Name: single-molecule analysis of sf9 purified superprocessive kinesin-3 family motors
Uploaded: 2022-07-27T13:00:00
Description: Watch this Scientific Journal Video about Single-Molecule Analysis of Sf9 Purified Superprocessive Kinesin-3 Family Motors at JoVE.com

V.S. and P.S. thank Prof. Kristen J. Verhey (University of Michigan, Ann Arbor, MI, USA) and Prof. Roop Mallik (Indian Institute of Technology Bombay (IITB), Mumbai, India) for their unconditional support throughout the study. P.S. thanks Dr. Sivapriya Kirubakaran for her support throughout the project. V.S. acknowledges funding through DBT (Grant No.: BT/PR15214/BRB/10/1449/2015 and BT/RLF/Re-entry/45/2015) and DST-SERB (Grant No.: ECR/2016/000913). P.K.N acknowledges ICMR for funding (Grant No. 5/13/13/2019/NCD-III). P.S. acknowledges funding from DST (Grant No.: SR/WOS-A/LS-73/2017). D.J.S acknowledges&#160;fellowship from IIT Gandhinagar.

1. Sf9 culture, transfection, and virus generation
NOTE: Maintain Sf9 cells in 30 mL of Sf-900/SFM medium in 100 mL sterile, disposable conical flask without any antibiotic/antimycotic at 28 &#176;C. Keep the suspension culture in an orbital shaker at 90 rpm. Supply of CO2 and humidity maintenance is not required. Cells are usually subcultured every fourth day by inoculating 0.5 x 106 cells/mL to reach 2.0 x 106 cells/mL density on the fourth day...

