Optical Tweezers to Study Viruses

  • J. Ricardo Arias-Gonzalez
Part of the Subcellular Biochemistry book series (SCBI, volume 68)


A virus is a complex molecular machine that propagates by channeling its genetic information from cell to cell. Unlike macroscopic engines, it operates in a nanoscopic world under continuous thermal agitation. Viruses have developed efficient passive and active strategies to pack and release nucleic acids. Some aspects of the dynamic behavior of viruses and their substrates can be studied using structural and biochemical techniques. Recently, physical techniques have been applied to dynamic studies of viruses in which their intrinsic mechanical activity can be measured directly. Optical tweezers are a technology that can be used to measure the force, torque and strain produced by molecular motors, as a function of time and at the single-molecule level. Thanks to this technique, some bacteriophages are now known to be powerful nanomachines; they exert force in the piconewton range and their motors work in a highly coordinated fashion for packaging the viral nucleic acid genome. Nucleic acids, whose elasticity and condensation behavior are inherently coupled to the viral packaging mechanisms, are also amenable to examination with optical tweezers. In this chapter, we provide a comprehensive analysis of this laser-based tool, its combination with imaging methods and its application to the study of viruses and viral molecules.


Biophysics Virus Bacteriophage Capsid DNA RNA Molecular motor Machine Single-molecule Mechanochemistry Optics Optical tweezers Magnetic tweezers Dynamics Manipulation Force Pressure Elasticity Condensation DNA packaging 



Three dimensional


Atomic force microscopy


Base pair










Numerical aperture





It is a pleasure to acknowledge J.R. Moffitt and J.L. Carrascosa for technical insights into different aspects of the chapter, R. Bocanegra, L. Quintana for careful reading of the manuscript, C. Mark and S. Hormeño for editorial and illustration assistance, respectively, and M. de la Guía for graphic design of Fig. 9.8. This work was funded by the Spanish Ministry of Science and Innovation under the “Ramon y Cajal” program (Grant No. RYC-2007-01765).

