Name: horizontal gel electrophoresis for enhanced detection of protein-rna complexes
Uploaded: 2017-07-28T14:00:00
Description: Watch this Scientific Journal Video about Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes at JoVE.com

We danken Laura Vanderploeg voor het voorbereiden van cijfers. Werk in het laboratorium Sheets wordt ondersteund door NSF grant 1050395 en NIH grant (R21HD076828). Werk in het Ryder lab wordt ondersteund door NIH subsidies R01GM117237 en R01GM117008. Megan Dowdle wordt ondersteund door een SciMed GRS Advanced Opportunity Fellowship door het University of Wisconsin-Madison Graduate School en Biotechnology Training Programma door het Nationaal Instituut voor Algemene Medische Wetenschappen van de National Institutes of Health (T32GM008349).

1. Bereiding van de Horizontale Native Polyacrylamide Gel 4 . <ol><li> Voorbereiding van de benodigde materialen. <ol><li> Voor het horizontale gelapparaat gebruik een gelendoos (37 cm x 24 cm) met een 27 cm x 21 cm lade en een capaciteit voor twee combinaties met 24 putjes. Deze installatie biedt in totaal 48 monsters die tegelijkertijd kunnen worden geanalyseerd. </li><li> Bereid de volgende reagentia voor: 40% Acrylamide-Bis 19: 1, 5x TBE (Tris-Borate-EDTA pH 8,0), TEMED en ...

<ol>
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G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrophoretic+mobility+shift+assay+(EMSA)+for+detecting+protein-nucleic+acid+interactions.">Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions.</a> Nat Protoc. 2 (8), 1849-1861 (2007).</li><li>Pagano, J. M., Farley, B. M., Essien, K. I., Ryder, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+recognition+by+the+embryonic+cell+fate+determinant+and+germline+totipotency+factor+MEX-3.">RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3.</a> Proc Natl Acad Sci USA. 106 (48), 20252-20257 (2009).</li><li>Royer, C. A., Scarlata, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+approaches+to+quantifying+biomolecular+interactions.">Fluorescence approaches to quantifying biomolecular interactions.</a> Meth Enzymol. 450, 79-106 (2008).</li><li>Su, C., Wang, F., Ciolek, D., Pan, Y. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrophoresis+of+proteins+and+protein-protein+complexes+in+native+polyacrylamide+gels+using+a+horizontal+gel+apparatus.">Electrophoresis of proteins and protein-protein complexes in native polyacrylamide gels using a horizontal gel apparatus.</a> Anal Biochem. 223, 93-98 (1994).</li><li>Buczek, P., Horvath, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermodynamic+Characterization+of+Binding+Oxytricha+nova+Single+Strand+Telomere+DNA+with+the+Alpha+Protein+N-terminal+Domain.">Thermodynamic Characterization of Binding Oxytricha nova Single Strand Telomere DNA with the Alpha Protein N-terminal Domain.</a> J Mol Biol. 359 (5), 1217-1234 (2006).</li><li>Zhang, Y., Park, S., Blaser, S., Sheets, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determinants+of+RNA+binding+and+translational+repression+by+the+Bicaudal-C+regulatory+protein.">Determinants of RNA binding and translational repression by the Bicaudal-C regulatory protein.</a> J Biol Chem. 289 (11), 7497-7504 (2014).</li><li>Gamberi, C., Lasko, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Bic-C+family+of+developmental+translational+regulators.">The Bic-C family of developmental translational regulators.</a> Comp Funct Genomics. , 141386 (2012).</li><li>Saffman, E. 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=Premature+translation+of+oskar+in+oocytes+lacking+the+RNA-binding+protein+bicaudal-C.">Premature translation of oskar in oocytes lacking the RNA-binding protein bicaudal-C.</a> Mol Cell Biol. 18 (8), 4855-4862 (1998).</li><li>Chicoine, 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=Bicaudal-C+recruits+CCR4-NOT+deadenylase+to+target+mRNAs+and+regulates+oogenesis,+cytoskeletal+organization,+and+its+own+expression.">Bicaudal-C recruits CCR4-NOT deadenylase to target mRNAs and regulates oogenesis, cytoskeletal organization, and its own expression.</a> Dev Cell. 13 (5), 691-704 (2007).</li><li>Zhang, 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=Bicaudal-C+spatially+controls+translation+of+vertebrate+maternal+mRNAs.">Bicaudal-C spatially controls translation of vertebrate maternal mRNAs.</a> RNA. 19 (11), 1575-1582 (2013).</li><li>Maisonneuve, C., 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=Bicaudal+C,+a+novel+regulator+of+Dvl+signaling+abutting+RNA-processing+bodies,+controls+cilia+orientation+and+leftward+flow.">Bicaudal C, a novel regulator of Dvl signaling abutting RNA-processing bodies, controls cilia orientation and leftward flow.</a> Development. 136 (17), 3019-3030 (2009).</li><li>Tran, U., 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=The+RNA-binding+protein+bicaudal+C+regulates+polycystin+2+in+the+kidney+by+antagonizing+miR-17+activity.">The RNA-binding protein bicaudal C regulates polycystin 2 in the kidney by antagonizing miR-17 activity.</a> Development. 137 (7), 1107-1116 (2010).</li><li>Pagano, J. M., Clingman, C. C., Ryder, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+approaches+to+monitor+protein-nucleic+acid+interactions+using+fluorescent+probes.">Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes.</a> RNA. 17 (1), 14-20 (2011).</li><li>Foley, T. L., 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=Platform+to+Enable+the+Pharmacological+Profiling+of+Small+Molecules+in+Gel-Based+Electrophoretic+Mobility+Shift+Assays.">Platform to Enable the Pharmacological Profiling of Small Molecules in Gel-Based Electrophoretic Mobility Shift Assays.</a> J Biomol Screen. 21 (10), 1125-1131 (2016).</li></ol>