<ol>
	<li>Vale, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+molecular+motor+toolbox+for+intracellular+transport.">The molecular motor toolbox for intracellular transport.</a> Cell. 112, 467-480 (2003).</li><li>Miki, H., Okada, Y., Hirokawa, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+the+kinesin+superfamily:+insights+into+structure+and+function.">Analysis of the kinesin superfamily: insights into structure and function.</a> Trends in Cell Biology. 15 (9), 467-476 (2005).</li><li>Hirokawa, N., Niwa, S., Tanaka, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+motors+in+neurons:+transport+mechanisms+and+roles+in+brain+function,+development,+and+disease.">Molecular motors in neurons: transport mechanisms and roles in brain function, development, and disease.</a> Neuron. 68 (4), 610-638 (2010).</li><li>Hirokawa, N., Takemura, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+motors+and+mechanisms+of+directional+transport+in+neurons.">Molecular motors and mechanisms of directional transport in neurons.</a> Nature Reviews Neuroscience. 6 (3), 201-214 (2005).</li><li>Patel, N. 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=KIF13A+motors+are+regulated+by+Rab22A+to+function+as+weak+dimers+inside+the+cell.">KIF13A motors are regulated by Rab22A to function as weak dimers inside the cell.</a> Scientific Advances. 7 (6), (2021).</li><li>Franker, M. A., Hoogenraad, C. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microtubule-based+transport+-+basic+mechanisms,+traffic+rules+and+role+in+neurological+pathogenesis.">Microtubule-based transport - basic mechanisms, traffic rules and role in neurological pathogenesis.</a> Journal of Cellular Science. 126, 2319-2329 (2013).</li><li>Gunawardena, S., Anderson, E. N., White, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Axonal+transport+and+neurodegenerative+disease:+vesicle-motor+complex+formation+and+their+regulation.">Axonal transport and neurodegenerative disease: vesicle-motor complex formation and their regulation.</a> Degernative Neurological and Neuromuscular Disease. 4, 29-47 (2014).</li><li>Rath, O., Kozielski, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinesins+and+cancer.">Kinesins and cancer.</a> Nature Reviews Cancer. 12 (8), 527-539 (2012).</li><li>Wang, Z. Z., 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=KIF14+promotes+cell+proliferation+via+activation+of+Akt+and+is+directly+targeted+by+miR-200c+in+colorectal+cancer.">KIF14 promotes cell proliferation via activation of Akt and is directly targeted by miR-200c in colorectal cancer.</a> International Journal of Oncology. 53 (5), 1939-1952 (2018).</li><li>Guo, S. K., Shi, X. X., Wang, P. Y., Xie, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Run+length+distribution+of+dimerized+kinesin-3+molecular+motors:+comparison+with+dimeric+kinesin-1.">Run length distribution of dimerized kinesin-3 molecular motors: comparison with dimeric kinesin-1.</a> Scientific Reports. 9 (1), 16973 (2019).</li><li>Scarabelli, G., 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=Mapping+the+processivity+determinants+of+the+Kinesin-3+motor+domain.">Mapping the processivity determinants of the Kinesin-3 motor domain.</a> Biophysical Journal. 109 (8), 1537-1540 (2015).</li><li>Soppina, V., 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=Dimerization+of+mammalian+kinesin-3+motors+results+in+superprocessive+motion.">Dimerization of mammalian kinesin-3 motors results in superprocessive motion.</a> Proceedings of the National Academy of Sciences of the United States of America. 111 (15), 5562-5567 (2014).</li><li>Soppina, V., Verhey, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+family-specific+K-loop+influences+the+microtubule+on-rate+but+not+the+superprocessivity+of+kinesin-3+motors.">The family-specific K-loop influences the microtubule on-rate but not the superprocessivity of kinesin-3 motors.</a> Molecular Biology Cell. 25 (14), 2161-2170 (2014).</li><li>Soppina, V., 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=Kinesin-3+motors+are+fine-tuned+at+the+molecular+level+to+endow+distinct+mechanical+outputs.">Kinesin-3 motors are fine-tuned at the molecular level to endow distinct mechanical outputs.</a> BMC Biology. , (2022).</li><li>Korten, T., Chaudhuri, S., Tavkin, E., Braun, M., Diez, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinesin-1+Expressed+in+insect+cells+improves+microtubule+in+vitro+gliding+performance,+long-term+stability+and+guiding+efficiency+in+nanostructures.">Kinesin-1 Expressed in insect cells improves microtubule in vitro gliding performance, long-term stability and guiding efficiency in nanostructures.</a> IEEE Transactions on Nanobioscience. 15 (1), 62-69 (2016).</li><li>Schmidt, F. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+expression+systems+in+the+pharmaceutical+industry.">Recombinant expression systems in the pharmaceutical industry.</a> Applied Microbiology and Biotechnology. 65 (4), 363-372 (2004).</li><li>Kurland, C., Gallant, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Errors+of+heterologous+protein+expression.">Errors of heterologous protein expression.</a> Current Opinions in Biotechnology. 7 (5), 489-493 (1996).</li><li>Tao, L., Scholey, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+and+assay+of+mitotic+motors.">Purification and assay of mitotic motors.</a> Methods. 51 (2), 233-241 (2010).</li><li>Kost, T. A., Condreay, J. P., Jarvis, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Baculovirus+as+versatile+vectors+for+protein+expression+in+insect+and+mammalian+cells.">Baculovirus as versatile vectors for protein expression in insect and mammalian cells.</a> Nature Biotechnology. 23 (5), 567-575 (2005).</li><li>Felberbaum, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+baculovirus+expression+vector+system:+A+commercial+manufacturing+platform+for+viral+vaccines+and+gene+therapy+vectors.">The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors.</a> Biotechnology Journal. 10 (5), 702-714 (2015).</li><li>Kumar, N., Pandey, D., Halder, A., Kumar, D., Gong, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Trends in Insect Molecular Biology and Biotechnology. , 163-191 (2018).</li><li>Nagano, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+fluorescent+probes+for+bioimaging+applications.">Development of fluorescent probes for bioimaging applications.</a> Proceedings of the Japan Academy. Series B. Physical and Biological Sciences. 86 (8), 837-847 (2010).</li><li>Hassan, M., Klaunberg, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biomedical+applications+of+fluorescence+imaging+in+vivo.">Biomedical applications of fluorescence imaging in vivo.</a> Comparative Medicine. 54 (6), 635-644 (2004).</li><li>Yang, Z., Samanta, S., Yan, W., Yu, B., Qu, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Super-resolution+microscopy+for+biological+imaging.">Super-resolution microscopy for biological imaging.</a> Advances in Experimental Medicine and Biology. 3233, 23-43 (2021).</li><li>Ettinger, A., Wittmann, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+live+cell+imaging.">Fluorescence live cell imaging.</a> Methods in Cell Biology. 123, 77-94 (2014).</li><li>Waters, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Live-cell+fluorescence+imaging.">Live-cell fluorescence imaging.</a> Methods in Cell Biology. 114, 125-150 (2013).</li><li>Zheng, Q., Jockusch, S., Zhou, Z., Blanchard, S. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+contribution+of+reactive+oxygen+species+to+the+photobleaching+of+organic+fluorophores.">The contribution of reactive oxygen species to the photobleaching of organic fluorophores.</a> Photochemistry and Photobiology. 90 (2), 448-454 (2014).</li><li>Wojtovich, A. P., Foster, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+control+of+ROS+production.">Optogenetic control of ROS production.</a> Redox Biology. 2, 368-376 (2014).</li><li>Cai, D., Verhey, K. J., Meyhofer, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tracking+single+Kinesin+molecules+in+the+cytoplasm+of+mammalian+cells.">Tracking single Kinesin molecules in the cytoplasm of mammalian cells.</a> Biophysical Journal. 92 (12), 4137-4144 (2007).</li><li>Bohm, K. J., Stracke, R., Baum, M., Zieren, M., Unger, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+temperature+on+kinesin-driven+microtubule+gliding+and+kinesin+ATPase+activity.">Effect of temperature on kinesin-driven microtubule gliding and kinesin ATPase activity.</a> FEBS Letters. 466, 59-62 (2000).</li><li>Porter, M. E., 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=Characterization+of+the+microtubule+movement+produced+by+sea+urchin+egg+kinesin.">Characterization of the microtubule movement produced by sea urchin egg kinesin.</a> The Journal of Biological Chemistry. 262 (6), 2794-2802 (1987).</li><li>Muyldermans, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanobodies:+natural+single-domain+antibodies.">Nanobodies: natural single-domain antibodies.</a> Annual Review of Biochemistry. 82, 775-797 (2013).</li><li>Verma, S., Kumar, N., Verma, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+paclitaxel+on+critical+nucleation+concentration+of+tubulin+and+its+effects+thereof.">Role of paclitaxel on critical nucleation concentration of tubulin and its effects thereof.</a> Biochemical and Biophysical Research Communications. 478 (3), 1350-1354 (2016).</li><li>Parness, J., Horwitz, S. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Taxol+binds+to+polymerized+tubulin+in+vitro.">Taxol binds to polymerized tubulin in vitro.</a> Journal of Cell Biology. 91 (2), 479-487 (1981).</li><li>Schiff, P. B., Fant, J., Horwitz, S. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Promotion+of+microtubule+assembly+in+vitro+by+taxol.">Promotion of microtubule assembly in vitro by taxol.</a> Nature. 277 (5698), 665-667 (1979).</li><li>Kato, T., Kageshima, A., Suzuki, F., Park, E. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+and+purification+of+human+(pro)renin+receptor+in+insect+cells+using+baculovirus+expression+system.">Expression and purification of human (pro)renin receptor in insect cells using baculovirus expression system.</a> Protein Expression and Purification. 58 (2), 242-248 (2008).</li><li>Liu, F., Wu, X., Li, L., Liu, Z., Wang, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+baculovirus+expression+system+for+generation+of+virus-like+particles:+successes+and+challenges.">Use of baculovirus expression system for generation of virus-like particles: successes and challenges.</a> Protein Expression and Purification. 90 (2), 104-116 (2013).</li><li>Terpe, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overview+of+tag+protein+fusions:+from+molecular+and+biochemical+fundamentals+to+commercial+systems.">Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems.</a> Applied Microbiology and Biotechnology. 60 (5), 523-533 (2003).</li><li>Huang, S. T., 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=Liposomal+paclitaxel+induces+fewer+hematopoietic+and+cardiovascular+complications+than+bioequivalent+doses+of+Taxol.">Liposomal paclitaxel induces fewer hematopoietic and cardiovascular complications than bioequivalent doses of Taxol.</a> International Journal of Oncology. 53 (3), 1105-1117 (2018).</li></ol>

The Sf9-baculovirus expression system is one of the most versatile and successful methods for high-throughput protein production19,36,37. The posttranslational modification ability of Sf9 cells is highly comparable to the mammalian system15. A considerable disadvantage of using this system is that it is slow and sensitive to contamination. One of the most critical steps is efficient infection and successf...

