Name: combining single-molecule manipulation and imaging for the study of protein-dna interactions
Uploaded: 2014-08-27T14:00:00
Description: Watch this Scientific Journal Video about Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions at JoVE.com

We thank Gijs Wuite, Erwin J.G.&#160;Peterman, and Peter Gross for help with the microfluidics and Alessia Tempestini for help with sample preparation. This research was funded by the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n&#176; 284464 and from the Italian Ministry for Education, University and Research FIRB 2011 RBAP11X42L006, Futuro in Ricerca 2013 RBFR13V4M2, and in the framework of the Flagship Project NANOMAX.

1. Optical Tweezers Setup with Nanometer Stability
The experimental setup must provide two optical tweezers with pointing stability at the nanometer level and intensity fluctuations of the trapping laser below 1%. Combination of these conditions will assure nanometer stability of the dumbbell under typical tension (1 pN - few tens of pN), trap stiffness (0.1 pN/nm) and measurement bandwidth (image acquisition rate 20 sec-1). A scheme of the experimental setup is depicted in Fi...

<ol>
	<li>Monico, C., Capitanio, M., Belcastro, G., Vanzi, F., Pavone, F. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+Methods+to+Study+Protein-DNA+Interactions+in+Vitro+and+in+Living+Cells+at+the+Single-Molecule+Level.">Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.</a> International journal of molecular sciences. 14, 3961-3992 (2013).</li><li>Tinoco, I., Gonzalez, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+mechanisms,+one+molecule+at+a+time.">Biological mechanisms, one molecule at a time.</a> Genes &amp; development. 25, 1205-1231 (2011).</li><li>Capitanio, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exploring+molecular+motors+and+switches+at+the+single-molecule+level.">Exploring molecular motors and switches at the single-molecule level.</a> Micr. Res. Tech. 65, 194-204 (2004).</li><li>Smith, S. B., Finzi, L., Bustamante, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+mechanical+measurements+of+the+elasticity+of+single+DNA+molecules+by+using+magnetic+beads.">Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.</a> Science. 258, 1122-1126 (1992).</li><li>Block, S. M., Goldstein, L. S., Schnapp, B. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bead+movement+by+single+kinesin+molecules+studied+with+optical+tweezers.">Bead movement by single kinesin molecules studied with optical tweezers.</a> Nature. 348, 348-352 (1990).</li><li>Wang, M. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Force+and+velocity+measured+for+single+molecules+of+RNA+polymerase.">Force and velocity measured for single molecules of RNA polymerase.</a> Science. 282, 902-907 (1998).</li><li>Capitanio, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrafast+force-clamp+spectroscopy+of+single+molecules+reveals+load+dependence+of+myosin+working+stroke.">Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke.</a> Nat Methods. 9, 1013-1019 (2012).</li><li>Thompson, R. E., Larson, D. R., Webb, W. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Precise+nanometer+localization+analysis+for+individual+fluorescent+probes.">Precise nanometer localization analysis for individual fluorescent probes.</a> Biophys J. 82, 2775-2783 (2002).</li><li>Yildiz, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Myosin+V+walks+hand-over-hand:+single+fluorophore+imaging+with+1.5-nm+localization.">Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization.</a> Science. 300, 2061-2065 (2003).</li><li>Biebricher, A., Wende, W., Escude, C., Pingoud, A., Desbiolles, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tracking+of+single+quantum+dot+labeled+EcoRV+sliding+along+DNA+manipulated+by+double+optical+tweezers.">Tracking of single quantum dot labeled EcoRV sliding along DNA manipulated by double optical tweezers.</a> Biophys J. 96, 50-52 (2009).</li><li>Candelli, A., Wuite, G. J., Peterman, E. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combining+optical+trapping,+fluorescence+microscopy+and+micro-fluidics+for+single+molecule+studies+of+DNA-protein+interactions.">Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA-protein interactions.</a> Physical chemistry chemical physics : PCCP. 13, 7263-7272 (2011).</li><li>Capitanio, M., Cicchi, R., Pavone, F. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Continuous+and+time-shared+multiple+optical+tweezers+for+the+study+of+single+motor+proteins.">Continuous and time-shared multiple optical tweezers for the study of single motor proteins.