Questo lavoro è stato sostenuto dal accademico Singapore Research Council (ARC) [codice di autorizzazione del 90/07]. Ringraziamo radiodurans per il sostegno.

Il protocollo testo completo e dettagliato per questa procedura sperimentale è disponibile nei protocolli di corrente in Biologia Molecolare. Dettagliate passo-passo le istruzioni per il montaggio del panino gel e gel per apparecchi possono essere trovati sul sito web BioRad 3. Attrezzatura richiesta: Lastre di vetro (interno ed esterno) 10 celle cm: 10,1 x 7,3 cm (disco interno), 10,1 x 8,2 cm (piastra esterna), BioRad 20 celle cm: 20 x 20 cm (lastra interna), 20 x 22,3 centimetri (piastra esterna), BioRad 0,5-1,5 pettine gel mm e distanziali Gel fusione stare Apparato gel con coperchio e cavi Alimentatore ad alta tensione Riscaldamento blocco o bagnomaria Pipette sierologiche e aiuto pipetta Pipette e puntali Gel essiccatore o uno scanner Reagenti e soluzioni: Urea (ultrapuro) Poliacrilammide soluzione al 40% (29:1) 10 x soluzione di TBE (Tris-borato, EDTA buffer) Deionizzata, acqua distillata TEMED 30% (w / v) di soluzione di persolfato di ammonio 0,5 x TBE soluzione Formammide EDTA Cyanol Xilene Blu di bromofenolo Metanolo Etanolo <table border="1" cellspacing="0" cellpadding="0"><tbody><tr><td> Volume </td><td colspan="3" style="text-align:center;"> 50 ml </td><td colspan="3" style="text-align:center;"> 60 ml </td><td colspan="3" style="text-align:center;"> 10 ml </td></tr><tr><td> Concentrazione di acrilamide </td><td> 10% </td><td> 12,5% </td><td> 15% </td><td> 10% </td><td> 12,5% </td><td> 15% </td><td> 10% </td><td> 12,5% </td><td> 15% </td></tr><tr><td> g UREA </td><td> 24 </td><td> 24 </td><td> 24 </td><td> 28,8 </td><td> 28,8 </td><td> 28,8 </td><td> 4,8 </td><td> 4,8 </td><td> 4,8 </td></tr><tr><td> ml 40% Acryl (29:1) </td><td> 12,5 </td><td> 15,625 </td><td> 18,75 </td><td> 15 </td><td> 18,75 </td><td> 22,5 </td><td> 2,5 </td><td> 3,125 </td><td> 3,75 </td></tr><tr><td> ul APS 30% </td><td> 166 </td><td> 166 </td><td> 166 </td><td> 199,2 </td><td> 199,2 </td><td> 199,2 </td><td> 33 </td><td> 33 </td><td> 33 </td></tr><tr><td> ul TEMED </td><td> 20 </td><td> 20 </td><td> 20 </td><td> 24 </td><td> 24 </td><td> 24 </td><td> 4 </td><td> 4 </td><td> 4 </td></tr><tr><td> 10 x TBE </td><td> 5 </td><td> 5 </td><td> 5 </td><td> 6 </td><td> 6 </td><td> 6 </td><td> 1 </td><td> 1 </td><td> 1 </td></tr><tr><td colspan="10"> Riempire il volume con acqua deionizzata, acqua distillata </td></tr></tbody></table> Tabella 1: Reagenti e soluzioni necessarie per le concentrazioni di acrilamide e vari volumi per la risoluzione di oligonucleotidi singolo filamento Gel di assemblaggio sandwich e gel di preparazione <ol><li> Montare il gel secondo la descrizione di produttori e fissare il gel in gel-casting da camera 3. Utilizzare distanziatori 0,5-1,5 mm di spessore. </li><li> Preparare la soluzione appropriata poliacrilamide in base alle attuali protocolli di biologia molecolare o come indicato nella Tabella 1. Per un gel di acrilammide denaturante di 20 cm x 22 cm x 1,5 mm, 60 ml di soluzione di gel e per un 10,1 x 8,2 centimetri x 1 mm gel 5 ml di soluzione di gel è sufficiente. Grandi gel sono usati quando i prodotti attesi / bande sono all&#39;interno della gamma di alcune basi, poi un gel più risolverà bande con una differenza di un singolo nucleotide. Se le bande atteso differiscono in più di 10 nucleotidi, piccoli gel sarà adatto a risolvere i frammenti. Scegli la percentuale di poliacrilammide che si adatta alle vostre esigenze di separazione, una più alta concentrazione di poliacrilamide risolverà inferiore frammenti di peso molecolare. Usa urea ultrapura e mescolare con la quantità desiderata di