An immensely crowded cell environment poses many challenges in sorting destined proteins and molecules. This intense workload of organization and spatiotemporal distribution of molecules within the cytoplasm is facilitated by molecular motors and cytoskeletal tracks. Molecular motors are the enzymes that hydrolyze the energy currencies such as ATP and utilize that energy during motion and force generation1. Based on the amino acid sequence similarity, kinesins are grouped into 14 families and despite this similarity, each motor contributes uniquely to the functioning of a cell. Kinesin-3 family motors constitute one of the largest, comprising five subfamilies (KIF1, KIF13, KIF14, KIF16, and KIF28)2, associated with diverse cellular and physiological functions, including vesicle transport, signaling, mitosis, nuclear migration, and development 3,4,5. Impairment in kinesin-3 transport function implicates in many neurodegenerative disorders, developmental defects, and cancer diseases6,7,8,9.
Recent work has demonstrated that kinesin-3 motors are monomers but undergo cargo-induced dimerization and result in fast and superprocessive motility compared to conventional kinesin10,11,12,13. Their biochemical and biophysical characterization needs a large quantity of purified, active proteins. However, their production in the prokaryotic expression system resulted in inactive or aggregated motors, presumably due to incompatible protein synthesis, folding and modification machinery14,15,16,17,18. To circumvent such limitations and increase the yield, here we have established a robust Sf9-baculovirus expression system to express and purify these motors.
The baculovirus expression system uses Sf9 insect cell lines as a host system for high-throughput eukaryotic recombinant protein expression19,20. Baculovirus possesses a strong polyhedrin promoter that assists in heterologous gene expression and the production of soluble recombinant proteins17. Due to its cost-effectiveness, safe to handle and high amount of active protein expression, it has become a powerful tool21. To express a protein of interest, a key step is to generate a recombinant bacmid. Since the commercially available bacmid generating kits are expensive and we will be working with more samples, we developed an in-house protocol for both large and small inserts of kinesin-3 motors into bacmids. Sf9-purified kinesin-3 motors were used to characterize in vitro single-molecule and multi-motor microtubule gliding properties using total internal reflection fluorescence (TIRF) microscopy. Motors are C-terminally tagged with 3-tandem fluorescent molecules (3xmCit) to provide enhanced signal and decreased photobleaching. Due to its increased signal-to-noise ratio, less phototoxicity, and selective imaging of a very small area close to the coverslip, TIRF imaging has been widely used to visualize protein dynamics at the single-molecule level in vivo and in vitro.
This study discusses the purification of kinesin-3 motors by employing Sf9-baculovirus expression system and in vitro single-molecule imaging and multi-motor gliding analysis of motors using TIRF microscopy. Altogether, this study shows that the motility properties of Sf9 purified motors are identical to that of motors prepared from mammalian cell lysates. Hence, we believe that the Sf9-baculovirus system can be adapted to express and purify any motor protein of interest.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Sf9 culture and transfection materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>anti-FLAG M2 affinity</td>
			<td>Biolegend</td>
			<td>651502</td>
			<td>For motility purification</td>
		</tr>
		<tr>
			<td>Aprotinin</td>
			<td>Sigma</td>
			<td>A6279</td>
			<td>For motility assay and purification</td>
		</tr>
		<tr>
			<td>Cellfectin</td>
			<td>Invitrogen</td>
			<td>10362100</td>
			<td>For Sf9 transfection</td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Sigma</td>
			<td>D5545</td>
			<td>For motility assay mixture</td>
		</tr>
		<tr>
			<td>FLAG peptide</td>
			<td>Sigma</td>
			<td>F3290</td>
			<td>For motility purification</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Sigma</td>
			<td>G5516</td>
			<td>For motility purification</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma</td>
			<td>H3375</td>
			<td>Preparing lysing Sf9 cells</td>
		</tr>
		<tr>
			<td>IGEPAL CA 630</td>
			<td>Sigma</td>
			<td>I8896</td>
			<td>Preparing lysing buffer for Sf9 cells</td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Sigma</td>
			<td>P9541</td>
			<td>For motility purification</td>
		</tr>
		<tr>
			<td>Leupeptin</td>
			<td>Sigma</td>
			<td>L2884</td>
			<td>For motility assay and purification</td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma</td>
			<td>M2670</td>
			<td>For preparing lysis buffer</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma</td>
			<td>S7653</td>
			<td>For preparing lysis buffer</td>
		</tr>
		<tr>
			<td>PMSF</td>
			<td>Sigma</td>
			<td>P7626</td>
			<td>For motility purification</td>
		</tr>
		<tr>
			<td>Sf9 cells</td>
			<td>Kind gift from Dr. Thomas Pucadyil (Indian Institute of Science Education and Research, Pune, India).</td>
			<td></td>
			<td>For baculovirs expression and purification</td>
		</tr>
		<tr>
			<td>Sf9 culture bottles</td>
			<td>Thermo Scientific</td>
			<td>4115-0125</td>
			<td>For suspension culture</td>
		</tr>
		<tr>
			<td>Sf-900/SFM medium (1X)</td>
			<td>Thermo Scientific</td>
			<td>10902-096 -500ml</td>
			<td>For culturing Sf9 cells</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sigma</td>
			<td>S1888</td>
			<td>Preparing lysing buffer for Sf9 cells</td>
		</tr>
		<tr>
			<td>Unsupplemented Grace&#8217;s media</td>