</a> Optics and Lasers in Engineering. 45, 450-457 (2007).</li><li>Harada, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+imaging+of+RNA+polymerase-DNA+interactions+in+real+time.">Single-molecule imaging of RNA polymerase-DNA interactions in real time.</a> Biophys J. 76, 709-715 (1999).</li><li>van Mameren, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Counting+RAD51+proteins+disassembling+from+nucleoprotein+filaments+under+tension.">Counting RAD51 proteins disassembling from nucleoprotein filaments under tension.</a> Nature. 457, 745-748 (2009).</li><li>Capitanio, M., Maggi, D., Vanzi, F., Pavone, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiona+in+the+trap:+the+advantages+of+combining+optical+tweezers+and+fluorescence.">Fiona in the trap: the advantages of combining optical tweezers and fluorescence.</a> J Opt A: Pure Appl Opt. 9, s157 (2007).</li><li>Dijk, M. A., Kapitein, L. C., Mameren, J., Schmidt, C. F., Peterman, E. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combining+optical+trapping+and+single-molecule+fluorescence+spectroscopy:+enhanced+photobleaching+of+fluorophores.">Combining optical trapping and single-molecule fluorescence spectroscopy: enhanced photobleaching of fluorophores.</a> J Phys Chem B. 108, 6479-6484 (2004).</li><li>Capitanio, M., Cicchi, R., Pavone, F. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Position+control+and+optical+manipulation+for+nanotechnology+applications.">Position control and optical manipulation for nanotechnology applications.</a> European Physical Journal B. 46, 1-8 (2005).</li><li>Capitanio, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calibration+of+optical+tweezers+with+differential+interference+contrast+signals.">Calibration of optical tweezers with differential interference contrast signals.</a> Review of Scientific Instruments. 73, 1687-1696 (2002).</li><li>Elangovan, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+integrated+in+vitro+and+in+situ+study+of+kinetics+of+myosin+II+from+frog+skeletal+muscle.">An integrated in vitro and in situ study of kinetics of myosin II from frog skeletal muscle.</a> J Physiol. 590, 1227-1242 (2012).</li><li>Wuite, G. J. L., Davenport, R. J., Rappaport, A., Bustamante, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+integrated+laser+trap/flow+control+video+microscope+for+the+study+of+single+biomolecules.">An integrated laser trap/flow control video microscope for the study of single biomolecules.</a> Biophysical Journal. 79, 1155-1167 (2000).</li><li>Brewer, L. R., Bianco, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laminar+flow+cells+for+single-molecule+studies+of+DNA-protein+interactions.">Laminar flow cells for single-molecule studies of DNA-protein interactions.</a> Nat Methods. 5, 517-525 (2008).</li><li>Rutkauskas, D., Zhan, H. L., Matthews, K. S., Pavone, F. S., Vanzi, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tetramer+opening+in+LacI-mediated+DNA+looping.">Tetramer opening in LacI-mediated DNA looping.</a> Proceedings of the National Academy of Sciences of the United States of America. 106, 16627-16632 (2009).</li><li>Marko, J. F., Siggia, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stretching+DNA.">Stretching DNA.</a> Macromolecules. 28, 8759-8770 (1995).</li><li>van Mameren, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unraveling+the+structure+of+DNA+during+overstretching+by+using+multicolor,+single-molecule+fluorescence+imaging.">Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging.</a> Proc Natl Acad Sci U S A. 106, 18231-18236 (2009).</li><li>Wang, M. D., Yin, H., Landick, R., Gelles, J., Block, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stretching+DNA+with+optical+tweezers.">Stretching DNA with optical tweezers.</a> Biophys J. 72, 1335-1346 (1997).</li><li>Ma, H., Long, F., Zeng, S., Huang, Z. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+and+precise+algorithm+based+on+maximum+radial+symmetry+for+single+molecule+localization.">Fast and precise algorithm based on maximum radial symmetry for single molecule localization.</a> Opt Lett. 37, 2481-2483 (2012).</li><li>Parthasarathy, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid,+accurate+particle+tracking+by+calculation+of+radial+symmetry+centers.">Rapid, accurate particle tracking by calculation of radial symmetry centers.</a> Nat Methods. 9, 724-726 (2012).</li></ol>