acrilamide. Aggiungi tampone TBE alla miscela di gel per ottenere una concentrazione finale di 0,5-1 x TBE e riempire il volume con acqua deionizzata, acqua distillata. Riscaldare la soluzione per 20 secondi nel microonde e mescolare delicatamente. Per i volumi gel più ripetere questo passaggio fino a quando la soluzione è la mano calda. </li><li> Versare il gel immediatamente con una pipetta sierologica e un aiuto pipetta automatica tra le due lastre di vetro. Evitare di introdurre bolle d&#39;aria. Inserire il pettine e lasciare polimerizzare il gel per 30-60 minuti. </li></ol> Sistemare il dispositivo di elettroforesi e prerun il gel <ol><li> Smontare il gel dalla camera di fusione e di montaggio per l&#39;apparato gel in base alle istruzioni produce 3. </li><li> Riempire la camera bassa del buffer buffer di ingegno in esecuzione (0.5-1 x TBE) che le lastre di vetro saranno subfuse 2-3 cm con tampone. Riempire la camera alta del buffer fino alla parte superiore del gel con la gestione del buffer. </li><li> Rimuovere con attenzione il pettine e lavare i pozzetti con tampone di corsa, utilizzando una pipetta e gel punte di carico. </li><li> Fissare il coperchio del sistema gel e collegare i cavi ad una alimentazione ad alta tensione. Prima di poter caricare i campioni è necessario prerun il gel per almeno 30 minuti per scaldare il gel e per rimuovere l&#39;urea rimanenti dal gel. La temperatura ottimale dovrebbe essere tra 45-55 ° C. Evitare temperature superiori a 60 ° C come bande potrebbe striscio o le lastre di vetro potrebbe rompersi. Scegli watt costante per il prerun (15-25 W per gel). </li></ol> Preparazione del campione <ol><li> Nel frattempo preparare i campioni. Quindi, aggiungere la quantità appropriata di 2 mix di caricamento del gel x per il campione. Il mix di caricamento di solito contiene il 90% formammide, 0,5% EDTA, cyanol 0,1% xilene e 0,1% blu di bromofenolo. </li><li> Prima che i campioni possono essere caricati sul gel, i campioni devono essere denaturato calore riscaldando i campioni tra i 70-90 ° C per qualche minuto. </li></ol> Caricare ed eseguire il gel <ol><li> Quando il prerun è terminata, togliere il coperchio e lavare accuratamente le tasche, come descritto prima che l&#39;urea ha colato nei pozzetti. </li><li> Applicare i campioni con attenzione dal fondo della tasca. Evitare di introdurre bolle d&#39;aria. Caricamento del buffer deve essere applicata a tasche vuote per mantenere la parità di condizioni durante la corsa. </li><li> Montare il coperchio ed eseguire il gel a watt costante per mantenere una temperatura gel di 55 ° C simile al prerun. Osservare la migrazione dei coloranti marcatore fino a quando il fronte del colorante raggiunge l&#39;estremità inferiore del gel. La durata di esecuzione dipende dalla percentuale di acrilammide utilizzati, forza ionica del tampone e lo spessore del gel. Una corsa può durare da 2-4 ore. Controllare la temperatura del gel. Un termometro gel può aiutare a controllare la giusta temperatura durante la corsa. </li></ol> Processo il gel <ol><li> Quando il fronte del colorante ha raggiunto la fine del gel messo il gel dalla camera bassa del buffer. Rimuovere il gel dalla camera e allentare i morsetti. Tirare fuori i distanziali e con attenzione dissimulare le lastre di vetro. Se necessario tagliare la parte superiore pozzetto contenente gel. </li><li> Con attenzione trasferire il gel in un piatto con una soluzione di gel di fissazione (stessa concentrazione di metanolo TBE più 5-10% ed etanolo). Lascia il gel nella soluzione per 5-10 minuti e cambia il buffer due volte. </li><li> Il gel è pronto per l&#39;ulteriore elaborazione con essiccatore gel vuoto o la scansione diretta del gel. </li></ol>