			<td>Thermo Scientific</td>
			<td>11595030 -500ml</td>
			<td>For Sf9 transfection</td>
		</tr>
		<tr>
			<td>Mirotubule Polymerization and Single molecule assay materails</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ATP</td>
			<td>Sigma</td>
			<td>A2647</td>
			<td>For motility and gliding assay</td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Sigma</td>
			<td>A2153</td>
			<td>For blocking motility chamber</td>
		</tr>
		<tr>
			<td>Catalase</td>
			<td>Sigma</td>
			<td>C9322</td>
			<td>For motility and gliding assay</td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma</td>
			<td>D5879</td>
			<td>For dissolving Rhodamine</td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td>Sigma</td>
			<td>3777</td>
			<td>For preparing buffers</td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Sigma</td>
			<td>G7021</td>
			<td>For motility and gliding assay</td>
		</tr>
		<tr>
			<td>Glucose oxidase</td>
			<td>Sigma</td>
			<td>G2133</td>
			<td>For motility and gliding assay</td>
		</tr>
		<tr>
			<td>GTP</td>
			<td>Sigma</td>
			<td>G8877</td>
			<td>For microtubule polymerization</td>
		</tr>
		<tr>
			<td>KOH</td>
			<td>Sigma</td>
			<td>P1767</td>
			<td>Preparing PIPES buffer pH 6.9</td>
		</tr>
		<tr>
			<td>PIPES</td>
			<td>Sigma</td>
			<td>P6757</td>
			<td>For motility and gliding assay</td>
		</tr>
		<tr>
			<td>Microtubule gliding assay materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>26G&#160; needle</td>
			<td>Dispovan</td>
			<td></td>
			<td>For shearing microtubules</td>
		</tr>
		<tr>
			<td>Casein</td>
			<td>Sigma</td>
			<td>C3400</td>
			<td>For microtubule glidning assay</td>
		</tr>
		<tr>
			<td>GFP nanobodies</td>
			<td>Gift from Dr. Sivaraj Sivaramakrishnan (University of Minnesota, USA)</td>
			<td></td>
			<td>For attaching motors to the coverslip</td>
		</tr>
		<tr>
			<td>Rhodamine</td>
			<td>Thermo Scientific</td>
			<td>46406</td>
			<td>For preparing labelling tubulin</td>
		</tr>
		<tr>
			<td>Microscope and other instruments</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>0.5ml, 1.5 and 2-ml microcentrifuge tubes</td>
			<td>Eppendorf</td>
			<td></td>
			<td>For Sf9 culture and purification</td>
		</tr>
		<tr>
			<td>10ml&#160; disposable sterile pipettes</td>
			<td>Eppendorf</td>
			<td></td>
			<td>For Sf9 culture and purification</td>
		</tr>
		<tr>
			<td>10ul, 200ul, 1ml micropipette tips</td>
			<td>Eppendorf</td>
			<td></td>
			<td>For Sf9 culture and purification</td>
		</tr>
		<tr>
			<td>15ml concal tubes</td>
			<td>Eppendorf</td>
			<td></td>
			<td>For Sf9 culture and purification</td>
		</tr>
		<tr>
			<td>35mm cell culture dish</td>
			<td>Cole Palmer</td>
			<td>15179-39</td>
			<td>For Sf9 culture</td>
		</tr>
		<tr>
			<td>Balance</td>
			<td>Sartorious</td>
			<td></td>
			<td>0.01g-300g</td>
		</tr>
		<tr>
			<td>Benchtop orbial shaking incubator</td>
			<td>REMI</td>
			<td></td>
			<td>For Sf9 suspenculture at 28oC</td>
		</tr>
		<tr>
			<td>Camera</td>
			<td>EMCCD Andor iXon Ultra 897</td>
			<td></td>
			<td>For TIRF imaging and acquesition</td>
		</tr>
		<tr>
			<td>Double sided tape</td>
			<td>Scotch</td>
			<td></td>
			<td>For making motility chamber</td>
		</tr>
		<tr>
			<td>Glass coverslip</td>
			<td>Fisherfinest</td>
			<td>12-548-5A</td>
			<td>size; 22X30</td>
		</tr>
		<tr>
			<td>Glass slide</td>
			<td>Blue Star</td>
			<td></td>
			<td>For making motility chamber</td>
		</tr>
		<tr>
			<td>Heating block</td>
			<td>Neuation</td>
			<td></td>
			<td>Dissolving paraffin wax</td>
		</tr>
		<tr>
			<td>Inverted microscope</td>
			<td>Nikon Eclipse Ti- U</td>
			<td></td>
			<td>To check protein expression</td>
		</tr>
		<tr>
			<td>Lasers</td>
			<td>488nm (100mW)</td>
			<td></td>
			<td>For TIRF imaging</td>
		</tr>
		<tr>
			<td>Liquid nitrogen</td>
			<td></td>
			<td></td>
			<td>For sample freezing and storage</td>
		</tr>
		<tr>
			<td>Microcapillary loading tip</td>
			<td>Eppendorf</td>
			<td>EP022491920</td>
			<td>For shearing microtubules</td>
		</tr>
		<tr>
			<td>Microscope</td>
			<td>Nikon Eclipse Ti2-E with DIC set up</td>
			<td></td>
			<td>For TIRF imaging</td>
		</tr>
		<tr>
			<td>Mini spin</td>
			<td>Genetix, BiotechAsia Pvt.Ltd</td>
			<td></td>
			<td>For quick spin</td>
		</tr>
		<tr>
			<td>Objective</td>
			<td>100X TIRF objective with 1.49NA oil immersion</td>
			<td></td>
			<td>For TIRF imaging</td>
		</tr>
		<tr>
			<td>Optima UltraCentrifuge XE</td>
			<td>Beckman Coulter</td>
			<td></td>
			<td>For protein purification</td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Eppendorf</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>pH-meter</td>
			<td>Corning</td>
			<td>Coring 430</td>
			<td>To adjust pH</td>
		</tr>
		<tr>
			<td>Pipette-boy</td>
			<td>VWR</td>
			<td></td>
			<td>For Sf9 culture and purification</td>
		</tr>
		<tr>
			<td>Sorvall Legend Micro 21</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td>For protein purification</td>
		</tr>
		<tr>
			<td>Sorvall ST8R centrifuge</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td>Protein purification</td>
		</tr>
		<tr>
			<td>ThermoMixer</td>
			<td>Eppendorf</td>
			<td></td>
			<td>For microtubule polymerization</td>
		</tr>
		<tr>
			<td>Ultracentrifuge rotor</td>
			<td>Beckman coulter</td>
			<td></td>
			<td>SW60Ti rotor</td>
		</tr>
		<tr>
			<td>Ultracentrifuge tubes</td>
			<td>Beckman</td>
			<td></td>
			<td>5 mL, Open-Top Thinwall Ultra-Clear Tube, 13 x 51mm</td>
		</tr>
		<tr>
			<td>Vortex mixer</td>
			<td>Neuation</td>
			<td></td>
			<td>Sample mixing</td>
		</tr>
		<tr>
			<td>Wax</td>
			<td>Sigma</td>
			<td>V001228</td>
			<td>To seal motility chamber</td>
		</tr>
	</tbody>
</table>

