2/18/09

Optical traps for single molecule biophysics


I worked closely with Fellow Tom Perkins on this techincal illustration of biophysical signals and optical-trapping geometries. I made the illustration late in 2008, but it did not get published to Laser & Photonics Reviews until Feb 2009. The top image is the final layout for the journal article with some visual adjustments by Tom Perkins.

Caption Text for Figure 3:
(online color at: www.lpr-journal.org) Comparison of different biophysical signals (a–g) and optical-trapping geometries (i–vii) used to study nucleic acids and nucleic-acid enzymes. (a) A “tug-of-war” signal between the biological molecule and the trap develops as an anchored protein (gold cone) moves along a nucleic acid (red and green) pulling the bead (blue sphere) in an optical trap (pink). (b) A ”conversion” signal uses the conversion from dsDNA (red and green) to ssDNA (green), or the reverse, to change the elastic properties of the tether and thereby measure enzymatic motion. (c) Opening of a nucleic-acid hairpin (through increased force, enzyme motion, or protein melting) leads to more single-stranded nucleic acid under tension and, therefore, motion of the trapped bead. (d) A “popping” signal occurs when sequestered nucleic-acid segments are released as the force in the trap is increased. This signal can be used to measure binding or looping of a protein (purple). (e) Fluorescent tracking of the motion of an enzyme (red cone) either by dye (green halos) displacement or a small fluorescent particle (green sphere) attached directly to the enzyme under study. (f) Fluorescence-resonance energy transfer (FRET) of two nearby fluorophores (D and A, donor and acceptor) leads to emission of red (acceptor) light if the fluorophores are close together. If the strands were separated by force or enzymatic motion, the FRET efficiency would change. (g) A torsional signal (enzyme rotational movement, nucleic-acid supercoiling) can be obtained by using birefringent particles (grey cylinder) and an optical trap which measures torque. (i) The nucleic acid is stretched between an anchor point on the surface and the trapped bead in the surface-coupled geometry. (ii) A micropipette holds one bead via suction while the other bead is optically trapped. (iii) Fluid flow (arrows) extends DNA attached to an optically trapped bead. (iv) Two traps holding two beads connected by a nucleic-acid molecule, often called a ”dumbbell” geometry. (v) Vertical stretching of a nucleic acid, similar to (i), but pulling straight up. (vi) A double dumbbell geometry, or ”quad” trap, allows precise manipulation and measurement of two nucleic-acid molecules for studying a protein (purple) which binds the two molecules together. (vii) Pulling a DNA molecule through a nanopore using an optical trap. Figures are schematic representations from references found in the main text. The biophysical signals shown can be measured through a variety of trapping geometries. For example, the enzyme moving along a nucleic acid which creates the “tug-of-war” signal could be anchored to a cover slip (i), a bead held by a micropipette (ii), or a second optically trapped bead (iv).

The Full citation: Laser & Photonics Reviews [article Fig 3], "Optical traps for single molecule biophysics: a primer", February 2009, Vol 3, Issue 1-2, Page 207

  • Client: Thomas Perkins

  • Related Links: Laser & Photonics Reviews article (Feb 2009, Vol 3 Iss 1-2, Pg 203-220) article
  • 1 comment:

    accumaximum said...

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