<ol>
	<li>Maniatis, T., Jeffrey, A., van deSande, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chain+length+determination+of+small+double-+and+single-stranded+DNA+molecules+by+polyacrylamide+gel+electrophoresis.">Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis.</a> Biochemistry. 14, 3787-3794 (1975).</li><li>Albright, L. M., Slatko, B. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Denaturing+polyacrylamide+gel+electrophoresis.">Denaturing polyacrylamide gel electrophoresis.</a> Curr Protoc Nucleic Acid Chem. , (2001).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> PROTEAN II xi Cell and PROTEAN II xi 2-D Cell Instruction Manual. , (2001).</li></ol>

The authors have nothing to disclose.

<ol><li> La nitidezza banda dipende da diversi fattori. Il volume di campione caricato per bande forte deve essere il più piccolo possibile, cioè idealmente tra 1-5 microlitri. Tuttavia, fino a 15 microlitri può essere caricato che assicura ancora la risoluzione accettabile. Meno volume risultati dei campioni in più nitide bande. </li><li> La qualità di banda dipende anche dallo spessore del gel. Diluente gel, come ad esempio 0,75 millimetri mostrano risultati migliori gel a 1,5 mm di spessore. </li><li> La forma delle bande può anche ess...

denaturing urea polyacrylamide gel electrophoresis (urea page)

PAGINA urea o denaturazione poliacrilammide gel elettroforesi urea impiega 6-8 M urea, che denatura il DNA o le strutture secondarie dell&#39;RNA e viene utilizzato per la loro separazione in una matrice di gel di poliacrilammide in base al peso molecolare. Frammenti da 2 a 500 basi, con differenze di lunghezza piccolo come un singolo nucleotide, possono essere separati con questo metodo 1. La migrazione del campione dipende dalla concentrazione di acrilamide scelto. Una percentuale più alta di poliacrilammide risolve frammenti di peso molecolare inferiore. La combinazione di urea e temperature di 45-55 ° C durante la corsa del gel consente la separazione del DNA non strutturati o di molecole di RNA. In generale, questo metodo è necessario per analizzare o purificare DNA a singolo filamento o di frammenti di RNA, come oligonucleotidi sintetizzati o etichettati o prodotti da reazioni enzimatiche scissione. In questo articolo mostriamo il video come preparare ed eseguire il gel di poliacrilammide denaturante di urea. Consigli tecnici sono inclusi, oltre ai 1,2 protocollo originale.

Watch this Scientific Journal Video about Denaturing Urea Polyacrylamide Gel Electrophoresis Urea PAGE at JoVE.com

Denaturing Urea Polyacrylamide Gel Electrophoresis Urea PAGE

Denaturazione poliacrilammide gel elettroforesi urea viene utilizzato per separare singolo filamento di DNA o RNA fino ad un limite di 500 nucleotidi. Urea in combinazione con i campioni di calore denatura e non strutturati singoli filamenti migrano all&#39;interno della matrice gel in base al loro peso molecolare.

Denaturazione Urea elettroforesi su gel poliacrilammide (PAG Urea)

Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their ...

denaturing-urea-polyacrylamide-gel-electrophoresis-urea-page

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JoVE Journal

Biology

Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE)

78.6K Views.  Nanyang Technological University, Singapore - NTU. Denaturazione poliacrilammide gel elettroforesi urea viene utilizzato per separare singolo filamento di DNA o RNA fino ad un limite di 500 nucleotidi. Urea in combinazione con i campioni di calore denatura e non strutturati singoli filamenti migrano all'interno della matrice gel in base al loro peso molecolare.