single-molecule analysis of sf9 purified superprocessive kinesin-3 family motors

A complex cellular environment poses challenges for single-molecule motility analysis. However, advancement in imaging techniques have improved single-molecule studies and has gained immense popularity in detecting and understanding the dynamic behavior of fluorescent-tagged molecules. Here, we describe a detailed method for&#160;in vitro single-molecule studies of kinesin-3 family motors using Total Internal Reflection Fluorescence (TIRF) microscopy. Kinesin-3 is a large family that plays critical roles in cellular and physiological functions ranging from intracellular cargo transport to cell division to development. We have shown previously that constitutively active dimeric kinesin-3 motors exhibit fast and superprocessive motility with high microtubule affinity at the single-molecule level using cell lysates prepared by expressing motor in mammalian cells. Our lab studies kinesin-3 motors and their regulatory mechanisms using cellular, biochemical and biophysical approaches, and such studies demand purified proteins at a large scale. Expression and purification of these motors using mammalian cells would be expensive and time-consuming, whereas expression in a prokaryotic expression system resulted in significantly aggregated and&#160;inactive protein. To overcome the limitations posed by bacterial purification systems and mammalian cell lysate, we have established a robust Sf9-baculovirus expression system to express and purify these motors. The kinesin-3 motors are C-terminally tagged with 3-tandem fluorescent proteins (3xmCitirine or 3xmCit) that provide enhanced signals and decreased photobleaching. In vitro single-molecule and multi-motor gliding analysis of Sf9 purified proteins demonstrate that kinesin-3 motors are fast and superprocessive akin to our previous studies using mammalian cell lysates. Other applications using these assays include detailed knowledge of oligomer conditions of motors, specific binding partners paralleling biochemical studies, and their kinetic state.

To express and purify active and functional recombinant motor proteins at a large scale using the Sf9-baculovirus expression, the system needs generation of viral particles stably carrying a coding sequence to infect Sf9 cells. To achieve this, Sf9 cells were transfected with recombinant bacmid encoding KIF1A(1-393LZ)-3xmCit-FLAG. After 72 h, a significant population of cells showed expression of green fluorescent protein (mCitrine) with enlarged cells and nuclei (Figure 1 and <strong class=...

Watch this Scientific Journal Video about Single-Molecule Analysis of Sf9 Purified Superprocessive Kinesin-3 Family Motors at JoVE.com

Single-Molecule Analysis of Sf9 Purified Superprocessive Kinesin-3 Family Motors

This study details purification of KIF1A(1-393LZ), a member of kinesin-3 family, using Sf9-baculovirus expression system. In vitro single-molecule and multi-motor gliding analysis of these purified motors exhibited robust motility properties comparable to motors from mammalian cell lysate. Thus, Sf9-baculovirus system is amenable to express and purify motor protein of interest.

A complex cellular environment poses challenges for single-molecule motility analysis. However, advancement in imaging techniques have improved ...