In the last decade, single molecule manipulation and imaging techniques have seen great progress in terms of spatial and temporal resolution. The combination of manipulation and imaging techniques is at the base of powerful instruments that now allow the control of the mechanical conditions of a single biological polymer, such as DNA, RNA or cytoskeletal filaments, and the simultaneous localization of single proteins interacting with the same polymer. Controlling the mechanical conditions of the trapped polymer is of par...

Single molecule (SM) techniques have greatly developed over the past thirty years to respond to the need of overcoming some of the limitations of traditional, bulk solution measurements 1-3. The manipulation of single biological molecules has created the opportunity to measure mechanical properties of biopolymers4 and control the mechanical parameters of protein-protein5 and protein-DNA interactions6,7. SM fluorescence detection, on the other hand, represents an incredibly versatile tool for studying protein activity in vitro and in vivo, leading to the possibility of localizing and tracking single molecules with nanometer precision. Through fitting of the instrument point-spread-function to the SM image, in fact, one can accomplish localization with a precision depending mainly on signal-to-noise ratio (SNR) and reaching a limit of about one nanometer8,9. These methodologies find powerful applications in the study of the dynamics of motor proteins, as well as of the diffusion processes underlying target search in DNA-binding proteins. The capability of determining diffusion constants as a function of the DNA sequence, residence time on the target and accurately measuring the DNA length explored during one-dimensional diffusion events, represent a powerful tool for the study of protein-DNA interaction dynamics and for the investigation of the mechanisms of specific target search.
Recently, the combination of these two techniques has produced a new generation of experimental setups10-14 enabling the simultaneous manipulation of a biological substrate (for example an actin filament or a DNA molecule) and detection/localization of an interacting partner enzyme (for example myosin or a DNA-binding protein). The advantages of these techniques mainly rest on the possibility of exerting mechanical control over the trapped polymer, thus enabling the study of interaction dynamics versus forces or torques. Also, the methodology allows measuring biochemical reactions far from the surface, avoiding one of the main limitations of classic SM methods, i.e., the need for immobilization of the molecules under study on a surface (glass slide or microspheres).
The combination of two single molecules techniques requires overcoming several technical difficulties, mainly arising from the requirements of mechanical stability and adequate SNR (especially when requiring localization with nm precision)15. Particularly, when coupling SM fluorescence detection with optical tweezers, the reduction of noise and photobleaching from the trapping infrared lasers16 and the control of biochemical buffers for assembly of the biological complexes and performance of the experimental measurements11 are of paramount importance. Here, we describe the methods for performing successful measurements in a dual trapping/SM Fluorescence localization setup. The methodology is illustrated with the example of lactose repressor protein (LacI) fluorescently labeled (with Atto532) and detected as it binds to a DNA molecule (trapped between two optical tweezers) containing specific LacI binding sequences (i.e., operators). We demonstrate the effectiveness of the method in detecting binding of LacI to DNA and diffusion along its contour in the target search process. The method is applicable to any combination of DNA sequence and DNA-binding protein, as well as to other systems (microtubules or actin filaments and the motor proteins interacting with them).