Video: Denaturing Urea Polyacrylamide Gel Electrophoresis Urea PAGE

Denaturing Gradient Gel Electrophoresis (DGGE)

Denaturing Gradient Gel Electrophoresis DGGE

Okay.Hi, my name is Celeste Peterson and I'm a fellow at Harvard University studying microbial bio film communities. So I am profiling the bacterial communities by looking at their 60 N sequence and how this sequence changes over time in space. And to do that, I'm using DDGE.This is not a normal acry of my well, it needs to be kept at 60 degrees when it's run and the buffer needs to be pumped continuously. So we're gonna warm up the buffer for about an hour until it's at 60 degrees, and then we can run the towel. Now I'm gonna wash this plate with dilute uc solution, peeling around for impurities, andone, light that up.Anything like that can cause regularities. It is important to wipe off all the water. So when I assemble the gel, I'll put that chip on the outside of the gel.So the gel will be in between these two pieces of glass and the chip will be on the outside and it won't affect the gel in between. So now I'm gonna assemble the gel in these clamps and then I squeeze them together and tighten by turning to the right. As with any gel, it's important to make sure that the bottom is flush.To prevent making, we now turn the gel around and put it in here to get sealed with the gasket. So it's important when you do this that the gel, that the plates are actually lined up with the gasket here. So these knobs on the side then go in and you press down to type the seal.So this is a 30 mil syringe. And this part and this part come with the bio red kit and it just on like this. And that's just to get rid of the excess water in the tubes.So put the tubing onto the gel to load the gel. First you put an adapter into the tubing and then a needle look with that small adapter and put it right in the center of the gel just so it's fairly below the bottom glass. Then this wire adapter goes into the long tubing and it's going to connect to equal syringes containing the high and the low density solution.So these are pre-prepared solutions. The blue one, I've added a dye here that just indicates that this is the most denaturing solution and this is the least fitting train solution, the low density one. And they have everything in them.And now I'm gonna to make, gonna be Actually I twice as much the week. And once you've got the tempt, you have about five to seven minutes to fill the gel before the colon rises. And now we fill the syringe juice with the solution.So I'm gonna fill it with about 15 the solution. And then to get rid of any air bubbles, I'll turn it upside down and squeeze gently until that top air bubble is gone. Now this little screw here is gonna go into this groove.This adapter is gonna line up with this clamp here, and it's gonna get C clamped in very tightly. And then this tubing is gonna attach to the syringe. And the same thing is done on the other side with the high density matrix where it's time to deliver.And so I'm gonna be turning this wheel in a steady clockwise motion. And first the blue solution is gonna go out first because that's the the most in nature, and it's gonna form the bottom part of the gel. And then after a little while, the clear solution will start filling in the gel and the Gradient will be formed.One moment is the gently on an angle to And as soon as you finish pouring the gel to wash out your tubes immediately because they will polymerize Going, It's the group there. And then press down. So this little, And on the other side, I'll do the same thing.Okay.Hi, my name is Celeste Peterson and I'm a fellow at Harvard University studying microbial bio communities. So I am profiling the bacterial communities by looking at their 60 F sequence and how the sequence changes over time in space. And to do that, I'm using DDGE.So DGE is Dena gel electrophoresis. And basically the idea is that there's a gradient and the DNA, as it runs down the gradient gets de natured. And so different 16 species will stop at different points along the gradient.And so it ends up being a fingerprint of the different sexiness species in the community. So the goal of my experiment is to see who is in the community and how that's changing over time and space. And I can run the sexiness DDD gel and then I can cut out the bands and identify the species that are represented in each community.So one of the biggest issues when, when doing A DDG gel is to figure out the gradient that's the best. And so that is just something that needs to be played around with and figuring out for a particular community which type of gradient. So the one I'm using today is 35 to 55%urea.One of the big problems that can happen with this technique is that smears come up in in the leans. And I found for that, for whatever reason, one of the best things to do is to run the gels for a really long time and then the smears disappear. Well, today I'm just using it for general bacterial communities, but this can also be used for a specific family of bacteria to see how those change over time, and those tend to be very clean gels.You can also look at mutations in single genes with DDGE.

Denaturazione gel elettroforesi gradiente (DGGE)

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Biologia

Screening for Amyloid Aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis

Amyloid aggregation is associated with numerous protein misfolding pathologies and underlies the infectious properties of prions, which are conformationally self-templating proteins that are thought to have beneficial roles in lower organisms.  Amyloids have been notoriously difficult to study due to their insolubility and structural heterogeneity.  However, resolution of amyloid polymers based on size and detergent insolubility has been made possible by Semi-Denaturing Detergent-Agarose Gel Electrophoresis (SDD-AGE).  This technique is finding widespread use for the detection and characterization of amyloid conformational variants.  Here, we demonstrate an adaptation of this technique that facilitates its use in large-scale applications, such as screens for novel prions and other amyloidogenic proteins.  The new SDD-AGE method uses capillary transfer for greater reliability and ease of use, and allows any sized gel to be accomodated.  Thus, a large number of samples, prepared from cells or purified proteins, can be processed simultaneously for the presence of SDS-insoluble conformers of tagged proteins.