The protocol offers a simple method for purifying active molecular motors using Sf9 baculovirus system. It also details single molecule motility and multi-motor gliding assays to study the regulatory mechanism of motor proteins. All that traditional vector expression Sf9 baculovirus expression and single step affinity purification, will lead pure and active motor protein to study the mechanistic details of Superprocessive Kinesins in single molecule and multi-motor systems.In addition to Kinesin motors, the protocol can be applied to study biochemical and biophysical properties of other cytoskeletal based proteins such as dionine and myosin. The protocol is detailed and easy to follow. Some suggestions are to handle Sf9 cells carefully as they are prone to contamination, and to follow notes provided in the protocol.Visual demonstration is highly effective, easy to follow and understand the critical steps, especially for those who have never performed these assays. Demonstrating the procedure will be Pushpanjali Soppina and Dipeshwari Shewale, PhD students working with me and Pradeep Naik. To begin, seed the cells in a 35 milliliter dish, at a density of 4.5 times 10 to the fifth cells per milliliter.After 24 hours, mix one microgram of bacmid DNA and 100 microliters of unsupplemented Grace's media in a tube. Mix six microliters of transfection reagent in another tube with 100 microliters of unsupplemented Grace's media. Carefully transfer the content of the first tube into the second tube.Mix them and incubate the mixture for 45 minutes at room temperature. Add 0.8 milliliters of unsupplemented Grace's media to the mixture. Mix and aspirate the Sf900 SFM media from the cells.Add the prepared transfection media drop-wise on the top of the cells and incubate the plate for six hours. Then carefully remove the transfection mixture. Add two milliliters of SF900 SFM media and incubate further at 28 degrees Celsius for 48 hours.Next, check the motor protein expression under an inverted fluorescence microscope. Harvest the media with infected cells, and spin for five minutes, at 500 G.Collect the supernatant and snap freeze the aliquots. Add 10 milliliters of SF900 SFM media with cells and one milliliter of P-zero virus stock, in a sterile, 100 milliliter, conical flask.Incubate at 28 degrees Celsius with constant shaking at 90 rpm. After 72 hours, spin down the cells in a 15 milliliter, sterile conical tube at 500 G for five minutes and collect the supernatant. For large scale protein expression, infect 30 milliliters of the suspension culture with one milliliter of P1 stock virus.72 hours post-infection, check the cells for protein expression and collect the cells in sterile, 50 milliliter, conical tubes. After spinning, discard the supernatant, and collect the cell pellet. To lyse the cells, add three milliliters of ice cold lysis buffer to the cell pellet.Spin the cell lysate at 150, 000 G for 30 minutes, at four degrees Celsius. Collect the supernatant and mix it with 40 microliters of 50%ANTI-FLAG M2 affinity resin. Incubate the mixture at four degrees Celsius for three hours with end-to-end tumbling.Now pellet the FLAG resin by spinning at 500 G for one minute at four degrees Celsius. Wash the FLAG resin pellet three times with ice cold wash buffer. And after the third wash, carefully drain the wash buffer.Next, add 70 microliters of wash buffer containing 100 micrograms per milliliter FLAG peptide, to the resin pellet, and incubate overnight at four degrees Celsius, as demonstrated earlier. After spinning, collect the supernatant containing purified protein into a fresh tube. Prepare a polymerization mix as described in the manuscript, and add 10 microliters of tubulin to the polymerization mixture.Transfer the tube into a heat block, pre-warmed at 37 degrees Celsius, and incubate for 30 minutes. After preparing the microtubule stabilization buffer, warm it, and add it to the polymerized microtubules. Once the motility flow cell chamber is prepared, flow 30 microliters of diluted microtubule solution through the chamber.After 30 minutes, flow 40 to 50 microliters of blocking buffer and incubate it. Prepare a motility mixture and add one microliter of the purified motor to it. Mix well and flow the solution into the motility chamber.Seal both ends of the motility chamber and image under TIRF illumination. Focus on the individual mCitirine tagged motors, moving processively. Mix rhodamine labeled tubulin with unlabeled tubulin in a ratio of one to 10.After 30 minutes of polymerization, gently add 30 microliters of pre-warmed microtubule stabilization buffer and incubate further, for five minutes, at 37 degrees Celsius. Shear the microtubules by pipetting with the capillary loading tip. After preparing the motility flow chamber, flow 50 microliters of Sf9 purified GFP nanobodies and incubate for 30 minutes.Block the cover slip surface by flowing 50 microliters of block buffer. Prepare 50 microliters of the motor mix. Flow it into the chamber after gently mixing the solution and incubate for 30 minutes.Wash the chamber, twice, with 50 microliters of P12-casein. Prepare the gliding assay mixture and mix it gently, before flowing it into the motility chamber. Seal the ends of the motility chamber, and image microtubule gliding under TIRF illumination.After 48 hours of transfection, the untransfected cells appear small, round and firmly attached. However, the transfected cells expressing protein, were loosely attached to the surface and showed enlarged cell diameter. After 72 hours, more than 90%of Sf9 cells expressed fluorescently tagged, kinesin-3 motor KIF1A, and cells were loosely bound to the surface.Kinesin-3 motor protein was purified from the transfected Sf9 cells. The kymograph depicts kinesin-3 motor walking processively, along the microtubule surface. Motility events showed an average velocity and run length of approximately 2.44 micrometers per second and 10.79 micrometers respectively.The kymograph indicates smooth microtubule gliding by the kinesin-3 motors, with an average velocity of approximately 1.37 micrometers per second. The most important thing is to add the stabilization buffer without disturbing the microtubule mix and not to shear the microtubule. The protocol would be useful for other applications, such as ATPase measurements, biophysical analysis, mechanisms, in vitro reconstitution assays, et cetera.Using sf9 purified motors, we've demonstrated recently that kinesin-3 motors are fast and superprocessive. Interestingly, these motors exhibit high ATP turnover rates compared to well-characterized motor, Kinesin-1.

single-molecule-analysis-sf9-purified-superprocessive-kinesin-3

Research

JoVE Journal

Biochemistry

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

A protocol on how to perform high-precision interdye distance measurements using F&#246;rster resonance energy transfer (FRET) at the single-molecule level in multiparameter fluorescence detection (MFD) mode is presented here. MFD maximizes the usage of all &#34;dimensions&#34; of fluorescence to reduce photophysical and experimental artifacts and allows for the measurement of interdye distance with an accuracy up to ~1 &#197; in rigid biomolecules. This method was used to identify three conformational states of the ligand-binding domain of the N-methyl-D-aspartate (NMDA) receptor to explain the activation of the receptor upon ligand binding. When comparing the known crystallographic structures with experimental measurements, they agreed within less than 3 &#197; for more dynamic biomolecules. Gathering a set of distance restraints that covers the entire dimensionality of the biomolecules would make it possible to provide a structural model of dynamic biomolecules.

A protocol for high-precision FRET experiments at the single molecule level is presented here. Additionally, this methodology can be used to identify three conformational states in the ligand-binding domain of the N-methyl-D-aspartate (NMDA) receptor. Determining precise distances is the first step towards building structural models based on FRET experiments.

A protocol on how to perform high-precision interdye distance measurements using F&#246;rster resonance energy transfer (FRET) at the single-molecule ...