Inheemse polyacrylamidegelen zijn een waardevol hulpmiddel om eiwit-RNA-interacties te onderzoeken en traditioneel worden deze gels verticaal 2 , 3 elektroforeseert. Wij hebben een wijziging van het protocol gebruikt dat de inheemse polyacrylamide gels creëert en horizontaal 1 , 4 , 6 , 7 , 15 elektr...

Elektroforetische mobiliteitsverschuivingsbepalingen (EMSA&#39;s) blijken een waardevol biochemisch instrument te zijn om specifieke eiwit-nucleïnezuurinteracties 1 , 2 , 3 te analyseren. Deze analyses kunnen belangrijke informatie verschaffen over de bindingsaffiniteit van eiwitten aan RNA of DNA 3 , de componentstochiometrie van nucleïnezuur-eiwitcomplexen 1 en verschaffen belangrijke nieuwe inzichten over de bindingsspecificiteit van RNA bindende eiwitten via substraatconcurrentie experimenten 1 . De traditionele experimentele opstelling voor deze analyses bestaat uit het mengen van gezuiverd eiwit met een radioactief gemerkt RNA-substraat. De resulterende complexen worden vervolgens geanalyseerd met niet-denaturerende (inheemse) polyacrylamidegelen die tussen twee glazen platen worden gegoten, gevolgd door monsterelektroforese in een verticaal apparaat 3. Hoewel deze benadering extensief is gebruikt om belangrijke inzichten te verschaffen in de biochemische mechanismen die de binding van eiwitten tot nucleïnezuren onderbouwen, heeft het ook verschillende beperkingen. Deze basisstrategie heeft bijvoorbeeld een relatief lage doorvoer en het is niet gemakkelijk aan te passen voor toepassingen waarbij parallel bindende reacties nodig zijn. Bovendien is het bij het traditionele verticale apparaat uitdagend om meerdere keren complexen mogelijk te houden tijdens elektroforese 3 , 4 . Hier presenteren we een aanpassing van de EMSA-analyse die gebruik maakt van inheemse polyacrylamidegels die worden gegoten in een flatbed apparaat, horizontale elektroforese en fluorescent gelabelde RNA substraten 4 , 5 , 6 , 7 . De opneming van deze relatief eenvoudige wijzigingen van de basis straTegy biedt een aantal sterke voordelen. In het bijzonder leent het horizontale platform formaat zich gemakkelijk om tientallen monsters tegelijkertijd 4 te analyseren. Ook voor sommige RNA-eiwitcomplexen, zoals die gevormd tussen het Bicaudal-C-eiwit en zijn RNA-substraatelektroforese in een horizontale gel, verschaft een verhoogd vermogen om afzonderlijke RNA-eiwitcomplexen op te lossen en deze te onderscheiden van het niet-gebonden RNA-substraat.