SDD-AGE is a useful technique for the detection and characterization of amyloid-like polymers in cells. Here we demonstrate an adaptation that makes this technique amenable to large-scale applications.

Lo screening per aggregazione amiloide di semi-denaturazione detergente-Agarosio elettroforesi su gel

Amyloid aggregation is associated with numerous protein misfolding pathologies and underlies the infectious properties of prions, which are ...

Fast and Sensitive Colloidal Coomassie G-250 Staining for Proteins in Polyacrylamide Gels

Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and high quantitation. Furthermore, it is completely compatible with mass spectrometric protein identification. But despite these advantages, CBB is regarded to be less sensitive than silver or fluorescence stainings and therefore rarely used for the detection of proteins in analytical gel-based proteomic approaches.
Several improvements of the original Coomassie protocol1 have been made to increase the sensitivity of CBB. Two major modifications were introduced to enhance the detection of low-abundant proteins by converting the dye molecules into colloidal particles: In 1988, Neuhoff and colleagues applied 20% methanol and higher concentrations of ammonium sulfate into the CBB G-250 based staining solution2, and in 2004 Candiano et al. established Blue Silver using CBB G-250 with phosphoric acid in the presence of ammonium sulfate and methanol3. Nevertheless, all these modifications just allow a detection of approximately 10 ng protein. A widely fameless protocol for colloidal Coomassie staining was published by Kang et al. in 2002 where they modified Neuhoff's colloidal CBB staining protocol regarding the complexing substances. Instead of ammonium sulfate they used aluminum sulfate and methanol was replaced by the less toxic ethanol4. The novel aluminum-based staining in Kang's study showed superior sensitivity that detects as low as 1 ng/band (phosphorylase b) with little sensitivity variation depending on proteins.
Here, we demonstrate application of Kang's protocol for fast and sensitive colloidal Coomassie staining of proteins in analytical purposes. We will illustrate the quick and easy protocol using two-dimensional gels routinely performed in our working group.

This video shall popularize a colloidal Coomassie G-250 staining protocol according to Kang et al. for the detection of average 4 ng protein in gels. The staining is completed within 2 hours and without any effort. We routinely use Kang's protocol for analytical purposes in gel-based proteomics.

Veloce e sensibile colloidale Coomassie G-250 colorazione per le proteine ​​in gel di poliacrilammide

Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and ...

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for Analysis of Multiprotein Complexes from Cellular Lysates

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other proteins (Sali, Glaeser et al. 2003). Thus, the study of protein-protein interaction networks requires the detailed characterization of MPCs to gain an integrative understanding of protein function and regulation. For identification and analysis, MPCs must be separated under native conditions. In this video, we describe the analysis of MPCs by blue native polyacrylamide gel electrophoresis (BN-PAGE). BN-PAGE is a technique that allows separation of MPCs in a native conformation with a higher resolution than offered by gel filtration or sucrose density ultracentrifugation, and is therefore useful to determine MPC size, composition, and relative abundance (Sch&auml;gger and von Jagow 1991); (Sch&auml;gger, Cramer et al. 1994). By this method, proteins are separated according to their hydrodynamic size and shape in a polyacrylamide matrix. Here, we demonstrate the analysis of MPCs of total cellular lysates, pointing out that lysate dialysis is the crucial step to make BN-PAGE applicable to these biological samples. Using a combination of first dimension BN- and second dimension SDS-PAGE, we show that MPCs separated by BN-PAGE can be further subdivided into their individual constituents by SDS-PAGE. Visualization of the MPC components upon gel separation is performed by standard immunoblotting. As an example for MPC analysis by BN-PAGE, we chose the well-characterized eukaryotic 19S, 20S, and 26S proteasomes.

Blue Native Polyacrylamide Gel Electrophoresis BN-PAGE for Analysis of Multiprotein Complexes from Cellular Lysates

In this video, we describe the characterization of multiprotein complexes (MPCs) by blue native polyacrylamide gel electrophoresis (BN-PAGE). In a first dimension, dialyzed cellular lysates are separated by BN-PAGE to identify individual MPCs. In a second dimension SDS-PAGE, MPCs of interest are further subdivided to analyze their constituents by immunoblotting.