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Non-canonical nucleic acid secondary structure G-quadruplexes (G4) are involved in diverse cellular processes, such as DNA replication, transcription, RNA processing, and telomere elongation. During these processes, various proteins bind and resolve G4 structures to perform their function. As the function of G4 often depends on the stability of its folded structure, it is important to investigate how G4 binding proteins regulate the stability of G4. This work presents a method to manipulate single G4 molecules using magnetic tweezers, which enables studies of the regulation of G4 binding proteins on a single G4 molecule in real time. In general, this method is suitable for a wide scope of applications in studies for proteins/ligands interactions and regulations on various DNA or RNA secondary structures.

A single-molecule magnetic tweezers platform to manipulate G-quadruplexes is reported, which allows for the study of G4 stability and regulation by various proteins.

Non-canonical nucleic acid secondary structure G-quadruplexes (G4) are involved in diverse cellular processes, such as DNA replication, transcription, RNA ...

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy

In recent years, atomic force microscopy (AFM) based single molecule force spectroscopy (SMFS) extended our understanding of molecular properties and functions. It gave us the opportunity to explore a multiplicity of biophysical mechanisms, e.g., how bacterial adhesins bind to host surface receptors in more detail. Among other factors, the success of SMFS experiments depends on the functional and native immobilization of the biomolecules of interest on solid surfaces and AFM tips. Here, we describe a straightforward protocol for the covalent coupling of proteins to silicon surfaces using silane-PEG-carboxyls and the well-established N-hydroxysuccinimid/1-ethyl-3-(3-dimethyl-aminopropyl)carbodiimid (EDC/NHS) chemistry in order to explore the interaction of pilus-1 adhesin RrgA from the Gram-positive bacterium Streptococcus pneumoniae (S. pneumoniae) with the extracellular matrix protein fibronectin (Fn). Our results show that the surface functionalization leads to a homogenous distribution of Fn on the glass surface and to an appropriate concentration of RrgA on the AFM cantilever tip, apparent by the target value of up to 20% of interaction events during SMFS measurements and revealed that RrgA binds to Fn with a mean force of 52 pN. The protocol can be adjusted to couple via site specific free thiol groups. This results in a predefined protein or molecule orientation and is suitable for other biophysical applications besides the SMFS.

This protocol describes the covalent immobilization of proteins with a heterobifunctional silane coupling agent to silicon-oxide surfaces designed for the atomic force microscopy based single molecule force spectroscopy which is exemplified by the interaction of RrgA (pilus-1 tip adhesin of S. pneumoniae) with fibronectin.

In recent years, atomic force microscopy (AFM) based single molecule force spectroscopy (SMFS) extended our understanding of molecular properties and ...

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Cell proteomes are often characterized using electrophoresis assays, where all species of proteins in the cells are non-specifically labeled with a fluorescent dye and are spotted by a photodetector following their separation. Single molecule fluorescence imaging can provide ultrasensitive protein detection with its ability for visualizing individual fluorescent molecules. However, the application of this powerful imaging method to electrophoresis assays is hampered by the lack of ways to characterize the homogeneity of fluorescent labeling of each protein species across the proteome. Here, we developed a method to evaluate the labeling homogeneity across the proteome based on a single molecule fluorescence imaging assay. In our measurement using a HeLa cell sample, the proportion of proteins labeled with at least one dye, which we termed &#8216;labeling occupancy&#8217; (LO), was determined to range from 50% to 90%, supporting the high potential of the application of single molecule imaging to sensitive and precise proteome analysis.

Here, we present a protocol to assess the labeling homogeneity for each protein species in a complex protein sample at the single molecule level.

Cell proteomes are often characterized using electrophoresis assays, where all species of proteins in the cells are non-specifically labeled with a ...

An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

Cap-dependent protein synthesis is the predominant translation pathway in eukaryotic cells. While various biochemical and genetic approaches have allowed extensive studies of cap-dependent translation and its regulation, high resolution kinetic characterization of this translation pathway is still lacking. Recently, we developed an in vitro assay to measure cap-dependent translation kinetics with single-molecule resolution. The assay is based on fluorescently labeled antibody binding to nascent epitope-tagged polypeptide. By imaging the binding and dissociation of antibodies to and from nascent peptide&#8211;ribosome&#8211;mRNA complexes, the translation progression on individual mRNAs can be tracked. Here, we present a protocol for establishing this assay, including mRNA and PEGylated slide preparations, real-time imaging of translation, and analysis of single molecule trajectories. This assay enables tracking of individual cap-dependent translation events and resolves key translation kinetics, such as initiation and elongation rates. The assay can be widely applied to distinct translation systems and should broadly benefit in vitro studies of cap-dependent translation kinetics and translational control mechanisms.

An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

Tracking individual translation events allows for high-resolution kinetic studies of cap-dependent translation mechanisms. Here we demonstrate an in vitro single-molecule assay based on imaging interactions between fluorescently labeled antibodies and epitope-tagged nascent peptides. This method enables single-molecule characterization of initiation and peptide elongation kinetics during active in vitro cap-dependent translation.

Cap-dependent protein synthesis is the predominant translation pathway in eukaryotic cells. While various biochemical and genetic approaches have allowed ...

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk population methods (Northern blot, PCR, and RNAseq) that measure mRNA levels lack the ability to provide information on cell-to-cell variation in responses. Precise single cell and allelic visualization and quantification is possible via single molecule RNA fluorescence in situ hybridization (smFISH). RNA-FISH is performed by hybridizing target RNAs with labeled oligonucleotide probes. These can be imaged in medium/high throughput modalities, and, through image analysis pipelines, provide quantitative data on both mature and nascent RNAs, all at the single cell level. The fixation, permeabilization, hybridization and imaging steps have been optimized in the lab over many years using the model system described herein, which results in successful and robust single cell analysis of smFISH labeling. The main goal with sample preparation and processing is to produce high quality images characterized by a high signal-to-noise ratio to reduce false positives and provide data that are more accurate. Here, we present a protocol describing the pipeline from sample preparation to data analysis in conjunction with suggestions and optimization steps to tailor to specific samples.&#160;

Single molecule RNA fluorescence in situ hybridization (smFISH) is a method to accurately quantify levels and localization of specific RNAs at the single cell level. Here, we report our validated lab protocols for wet-bench processing, imaging and image analysis for single cell quantification of specific RNAs.

Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk ...

Single-Molecule Dwell-Time Analysis of Restriction Endonuclease-Mediated DNA Cleavage

This novel total internal reflection fluorescence microscopy-based assay facilitates the simultaneous measurement of the length of the catalytic cycle for hundreds of individual restriction endonuclease (REase) molecules in one experiment. This assay does not require protein labeling and can be carried out with a single imaging channel. In addition, the results of multiple individual experiments can be pooled to generate well-populated dwell-time distributions. Analysis of the resulting dwell-time distributions can help elucidate the DNA cleavage mechanism by revealing the presence of kinetic steps that cannot be directly observed. Example data collected using this assay with the well-studied REase, EcoRV - a dimeric Type IIP restriction endonuclease that cleaves the palindromic sequence GAT&#8595;ATC (where &#8595; is the cut site) - are in agreement with prior studies. These results suggest that there are at least three steps in the pathway to DNA cleavage that is initiated by introducing magnesium after EcoRV binds DNA in its absence, with an average rate of 0.17 s-1 for each step.

Using quantum-dot-labeled DNA and total internal reflection fluorescence microscopy, we can investigate the reaction mechanism of restriction endonucleases while using unlabeled protein. This single-molecule technique allows for massively multiplexed observation of individual protein-DNA interactions, and data can be pooled to generate well-populated dwell-time distributions.

This novel total internal reflection fluorescence microscopy-based assay facilitates the simultaneous measurement of the length of the catalytic cycle for ...

Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis

The ribosome is a large ribonucleoprotein complex that assembles proteins processively along mRNA templates. The diameter of the ribosome is approximately 20 nm to accommodate large tRNA substrates at the A-, P- and E-sites. Consequently, the ribosome dynamics are naturally de-phased quickly. Single molecule method can detect each ribosome separately and distinguish inhomogeneous populations, which is essential to reveal the complicated mechanisms of multi-component systems. We report the details of a smFRET method based on the Nikon Ti2 inverted microscope to probe the ribosome dynamics between the ribosomal protein L27 and tRNAs. The L27 is labeled at its unique Cys 53 position and reconstituted into a ribosome that is engineered to lack L27. The tRNA is labeled at its elbow region. As the tRNA moves to different locations inside the ribosome during the elongation cycle, such as pre- and post- translocation, the FRET efficiencies and dynamics exhibit differences, which have suggested multiple subpopulations. These subpopulations are not detectable by ensemble methods. The TIRF-based smFRET microscope is built on a manual or motorized inverted microscope, with home-built laser illumination. The ribosome samples are purified by ultracentrifugation, loaded into a home-built multi-channel sample cell and then illuminated via an evanescent laser field. The reflection laser spot can be used to achieve feedback control of perfect focus. The fluorescence signals are separated by a motorized filter-turret and collected by two digital CMOS cameras. The intensities are retrieved via the NIS-Elements software.

Single molecule fluorescence energy transfer is a method that tracks the tRNA dynamics during ribosomal protein synthesis. By tracking individual ribosomes, inhomogeneous populations are identified, which shed light on mechanisms. This method can be used to track biological conformational changes in general to reveal dynamic-function relationships in many other complexed biosystems. Single molecule methods can observe non-rate limiting steps and low-populated key intermediates, which are not accessible by conventional ensemble methods due to the average effect.

The ribosome is a large ribonucleoprotein complex that assembles proteins processively along mRNA templates. The diameter of the ribosome is approximately ...

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA

The fusion genes resulting from chromosomal translocation have been found in many solid tumors or leukemia. EWS-FLI1, which belongs to the FUS/EWS/TAF15 (FET) family of fusion oncoproteins, is one of the most frequently involved fusion genes in Ewing sarcoma. These FET family fusion proteins typically harbor a low-complexity domain (LCD) of FET protein at their N-terminus and a DNA-binding domain (DBD) at their C-terminus. EWS-FLI1 has been confirmed to form biomolecular condensates at its target binding loci due to LCD-LCD and LCD-DBD interactions, and these condensates can recruit RNA polymerase II to enhance gene transcription. However, how these condensates are assembled at their binding sites remains unclear. Recently, a single-molecule biophysics method-DNA Curtains-was applied to visualize these assembling processes of EWS-FLI1 condensates. Here, the detailed experimental protocol and data analysis approaches are discussed for the application of DNA Curtains in studying the biomolecular condensates assembling on target DNA.

Here, we describe the use of the single-molecule imaging method, DNA Curtains, to study the biophysical mechanism of EWS-FLI1 condensates assembling on DNA.

The fusion genes resulting from chromosomal translocation have been found in many solid tumors or leukemia. EWS-FLI1, which belongs to the FUS/EWS/TAF15 ...

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to measure protein phosphorylation cannot preserve the heterogeneity in phosphorylation across individual proteins. The single-molecule pull-down (SiMPull) assay was developed to investigate the composition of macromolecular complexes via immunoprecipitation of proteins on a glass coverslip followed by single-molecule imaging. The current technique is an adaptation of SiMPull that provides robust quantification of the phosphorylation state of full-length membrane receptors at the single-molecule level. Imaging thousands of individual receptors in this way allows for quantifying protein phosphorylation patterns. The present protocol details the optimized SiMPull procedure, from sample preparation to imaging. Optimization of glass preparation and antibody fixation protocols further enhances data quality. The current protocol provides code for the single-molecule data analysis that calculates the fraction of receptors phosphorylated within a sample. While this work focuses on phosphorylation of the epidermal growth factor receptor (EGFR), the protocol can be generalized to other membrane receptors and cytosolic signaling molecules.

The present protocol describes sample preparation and data analysis to quantify protein phosphorylation using an improved single-molecule pull-down (SiMPull) assay.

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to ...