Optical Tweezers for Mechanical Control Over DNA in a Nanopore

  • Ulrich F. KeyserEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 870)


The translocation of long-chain molecules, such as DNA or peptides, through membranes is an integral process for the function of living cells. During the translocation process, a number of interactions of electrostatic or hydrophobic nature govern the translocation velocity. Most of these interactions remain largely unexplored on the single-molecule level due to a lack of suitable instrumentation. We have shown that a combination of optical tweezers, single solid-state nanopores, and electrophysiological ionic current detection can provide further insight into the behavior of polymers in confinement. Here, we describe the experimental procedures necessary for manipulation of single biopolymers in a single nanopore not only by electrical fields, but also through mechanical forces using optical tweezers.

Key words

Nanopore Optical tweezers DNA translocation Biopolymers Polymer transport Single-molecule sensors Single-channel recording 



I would like to thank Cees Dekker, Nynke, Dekker, Serge Lemay, Jelle van der Does, Stijn van Dorp, Bernard Koeleman, Oliver Otto, Benjamin Gollnick, Christof Gutsche, Friedrich Kremer, and Derek Stein for their help and discussions. Peter Veenhuizen, Ya-Hui Chen, and Suzanne Hage are acknowledged for preparing the biotinylated lambda-DNA, and Bernadette Quinn for help with electrochemical questions. Ralph Smeets, Diego Krapf, and Meng-Yue Wu mastered the fabrication of the nanpores. Stijn van Dorp, Bernard Koeleman, and Oliver Otto are especially acknowledged for taking some of the data presented here. I would like to thank Jo Gornall for proofreading the manuscript. Financial support of FOM, NWO, and the Emmy Noether program of the DFG is gratefully acknowledged.


  1. 1.
    Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166–169CrossRefGoogle Scholar
  2. 2.
    Dekker C (2007) Solid-state nanopores. Nature Nanotechnology 2:209–215CrossRefGoogle Scholar
  3. 3.
    Bezrukov SM (2000) Ion channels as molecular coulter counters to probe metabolite transport. J Membr Biol 174:1–13CrossRefGoogle Scholar
  4. 4.
    Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2:537–540CrossRefGoogle Scholar
  5. 5.
    Smeets RMM, Keyser UF, Krapf D, Wu MY, Dekker NH, Dekker C (2006) Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Letters 6:89–95CrossRefGoogle Scholar
  6. 6.
    Gerland U, Bundschuh R, Hwa T (2004) Translocation of structured polynucleotides through nanopores. Physical Biology 1:19–26CrossRefGoogle Scholar
  7. 7.
    Neuman K, Block S (2004) Optical trapping. Rev Sci Instrum 75:2787–2809CrossRefGoogle Scholar
  8. 8.
    Sischka A, Kleimann C, Hachmann W, Schafer MM, Seuffert I, Tonsing K, Anselmetti D (2008) Single beam optical tweezers setup with backscattered light detection for three-dimensional measurements on DNA and nanopores. Rev Sci Instrum 79:063702CrossRefGoogle Scholar
  9. 9.
    Trepagnier EH, Radenovic A, Sivak D, Geissler P, Liphardt J (2007) Controlling DNA capture and propagation through artificial nanopores. Nano Lett 7:2824–2830CrossRefGoogle Scholar
  10. 10.
    Peng H, Ling XS (2009) Reverse DNA ­translocation through a solid-state nanopore by magnetic tweezers. Nanotechnology 20: 185101CrossRefGoogle Scholar
  11. 11.
    Visscher K, Block SM (1998) Versatile optical traps with feedback control. Molecular Motors and the Cytoskeleton, Pt B 298:460–489CrossRefGoogle Scholar
  12. 12.
    Semenov I, Otto O, Stober G, Papadopoulos P, Keyser UF, Kremer F (2009) Single colloid electrophoresis. J Colloid Interface Sci 337: 260–264CrossRefGoogle Scholar
  13. 13.
    Otto, O., Gutsche, C., Kremer, F., and Keyser, U. F. (2008). Optical tweezers with 2.5 kHz bandwidth video detection for single-colloid electrophoresis. Rev Sci Instrum, 79, 023710.Google Scholar
  14. 14.
    Soni GV, Singer A, Yu Z, Sun Y, McNally B, Meller A (2010) Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores. Rev Sci Instrum 81:014301CrossRefGoogle Scholar
  15. 15.
    Krapf D, Wu MY, Smeets RMM, Zandbergen HW, Dekker C, Lemay SG (2006) Fabrication and characterization of nanopore-based electrodes with radii down to 2 nm. Nano Letters 6:105–109CrossRefGoogle Scholar
  16. 16.
    Keyser UF, Krapf D, Koeleman BN, Smeets RMM, Dekker NH, Dekker C (2005) Nanopore tomography of a laser focus. Nano Letters 5:2253–2256CrossRefGoogle Scholar
  17. 17.
    Smeets, R. M. M., Keyser, U. F., Wu, M. Y., Dekker, N. H., and Dekker, C. (2006). Nanobubbles in solid-state nanopores. Physical Review Letters, 97, -.Google Scholar
  18. 18.
    Strick TR, Allemand JF, Bensimon D, Bensimon A, Croquette V (1996) The elasticity of a single supercoiled DNA molecule. Science 271:1835–1837CrossRefGoogle Scholar
  19. 19.
    M. van den Hout, I.D. Vilfan, S. Hage, and N.H. Dekker (2010) Direct Force Measurements on Double-Stranded RNA Molecules in Solid-State Nanopores Nano Letters 10:701–707CrossRefGoogle Scholar
  20. 20.
    Davison PF (1959) The Effect of Hydrodynamic Shear on the Deoxyribonucleic Acid from T(2) and T(4) Bacteriophages. Proc Natl Acad Sci U S A 45:1560–1568CrossRefGoogle Scholar
  21. 21.
    Tong HD, Jansen HV, Gadgil VJ, Bostan CG, Berenschot E, van Rijn CJM, Elwenspoek M (2004) Silicon nitride nanosieve membrane. Nano Letters 4:283–287CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Cavendish LaboratoryUniversity of CambridgeCambridgeUK

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