<table border="0" cellpadding="0" cellspacing="0" width="863">
	<tbody>
		<tr height="42">
			<td height="42" style="height:43px;width:203px;">Name of Material/ Equipment</td>
			<td style="width:141px;">Company</td>
			<td style="width:167px;">Catalog Number</td>
			<td style="width:151px;">Comments/Description</td>
			<td style="width:203px;">Web Address</td>
		</tr>
		<tr height="114">
			<td height="114" style="height:115px;">elastomeric isolators</td>
			<td style="width:141px;">Newport</td>
			<td style="width:167px;">Newdamp</td>
			<td style="width:151px;">Choose the appropriate Newdamp elastomer depending on the microscope weight and resonance frequencies</td>
			<td><a href="http://www.newport.com/">http://www.newport.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">optical isolator</td>
			<td style="width:141px;">Optics for Research</td>
			<td style="width:167px;">IO-3-YAG-VHP</td>
			<td></td>
			<td><a href="http://www.ofr.com/">http://www.ofr.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nd:YAG laser, 1064 nm wavelength</td>
			<td style="width:141px;">Spectra-Physics</td>
			<td style="width:167px;">Millennia IR</td>
			<td></td>
			<td><a href="http://www.newport.com/">http://www.newport.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">acousto-optic deflectors (AODs)</td>
			<td style="width:141px;">A&#38;A optoelectronic</td>
			<td style="width:167px;">DTS-XY 250</td>
			<td></td>
			<td><a href="http://www.aaoptoelectronic.com/">http://www.aaoptoelectronic.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Direct Digital Synthesizers</td>
			<td style="width:141px;">Analog Devices</td>
			<td style="width:167px;"></td>
			<td></td>
			<td><a href="http://www.analog.com/">http://www.analog.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">quadrant detector photodiodes</td>
			<td style="width:141px;">OSI optoelectronics</td>
			<td style="width:167px;">SPOT-15-YAG</td>
			<td></td>
			<td><a href="http://www.osioptoelectronics.com/">http://www.osioptoelectronics.com</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">DIO and FPGA board</td>
			<td style="width:141px;">National Instruments</td>
			<td style="width:167px;">NI-PCI-7830R</td>
			<td></td>
			<td><a href="http://www.ni.com/">http://www.ni.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Halogen lamp</td>
			<td style="width:141px;">Schott</td>
			<td style="width:167px;">KL 1500 LCD</td>
			<td></td>
			<td><a href="http://www.schott.com/">http://www.schott.com</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">Condenser</td>
			<td style="width:141px;">Olympus</td>
			<td style="width:167px;">U-AAC 1.4NA Aplanat Apchromat</td>
			<td></td>
			<td><a href="http://www.olympus-global.com/en/">http://www.olympus-global.com/en/</a></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:203px;">Objective</td>
			<td style="width:141px;">Nikon</td>
			<td style="width:167px;">CFI Plan Apochromat 60x 1.2NA water immersion</td>
			<td></td>
			<td><a href="http://www.nikoninstruments.com/">http://www.nikoninstruments.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">532 nm laser</td>
			<td style="width:141px;">Coherent</td>
			<td style="width:167px;">Sapphire</td>
			<td></td>
			<td><a href="http://www.coherent.com/">http://www.coherent.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">CCD 200X and 2000X</td>
			<td style="width:141px;">Hamamatsu&#160;</td>
			<td style="width:167px;">XC-ST70 CE</td>
			<td></td>
			<td><a href="http://www.hamamatsu.com/">http://www.hamamatsu.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">electron-multiplied CCD</td>
			<td style="width:141px;">Hamamatsu&#160;</td>
			<td style="width:167px;">C9100-13</td>
			<td></td>
			<td><a href="http://www.hamamatsu.com/">http://www.hamamatsu.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">piezo stage with nm-accuracy</td>
			<td style="width:141px;">Physik Instrumente</td>
			<td style="width:167px;">P-527.2CL&#160;</td>
			<td></td>
			<td><a href="http://www.physikinstrumente.com/">http://www.physikinstrumente.com/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">Emission Filter</td>
			<td style="width:141px;">Chroma Technologies</td>
			<td style="width:167px;">600/100m</td>
			<td></td>
			<td><a href="http://www.chroma.com/">http://www.chroma.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">silica beads (1.54 mm)</td>
			<td style="width:141px;">Bangs Laboratories</td>
			<td style="width:167px;">SS04N/5303</td>
			<td></td>
			<td><a href="http://www.bangslabs.com/">http://www.bangslabs.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Albumin from bovine serum (BSA)</td>
			<td style="width:141px;">Sigma Aldrich</td>
			<td style="width:167px;">B4287</td>
			<td></td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">pentyl acetate&#160;</td>
			<td>Sigma Aldrich</td>
			<td style="width:167px;">46022</td>
			<td style="width:151px;">Flammable liquid and vapour (No 1272/2008)</td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">nitrocellulose</td>