<table border="0" cellpadding="0" cellspacing="0" width="1432">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:373px;">Horizontal Gel Box</td>
			<td style="width:112px;">OWL</td>
			<td style="width:116px;">N/A</td>
			<td style="width:831px;">Product no longer made. Similar gel boxes can be found at Thermo Scientific, A-series gel boxes. Catalog Number: A2-BP</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">24-well large large horizontal gel electrophoresis combs</td>
			<td>OWL</td>
			<td>N/A</td>
			<td>Product no longer made. Similar gel boxes can be found at Thermo Scientific, A-series gel box combs. Catalog Number: A2-24C</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Powerpac 300</td>
			<td>Bio-Rad</td>
			<td>1655050</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mini-Protean II Electrophoresis Cell</td>
			<td>Bio-Rad</td>
			<td>165-2940</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">InstaPAGE-19 40% 19:1 Acrylamide/Bis</td>
			<td>IBI</td>
			<td>IB70015</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TEMED</td>
			<td>IBI</td>
			<td>IB70120</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">APS</td>
			<td>IBI</td>
			<td>IB70080</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Yeast tRNAs</td>
			<td>Ambion</td>
			<td>AM7119</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fluorescein labeled RNA</td>
			<td>IDT</td>
			<td>N/A</td>
			<td>Order can be made custom to length and desired sequence</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">EDTA tetrasodium salt hydrate</td>
			<td>Sigma-Aldrich</td>
			<td>E5391-1KG</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>H4034-500G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tris Base Ultrapure</td>
			<td>US Biological</td>
			<td>T8600</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Boric Acid</td>
			<td>Fisher Scientific</td>
			<td>BP168-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Potassium Chloride</td>
			<td>Fisher Scientific</td>
			<td>BP366-1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tween-20</td>
			<td>Fisher Scientific</td>
			<td>BP337-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DEPC</td>
			<td>Sigma-Aldrich</td>
			<td>1609-47-8</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dithiothreitol (DTT)</td>
			<td>Sigma-Aldrich</td>
			<td>3483 12 3</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bovine Serum Albumin (BSA)</td>
			<td>Sigma-Aldrich</td>
			<td>9048-46-8</td>
			<td></td>
		</tr>
	</tbody>
</table>

horizontal gel electrophoresis for enhanced detection of protein-rna complexes

Inheemse polyacrylamide gelelektroforese is een fundamenteel instrument van moleculaire biologie die extensief is gebruikt voor de biochemische analyse van RNA-eiwitinteracties. Deze interacties zijn traditioneel geanalyseerd met polyacrylamidegels die worden gegenereerd tussen twee glazen platen en monsters die verticaal worden geforoteerd. Polyacrylamide gels die in bakken worden gegoten en elektroforeseer horizontaal bieden echter verschillende voordelen. Bijvoorbeeld, horizontale gels die gebruikt worden om complexen te analyseren tussen fluorescerende RNA-substraten en specifieke eiwitten kunnen meerdere malen worden weergegeven als elektroforese vordert. Dit biedt de unieke mogelijkheid om RNA-eiwitcomplexen op verschillende punten tijdens het experiment te volgen. Daarnaast maakt horizontale gelelektroforese het mogelijk om veel monsters parallel te analyseren. Dit kan de tijdcursusproeven aanzienlijk vergemakkelijken en meerdere reacties tegelijk analyseren om verschillende componenten en condities te vergelijken. Hier prOvide een gedetailleerd protocol voor het genereren en gebruiken van horizontale inheemse gelelektroforese voor het analyseren van RNA-eiwitinteracties.

Om de kracht en de veelzijdigheid van de horizontale inheemse gelelektroforese te demonstreren hebben we de binding van het Xenopus Bicaudal-C (Bicc1) eiwit geanalyseerd aan een fluorescent gemerkt RNA dat een Bicc1 bindingsplaats bevat. Bicc1-eiwitten functioneren als mRNA-specifieke translatie-repressors om de beslissingen van het celfeest tijdens de moederstadia van dierlijke ontwikkeling 9 , 10 , <sup clas...

Watch this Scientific Journal Video about Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes at JoVE.com

Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

Inheemse polyacrylamide gelelektroforese is een fundamenteel hulpmiddel voor het analyseren van RNA-eiwitinteracties. Traditioneel hebben de meeste experimenten verticale gels gebruikt. Horizontale gels verschaffen echter verschillende voordelen, zoals de mogelijkheid om complexen te monitoren tijdens elektroforese. Wij bieden een gedetailleerd protocol voor het genereren en gebruiken van horizontale inheemse gelelektroforese.

Horizontale Gel Electroforese voor Verbeterde Detectie van Proteïne-RNA Complexen

Native polyacrylamide gel electrophoresis is a fundamental tool of molecular biology that has been used extensively for the biochemical analysis of ...

