADS  Google Scholar 

  • Xu F, Ren K, Gouesbet G, et al. (2007). Generalized Lorenz-Mie theory for an arbitrarily oriented, located, and shaped beam scatted by a homogeneous spheroid. J Opt Soc Am A 24:119–131.

    Article  ADS  MATH  Google Scholar 

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Acknowledgments

We thank Cuauhtémoc García-García for critical reading of the manuscript and Charles Asbury, Joshua Shaevitz, and Kristina Herbert for providing the raw data used in Figures 12.10 and 12.11. MTV is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.

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Authors and Affiliations

  1. National Institute for Nanotechnology, National Research Council of Canada, and Department of Physics, University of Alberta, Alberta, Canada

    Michael T. Woodside

  2. Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA

    Megan T. Valentine

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  1. Michael T. Woodside
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  2. Megan T. Valentine
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Editors and Affiliations

  1. Institut für Biophysik, Universität Linz, Altenberger Straße 69, Linz, 4040, Austria

    Peter Hinterdorfer

  2. Harvard Medical School, Harvard University, Longwood Ave. 250, Boston, 02115, U.S.A.

    Antoine Oijen

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Woodside, M.T., Valentine, M.T. (2009). Single-Molecule Manipulation Using Optical Traps. In: Hinterdorfer, P., Oijen, A. (eds) Handbook of Single-Molecule Biophysics. Springer, New York, NY. https://doi.org/10.1007/978-0-387-76497-9_12

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