References and Further Reading

  1. 1.
    Hormeno S, Arias-Gonzalez JR (2006) Exploring mechanochemical processes in the cell with optical tweezers. Biol Cell 98:679–695PubMedCrossRefGoogle Scholar
  2. 2.
    Svoboda K, Block SM (1994) Biological applications of optical forces. Annu Rev Biophys Biomol Struct 23:247–285PubMedCrossRefGoogle Scholar
  3. 3.
    Bustamante C (2008) In singulo biochemistry: when less is more. Annu Rev Biochem 77:45–50PubMedCrossRefGoogle Scholar
  4. 4.
    Oster G, Wang H (2003) How protein motors convert chemical energy into mechanical work. In: Schliwa M (ed) Molecular motors. Wiley-VCH, Weinheim, pp 207–227Google Scholar
  5. 5.
    Ketterle W (1999) Experimental studies of Bose-Einstein condensation. Phys Today 52:30–35CrossRefGoogle Scholar
  6. 6.
    Smith SB, Cui Y, Bustamante C (2003) Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol 361:134–162PubMedCrossRefGoogle Scholar
  7. 7.
    Moffitt JR, Chemla YR, Smith SB, Bustamante C (2008) Recent advances in optical tweezers. Annu Rev Biochem 77:205–228PubMedCrossRefGoogle Scholar
  8. 8.
    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 U S A 103:9006–9011PubMedCrossRefGoogle Scholar
  9. 9.
    Hormeno S, Ibarra B, Chichon FJ, Habermann K, Lange BM, Valpuesta JM, Carrascosa JL, Arias-Gonzalez JR (2009) Single centrosome manipulation reveals its electric charge and associated dynamic structure. Biophys J 97:1022–1030PubMedCrossRefGoogle Scholar
  10. 10.
    Jackson JD (1999) Classical electrodynamics. Wiley Hoboken, USAGoogle Scholar
  11. 11.
    Arias-Gonzalez JR, Nieto-Vesperinas M (2003) Optical forces on small particles: attractive and repulsive nature and Plasmon-resonance conditions. J Opt Soc Am A 20:1201–1209CrossRefGoogle Scholar
  12. 12.
    Tanase M, Biais N, Sheetz M (2007) Magnetic tweezers in cell biology. In: Yu‐Li W, Dennis ED (eds) Methods in cell biology, vol 83. Academic Press, pp 473–493, vol 83Google Scholar
  13. 13.
    Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5:491–505PubMedCrossRefGoogle Scholar
  14. 14.
    Bustamante C, Macosko JC, Wuite GJ (2000) Grabbing the cat by the tail: manipulating molecules one by one. Nat Rev Mol Cell Biol 1:130–136PubMedCrossRefGoogle Scholar
  15. 15.
    Hormeno S, Moreno-Herrero F, Ibarra B, Carrascosa JL, Valpuesta JM, Arias-Gonzalez JR (2011) Condensation prevails over B-a transition in the structure of DNA at low humidity. Biophys J 100:2006–2015PubMedCrossRefGoogle Scholar
  16. 16.
    Rickgauer JP, Fuller DN, Grimes S, Jardine PJ, Anderson DL, Smith DE (2008) Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage phi29. Biophys J 94:159–167PubMedCrossRefGoogle Scholar
  17. 17.
    Smith DE, Tans SJ, Smith SB, Grimes S, Anderson DL, Bustamante C (2001) The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature 413:748–752PubMedCrossRefGoogle Scholar
  18. 18.
    Li PT, Collin D, Smith SB, Bustamante C, Tinoco I Jr (2006) Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J 90:250–260PubMedCrossRefGoogle Scholar
  19. 19.
    Bustamante C, Bryant Z, Smith SB (2003) Ten years of tension: single-molecule DNA mechanics. Nature 421:423–427PubMedCrossRefGoogle Scholar
  20. 20.
    Williams MC, Rouzina I, Bloomfield VA (2002) Thermodynamics of DNA interactions from single molecule stretching experiments. Acc Chem Res 35:159–166PubMedCrossRefGoogle Scholar
  21. 21.
    Mao H, Arias-Gonzalez JR, Smith SB, Tinoco I Jr, Bustamante C (2005) Temperature control methods in a laser tweezers system. Biophys J 89:1308–1316PubMedCrossRefGoogle Scholar
  22. 22.
    Hormeno S, Ibarra B, Valpuesta JM, Carrascosa JL, Arias-Gonzalez JR (2012) Mechanical stability of low-humidity single DNA molecules. Biopolymers 97:199–208PubMedCrossRefGoogle Scholar
  23. 23.
    Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC (2010) Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 7:299–341PubMedCrossRefGoogle Scholar
  24. 24.
    Casjens SR (2011) The DNA-packaging nanomotor of tailed bacteriophages. Nat Rev Microbiol 9:647–657PubMedCrossRefGoogle Scholar
  25. 25.
    Chemla YR, Smith DE (2012) Single-molecule studies of viral DNA packaging. Adv Exp Med Biol 726:549–584PubMedCrossRefGoogle Scholar
  26. 26.
    Feiss M, Rao VB (2012) The bacteriophage DNA packaging machine. Adv Exp Med Biol 726:489–509PubMedCrossRefGoogle Scholar
  27. 27.
    Tang J, Olson N, Jardine PJ, Grimes S, Anderson DL, Baker TS (2008) DNA poised for release in bacteriophage phi29. Structure 16:935–943PubMedCrossRefGoogle Scholar
  28. 28.
    Moffitt JR, Chemla YR, Aathavan K, Grimes S, Jardine PJ, Anderson DL, Bustamante C (2009) Intersubunit coordination in a homomeric ring ATPase. Nature 457:446–450PubMedCrossRefGoogle Scholar
  29. 29.
    Fuller DN, Raymer DM, Kottadiel VI, Rao VB, Smith DE (2007) Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc Natl Acad Sci U S A 104:16868–16873PubMedCrossRefGoogle Scholar
  30. 30.
    Fuller DN, Raymer DM, Rickgauer JP, Robertson RM, Catalano CE, Anderson DL, Grimes S, Smith DE (2007) Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. J Mol Biol 373:1113–1122PubMedCrossRefGoogle Scholar
  31. 31.
    Fuller DN, Rickgauer JP, Jardine PJ, Grimes S, Anderson DL, Smith DE (2007) Ionic effects on viral DNA packaging and portal motor function in bacteriophage phi 29. Proc Natl Acad Sci U S A 104:11245–11250PubMedCrossRefGoogle Scholar
  32. 32.