			<td>Sigma Aldrich</td>
			<td style="width:167px;">N8267-5EA</td>
			<td style="width:151px;">Flammable solid&#160; (No 1272/2008)</td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">heat block</td>
			<td style="width:141px;">MPM Instruments Srl</td>
			<td style="width:167px;">M502-HBD</td>
			<td style="width:151px;">with 2 removable blocks; preheated at 120&#176; C</td>
			<td><a href="http://www.mpminstruments.com/">http://www.mpminstruments.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NanoPort assemblies</td>
			<td style="width:141px;">Upchurch Scientific Inc.</td>
			<td style="width:167px;">N-333</td>
			<td></td>
			<td><a href="http://www.upchurch.com/">http://www.upchurch.com/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">polyetheretherketone tubing&#160;</td>
			<td style="width:141px;">Upchurch Scientific Inc.</td>
			<td style="width:167px;">1535</td>
			<td></td>
			<td><a href="http://www.upchurch.com/">http://www.upchurch.com/</a></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:203px;">home-made metallic holder for the assembly of the flow-chamber pressure reservoir made of Plexiglass</td>
			<td style="width:141px;"></td>
			<td style="width:167px;"></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">luer lock-tip syringes 2.5 mL</td>
			<td style="width:141px;">Terumo</td>
			<td style="width:167px;">SS 02LZ1</td>
			<td></td>
			<td><a href="http://www.terumomedical.com/">http://www.terumomedical.com</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">shut-off valves&#160;</td>
			<td style="width:141px;">Upchurch Scientific, Inc.</td>
			<td style="width:167px;">P-732</td>
			<td></td>
			<td><a href="http://www.upchurch.com/">http://www.upchurch.com/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">flangeless fittings&#160;</td>
			<td style="width:141px;">Upchurch Scientific, Inc.</td>
			<td style="width:167px;">LT-111</td>
			<td></td>
			<td><a href="http://www.upchurch.com/">http://www.upchurch.com/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">fluorinated ethylene propylene tubing&#160;</td>
			<td style="width:141px;">Upchurch Scientific, Inc.</td>
			<td style="width:167px;">1549</td>
			<td></td>
			<td><a href="http://www.upchurch.com/">http://www.upchurch.com/</a></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:203px;">two computer-controlled solenoid valves</td>
			<td style="width:141px;">Clippard, Cincinnati, USA</td>
			<td style="width:167px;">ET-2-H-M5</td>
			<td></td>
			<td><a href="http://www.clippard.com/">http://www.clippard.com</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pressure transducer</td>
			<td style="width:141px;">Druck LTD</td>
			<td style="width:167px;">PTX 1400</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">biotin-14-dCTP&#160;</td>
			<td style="width:141px;">Life Technologies</td>
			<td style="width:167px;">19518-018</td>
			<td></td>
			<td><a href="http://www.lifetechnologies.com/">http://www.lifetechnologies.com/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">Terminal deoxynucleotidyl Transferase (TdT)</td>
			<td style="width:141px;">Thermoscientific</td>
			<td style="width:167px;">EP0161</td>
			<td></td>
			<td><a href="http://www.thermoscientificbio.com/">http://www.thermoscientificbio.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ATTO532 maleimide</td>
			<td>Sigma Aldrich</td>
			<td style="width:167px;">68499</td>
			<td></td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="157">
			<td height="157" style="height:157px;width:203px;">N,N-dimethylformamide (DMF)&#160;</td>
			<td>Sigma Aldrich</td>
			<td style="width:167px;">227056</td>
			<td style="width:151px;">Combustible Liquid, Harmful by skin absorption., Irritant, Teratogen. H226; H303; H312; H316; H319; H331; H360; P201; P261; P280;P305; P351; P338; P311</td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Tris-(2-carboxyethyl)phosphine hydrochloride (TCEP)&#160;</td>
			<td>Sigma Aldrich</td>
			<td style="width:167px;">C4706</td>
			<td></td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="45">
			<td height="45" style="height:45px;width:203px;">L-Glutathione reduced (GSH)</td>
			<td>Sigma Aldrich</td>
			<td style="width:167px;">G4251</td>
			<td style="width:151px;">Acute toxicity, Oral (Category 5), H303</td>
			<td><a href="http://www.sigmaaldrich.com/">http://www.sigmaaldrich.com/</a></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:203px;">Amicon Ultra-15, PLQK Ultracel-PL Membrane, 10&#160;kDa cutoff spin concentrators</td>
			<td style="width:141px;">Merck Millipore</td>
			<td style="width:167px;">UFC901024</td>
			<td></td>
			<td><a href="http://www.merckmillipore.it/">http://www.merckmillipore.it/</a></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;">streptavidin-coated polystyrene beads 1,87 &#181;m</td>
			<td style="width:141px;">Spherotech, Inc.</td>
			<td style="width:167px;">SVP-15-5</td>
			<td></td>
			<td><a href="http://www.spherotech.com/">http://www.spherotech.com/</a></td>
		</tr>
	</tbody>
</table>

