Magnetic Tweezers

Abstract

Magnetic tweezers is a technique that allows applying a constant pulling force and torque on a nucleic acid molecule while measuring its elongation in real time. By means of two magnets, the polymer is stretched and twisted between a magnetic bead and the surface of a glass cover slide. In the course of an experiment, the position of the magnetic bead is followed in real time while a buffer containing proteins, adenosine triphosphate (ATP), etc. is introduced in the experiment chamber. This approach has been used to study deoxyribonucleic acid (DNA) condensation, mechanical properties of nucleic acids and dynamics of protein–DNA interactions. In this article an introduction to the Magnetic Tweezers technique is given and some examples of application presented.

Key Concepts:

  • Magnetic Tweezers allow stretching and twisting nucleic acids (NA) using magnetic microspheres and a magnetic field.

  • An NA is attached at one end to a magnetic bead and at the other end to a transparent glass surface.

  • The position of the bead is determined from the optical image given by a video camera.

  • The force acting on the NA is calculated from the movements of the tethered magnetic bead.

  • Magnetic Tweezers are used to study mechanical properties of NA and real‐time dynamics of protein–DNA interactions.

Keywords: single molecule; magnetic tweezers; DNA; protein–DNA interactions; real‐time measurements

Figure 1.

(a) Sketch of a Magnetic Tweezers setup. The transparent flow cell is mounted on an inverted optical microscope whose focus is controlled by a piezo stage. The molecule‐bead sample is flowed into the liquid cell and a CCD camera records the sample image. A computer is connected to the CCD camera in order to analyse the images. The magnets and light illumination are above the flow cell. (b) Cartoon of a DNA molecule attached by dig‐antidig bonds with the bottom surface and by biotin‐streptavidin bonds with the magnetic bead. The vertical and rotational movement of the magnets can vary the stretching force and supercoiling state of the molecules, respectively. A bead reference attached to the bottom of the flow cell is used to measure height differences. (c) CCD image of the sample obtained with a 100× oil immersion objective. The bead on the right is in focus and at the glass surface (reference bead). The bead on the left (DNA bead) is above the surface and out of focus as shown by its diffraction rings.

Figure 2.

(a) (i–iv) Optical images of a 1 μm‐size magnetic bead obtained at different objective's focal plane positions (0, 3, 4.5, 9.7 μm, respectively). (b) Calibration profile for a 1‐μm‐size reference bead. Data extracted from images in (a) are indicated by arrows. To calculate the vertical position, the radial intensity profile of the tethered bead is compared in real time with this calibration image.

Figure 3.

Cartoon of the bead‐DNA system subjected to a magnetic pulling force Fm in the vertical direction. l is the end‐to‐end distance or DNA extension. The bead is moved out the equilibrium position at a distance dx due to collisions with the surrounding water molecules.

Figure 4.

(a) x and y in‐plane displacements of a 1‐μm‐size magnetic bead tethered to a single DNA molecule and subjected to different stretching forces: 3.9 pN, 2.8 pN, 1.4 pN and 0.68 pN. As the force increases (the magnet position decreases), the Brownian motion of the bead decreases. (b) Force versus magnet distance calibration curve. The experimental data are fitted to an exponential function (red line).

Figure 5.

(a) Force versus extension curve for a 5 kbp (1.8 μm) long unnicked DNA molecule. Data are fitted by the Worm‐like Chain (WLC) model to obtain a persistence length of 50 nm and the total length of the molecule. (b) Extension versus rotation curves at different stretching forces: 0.068 pN (black), 0.18 pN (red), 0.34 pN (blue), 0.67 pN (green), 1.5 pN (pink) and at 2.7 pN (brown). At low forces, the DNA extension decreases for positive and negative rotations. At high forces, DNA extension decreases only for positive rotation and remains constant for negative rotations due to denaturation of the double helix. From a rotation curve at low forces, the point of zero supercoils can be obtained.

Figure 6.

(a) Cartoon of the experimental setup used to monitor real‐time dynamics of EcoR124I type I restriction enzyme. Although the MTase unit stays bound at the recognition site, the HsdR units pull in the DNA (red arrows). (b) View of a single translocation event. Adapted from Seidel et al.. Reproduced by permission of Nature Structural & Molecular Biology.

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References

Abels JA, Moreno‐Herrero F, van der Heijden T, Dekker C and Dekker NH (2005) Single‐molecule measurements of the persistence length of double‐stranded RNA. Biophysics Journal 88: 2737–2744.

Bouchiat C, Wang MD, Allemand J et al. (1999) Estimating the persistence length of a worm‐like chain molecule from force‐extension measurements. Biophysics Journal 76: 409–413.

Bustamante C, Bryant Z and Smith SB (2003) Ten years of tension: single‐molecule DNA mechanics. Nature 421: 423–427.

Bustamante C, Marko JF, Siggia ED and Smith S (1994) Entropic elasticity of lambda‐phage DNA. Science 265: 1599–1600.

Cluzel P, Lebrun A, Heller C et al. (1996) DNA: an extensible molecule. Science 271: 792–794.

Gelles J, Schnapp BJ and Sheetz MP (1988) Tracking kinesin‐driven movements with nanometre‐scale precision. Nature 331: 450–453.

Gosse C and Croquette V (2002) Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophysics Journal 82: 3314–3329.

Jackson JD (1999). Classical Electrodynamics (New York).

Koster DA, Croquette V, Dekker C, Shuman S and Dekker NH (2005) Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434: 671–674.

Lipfert J, Hao X and Dekker NH (2009) Quantitative modeling and optimization of magnetic tweezers. Biophysics Journal 96: 5040–5049.

Lipfert J, Klijnhout S and Dekker NH (2010) Torsional sensing of small‐molecule binding using magnetic tweezers. Nucleic Acids Research 38: 7122–7132.

Manosas M, Spiering MM, Zhuang Z, Benkovic SJ and Croquette V (2009) Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome. Nature Chemical Biology 5: 904–912.

Marko JF and Siggia ED (1994) Fluctuations and supercoiling of DNA. Science 265: 506–508.

Schnapp BJ, Gelles J and Sheetz MP (1988) Nanometer‐scale measurements using video light microscopy. Cell Motility and the Cytoskeleton 10: 47–53.

Seidel R, van Noort J, van der Scheer C et al. (2004) Real‐time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nature Structural & Molecular Biology 11: 838–843.

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

Strick TR, Allemand JF, Bensimon D, Bensimon A and Croquette V (1996) The elasticity of a single supercoiled DNA molecule. Science 271: 1835–1837.

Strick TR, Allemand JF, Bensimon D and Croquette V (1998) Behavior of supercoiled DNA. Biophysics Journal 74: 2016–2028.

Wong WP and Halvorsen K (2006) The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur. Optics Express 14: 12517–12531.

Wuite GJ, Smith SB, Young M, Keller D and Bustamante C (2000) Single‐molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404: 103–106.

Further Reading

Neuman KC, Lionnet T and Allemand J‐F (2007) Single‐Molecule Micromanipulation Techniques. Annual Review of Materials Research 37: 33–67.

Tanase M, Biais N and Sheetz M (2007) Magnetic tweezers in cell biology. Methods in Cell Biology 83: 473–493.

Vilfan ID, Lipfert J, Koster DA, Lemay SG and Dekker NH (2009) Magnetic Tweezers for single‐molecule experiments. In: Hinterdorfer P and van Oijen A (eds) Handbook of Single‐Molecule Biophysics. New York: Springer Science.

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How to Cite close
Carrasco Pulido, Carolina, and Moreno‐Herrero, Fernando(Apr 2011) Magnetic Tweezers. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023173]