    Ivanovska IL, de Pablo PJ, Ibarra B, Sgalari G, MacKintosh FC, Carrascosa JL, Schmidt CF, Wuite GJ (2004) Bacteriophage capsids: tough nanoshells with complex elastic properties. Proc Natl Acad Sci U S A 101:7600–7605PubMedCrossRefGoogle Scholar
  33. 33.
    Tsay JM, Sippy J, DelToro D, Andrews BT, Draper B, Rao V, Catalano CE, Feiss M, Smith DE (2010) Mutations altering a structurally conserved loop-helix-loop region of a viral packaging motor change DNA translocation velocity and processivity. J Biol Chem 285:24282–24289PubMedCrossRefGoogle Scholar
  34. 34.
    Tsay JM, Sippy J, Feiss M, Smith DE (2009) The Q motif of a viral packaging motor governs its force generation and communicates ATP recognition to DNA interaction. Proc Natl Acad Sci U S A 106:14355–14360PubMedCrossRefGoogle Scholar
  35. 35.
    Chemla YR, Aathavan K, Michaelis J, Grimes S, Jardine PJ, Anderson DL, Bustamante C (2005) Mechanism of force generation of a viral DNA packaging motor. Cell 122:683–692PubMedCrossRefGoogle Scholar
  36. 36.
    Aathavan K, Politzer AT, Kaplan A, Moffitt JR, Chemla YR, Grimes S, Jardine PJ, Anderson DL, Bustamante C (2009) Substrate interactions and promiscuity in a viral DNA packaging motor. Nature 461:669–673PubMedCrossRefGoogle Scholar
  37. 37.
    Zhang Z, Kottadiel VI, Vafabakhsh R, Dai L, Chemla YR, Ha T, Rao VB (2011) A promiscuous DNA packaging machine from bacteriophage T4. PLoS Biol 9:e1000592PubMedCrossRefGoogle Scholar
  38. 38.
    Hugel T, Michaelis J, Hetherington CL, Jardine PJ, Grimes S, Walter JM, Falk W, Anderson DL, Bustamante C (2007) Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids. PLoS Biol 5:e59PubMedCrossRefGoogle Scholar
  39. 39.
    Purohit PK, Kondev J, Phillips R (2003) Mechanics of DNA packaging in viruses. Proc Natl Acad Sci U S A 100:3173–3178PubMedCrossRefGoogle Scholar
  40. 40.
    Yu J, Moffitt J, Hetherington CL, Bustamante C, Oster G (2010) Mechanochemistry of a viral DNA packaging motor. J Mol Biol 400:186–203PubMedCrossRefGoogle Scholar
  41. 41.
    Ashkin A, Dziedzic JM (1987) Optical trapping and manipulation of viruses and bacteria. Science 235:1517–1520PubMedCrossRefGoogle Scholar
  42. 42.
    Sieben C, Kappel C, Zhu R, Wozniak A, Rankl C, Hinterdorfer P, Grubmuller H, Herrmann A (2012) Influenza virus binds its host cell using multiple dynamic interactions. Proc Natl Acad Sci U S A 109:13626–13631PubMedCrossRefGoogle Scholar
  43. 43.
    McNerney GP, Hubner W, Chen BK, Huser T (2010) Manipulating CD4+ T cells by optical tweezers for the initiation of cell-cell transfer of HIV-1. J Biophoton 3:216–223CrossRefGoogle Scholar
  44. 44.
    Herbert KM, Greenleaf WJ, Block SM (2008) Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem 77:149–176PubMedCrossRefGoogle Scholar
  45. 45.
    Pyle AM (2008) Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 37:317–336PubMedCrossRefGoogle Scholar
  46. 46.
    van Oijen AM, Loparo JJ (2010) Single-molecule studies of the replisome. Annu Rev Biophys 39:429–448PubMedCrossRefGoogle Scholar
  47. 47.
    Ashkin A (1970) Acceleration and trapping of particles by radiation pressure. Phys Rev Lett 24:156–159CrossRefGoogle Scholar
  48. 48.
    Grier DG (2003) A revolution in optical manipulation. Nature 424:810–816PubMedCrossRefGoogle Scholar
  49. 49.
    Dame RT, Noom MC, Wuite GJ (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444:387–390PubMedCrossRefGoogle Scholar
  50. 50.
    Gutierrez-Medina B, Andreasson JO, Greenleaf WJ, Laporta A, Block SM (2010) An optical apparatus for rotation and trapping. Methods Enzymol 475:377–404PubMedCrossRefGoogle Scholar
  51. 51.
    Parkin S, Knoner G, Singer W, Nieminen TA, Heckenberg NR, Rubinsztein-Dunlop H (2007) Optical torque on microscopic objects. Methods Cell Biol 82:525–561PubMedCrossRefGoogle Scholar
  52. 52.
    van Mameren J, Peterman EJ, Wuite GJ (2008) See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucleic Acids Res 36:4381–4389PubMedCrossRefGoogle Scholar
  53. 53.
    Lang MJ, Fordyce PM, Engh AM, Neuman KC, Block SM (2004) Simultaneous, coincident optical trapping and single-molecule fluorescence. Nat Methods 1:133–139PubMedCrossRefGoogle Scholar
  54. 54.
    Richardson AC, Reihani N, Oddershede LB (2006) In: Dholakia K, Spalding GC (eds) Combining confocal microscopy with precise force-scope optical tweezers, vol 6326. SPIE, San Diego, pp 632628–632637Google Scholar
  55. 55.
    Vossen DLJ, van der Horst A, Dogterom M, van Blaaderen A (2004) Optical tweezers and confocal microscopy for simultaneous three-dimensional manipulation and imaging in concentrated colloidal dispersions. Rev Sci Instrum 75:2960–2970CrossRefGoogle Scholar
  56. 56.
    Toprak E, Selvin PR (2007) New fluorescent tools for watching nanometer-scale conformational changes of single molecules. Annu Rev Biophys Biomol Struct 36:349–369PubMedCrossRefGoogle Scholar

Further Reading3

  1. Berns MW, Greulich KO (2007) Laser manipulation of cells and tissues. Methods Cell Biol 82Google Scholar
  2. Schliwa M (ed) (2003) Molecular motors. Wiley-VCH Weinheim (Germany)Google Scholar
  3. Sheetz MP (1998) Laser tweezers in cell biology. Methods Cell Biol 55Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia)MadridSpain
  2. 2.Department of Macromolecular StructureCentro Nacional de Biotecnología (CSIC)MadridSpain
  3. 3.CNB-CSIC-IMDEA Nanociencia associated unit “Unidad de Nanobiotecnología”MadridSpain

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