The overall of this protocol is to analyze RNA protein interactions using horizontal native gel electrophoresis. This method can help answer key questions in RNA biochemistry, such as defining the characteristics of specific RNA protein interactions. The main advantage of this technique is that it allows complex formation to be monitored multiple times during electrophoresis.For the horizontal gel apparatus, use a gel box with a 27 centimeter by 21 centimeter casting tray and a capacity for two 24 well combs. This set up provides a total of 48 samples that can be analyzed simultaneously. Prepare two liters of 1x TBE running buffer by diluting 400 milliliters of 5x TBE with 1, 600 milliliters of water and mixing.Place the TBE buffer in the cold room to cool. Prepare the following reagents following standard procedures, 40%acrylamide best 19:1, 5x TBE, temed and 10%ammonium per sulfate. To make a 10%native acrylamide gel, add the following to a 500 milliliter flask:80 milliliters of 5x TBE, 100 milliliters of 40%acrylamide and water to a final volume of 400 milliliters.Add four milliliters of 10%ammonium per sulfate and 400 microliters of temed and mix well. Pour the mix into the horizontal casting tray and allow the gel to polymerize in the fume hood for 30 minutes. The polymerized gel will be approximately two centimeters thick and a thin layer of liquid will remain on top of the gel.Place the gel into the gel box and take it into the cold room. Next, pour the liquid off and rinse with running buffer. Remove the combs carefully, add two liters of cold running buffer to the gel box and then use a syringe to rinse the wells with running buffer.Pre-run the gel at 120 volts for one hour at four degrees celsius in a cold room. While the gel is being prerun, prepare the binding reactions. Add the following binding reaction components to each RNA free microcentrifuge tube in this order:five microliters of 10 millimolar BSA, five microliters of 20 millimolar DTT, five microliters of 10 millimolar yeast tRNAs, 10 microliters of 5x binding buffer, bicaudal-c protein to a final concentration of 250 nanomolar in 50 microliters, DEPC-treated water to a final volume of 45 microliters and five microliters of fluorescently labeled RNA substrate.Close the tubes and flick gently to mix, centrifuge the tubes briefly and incubate in the dark for 30 minutes at room temperature. When the binding reactions are complete, add 15 microliters of 50%glycerol to each reaction and mix gently. Carefully load 30 microliters of each reaction into the wells of the gel, the amount of sample that can be loaded into a single well varies depending on the thickness of the gel and the size of the wells.The power supply to the gel apparatus, switch on the power, adjust the voltage to 120 volts and run the gel in four degree celsius. To prevent damaging or bleaching of the fluorescently labeled RNA, conduct electrophoresis in the dark. Electrophoresis times will vary depending upon the specifics of the RNA protein complex being analyzed.A major advantage of the horizontal electrophorated mobility shift assay analysis, is that electrophoresis can be stopped in the gel image prior to completion of the run. Perform analysis with any instrument designed for detecting an imaging fluorescent substrates. Adjust the imager settings, for fluorescently labeled ligands, use the following settings.Fluorescein wavelength of 473 nanometers, photomultiplier voltage of 750 volts and pixel size of 100 micrometers. Scan the gel to capture the image. After imaging, the gel can be placed back into the apparatus and electrophoresis can be continued for longer times.The binding of the xenopus bicaudal-C or Bicc1 protein to a fluorescently labeled Cripto1 mRNA containing a Bicc1 binding site, was analyzed by both vertical and horizontal native gel electrophoresis, as a negative control, Bicc1 was mixed with a fluorescently labeled RNA derived from CyclinB1 mRNA. It was readily apparent using either method, that Bicc1 binds to the Cripto1 RNA and forms a specific complex. However, the Bicc1, Cripto1 complexes were significantly more distinct when analyzed with the horizontal gel, facilitating their detection and allowing the discrimination of protein RNA complexes from unbound RNA.After imaging, the gel was returned to the gel apparatus, electrophoresis for an additional three and a half hours, and reimaged. As shown here, the complexes had migrated further and were still readily detectable, indicating their stability. Once mastered, this technique can be done in four to five hours, if it is performed properly.After watching this video, you should have a good understanding of how to analyze RNA protein interactions using horizontal native gel electrophoresis.

Research

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Biochemistry

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Detectie en visualisatie van DNA-schade-geïnduceerde eiwitcomplexen in suspensiecellenculturen met behulp van de proximity-liggingsassay

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For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis ...

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Amyloid or amyloid-like fibers have been associated with many human diseases, and are now being discovered to be important for many signaling pathways. ...

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