combining single-molecule manipulation and imaging for the study of protein-dna interactions

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method offers the opportunity of investigating interactions occurring in solution (thus avoiding problems due to closeby surfaces as in other single molecule methods), controlling the DNA extension and tracking interaction dynamics as a function of both mechanical parameters and DNA sequence. The methods for establishing successful optical trapping and nanometer localization of single molecules are illustrated. We illustrate the experimental conditions allowing the study of interaction of lactose repressor (lacI), labeled with Atto532, with a DNA molecule containing specific target sequences (operators) for LacI binding. The method allows the observation of specific interactions at the operators, as well as one-dimensional diffusion of the protein during the process of target search. The method is broadly applicable to the study of protein-DNA interactions but also to molecular motors, where control of the tension applied to the partner track polymer (for example actin or microtubules) is desirable.

In a successful experiment, one (or more) labeled proteins undergo binding/unbinding and/or monodimensional diffusion along the DNA molecule (Figure 3A). Localization of proteins along the DNA molecule allows the quantification of kinetic parameters as a function of the DNA sequence. When buffer conditions causing 1D diffusion are applied, it is possible to follow protein trajectories, and determine, for example, the diffusion coefficient D1D.
The precise position o...

Watch this Scientific Journal Video about Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions at JoVE.com

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Here we describe the instrumentation and methods for detecting single fluorescently-labeled protein molecules interacting with a single DNA molecule suspended between two optically trapped microspheres.

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

Research

JoVE Journal

Biology

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Single-Molecule Imaging of Nuclear Transport

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Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

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Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

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Protein-protein interactions are important for understanding cellular signaling cascades and identifying novel pathway components and protein dynamics. ...

Probing mRNA Kinetics in Space and Time in Escherichia coli using Two-Color Single-Molecule Fluorescence In Situ Hybridization

Probing mRNA Kinetics in Space and Time in Escherichia coli using Two-Color Single-Molecule Fluorescence In Situ Hybridization

Single-molecule fluorescence in situ hybridization (smFISH) allows for counting the absolute number of mRNAs in individual cells. Here, we describe an ...