Blu nativi poliacrilammide gel elettroforesi (BN-PAGE) per l&#39;analisi di complessi multiproteici da lisati cellulari

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other ...

Agarose Gel Electrophoresis for the Separation of DNA Fragments

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits2. During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel&#39;s molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight3. The leading model for DNA movement through an agarose gel is &#34;biased reptation&#34;, whereby the leading edge moves forward and pulls the rest of the molecule along4. The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation5; 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: 
 
1. Understand the mechanism by which DNA fragments are separated within a gel matrix 
2. Understand how conformation of the DNA molecule will determine its mobility through a gel matrix 
3. Identify an agarose solution of appropriate concentration for their needs 
4. Prepare an agarose gel for electrophoresis of DNA samples 
5. Set up the gel electrophoresis apparatus and power supply 
6. Select an appropriate voltage for the separation of DNA fragments 
7. Understand the mechanism by which ethidium bromide allows for the visualization of DNA bands 
8. Determine the sizes of separated DNA fragments 
&#160;

A basic protocol for the separation of DNA fragments using agarose gel electrophoresis is described.

Elettroforesi su gel agarosio per la separazione di frammenti di DNA

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from ...

Preparation of DNA-crosslinked Polyacrylamide Hydrogels

Mechanobiology is an emerging scientific area that addresses the critical role of physical cues in directing cell morphology and function. For example, the effect of tissue elasticity on cell function is a major area of mechanobiology research because tissue stiffness modulates with disease, development, and injury. Static tissue-mimicking materials, or materials that cannot alter stiffness once cells are plated, are predominately used to investigate the effects of tissue stiffness on cell functions. While information gathered from static studies is valuable, these studies are not indicative of the dynamic nature of the cellular microenvironment in vivo. To better address the effects of dynamic stiffness on cell function, we developed a DNA-crosslinked polyacrylamide hydrogel system (DNA gels). Unlike other dynamic substrates, DNA gels have the ability to decrease or increase in stiffness after fabrication without stimuli. DNA gels consist of DNA crosslinks that are polymerized into a polyacrylamide backbone. Adding and removing crosslinks via delivery of single-stranded DNA allows temporal, spatial, and reversible control of gel elasticity. We have shown in previous reports that dynamic modulation of DNA gel elasticity influences fibroblast and neuron behavior. In this report and video, we provide a schematic that describes the DNA gel crosslinking mechanisms and step-by-step instructions on the preparation DNA gels.

Our laboratory has developed DNA-crosslinked polyacrylamide hydrogels, a dynamic hydrogel system, to better understand the effects of modulating tissue stiffness on cell function. Here, we provide schematics, descriptions, and protocols to prepare these hydrogels.

Preparazione di DNA-reticolato poliacrilammide idrogel

Mechanobiology is an emerging scientific area that addresses the critical role of physical cues in directing cell morphology and function. For example, ...

Mucin Agarose Gel Electrophoresis: Western Blotting for High-molecular-weight Glycoproteins

Mucins, the heavily-glycosylated proteins lining mucosal surfaces, have evolved as a key component of innate defense by protecting the epithelium against invading pathogens. The main role of these macromolecules is to facilitate particle trapping and clearance while promoting lubrication of the mucosa. During protein synthesis, mucins undergo intense O-glycosylation and multimerization, which dramatically increase the mass and size of these molecules. These post-translational modifications are critical for the viscoelastic properties of mucus. As a result of the complex biochemical and biophysical nature of these molecules, working with mucins provides many challenges that cannot be overcome by conventional protein analysis methods. For instance, their high-molecular-weight prevents electrophoretic migration via regular polyacrylamide gels and their sticky nature causes adhesion to experimental tubing. However, investigating the role of mucins in health (e.g., maintaining mucosal integrity) and disease (e.g., hyperconcentration, mucostasis, cancer) has recently gained interest and mucins are being investigated as a therapeutic target. A better understanding of the production and function of mucin macromolecules may lead to novel pharmaceutical approaches, e.g., inhibitors of mucin granule exocytosis and/or mucolytic agents. Therefore, consistent and reliable protocols to investigate mucin biology are critical for scientific advancement. Here, we describe conventional methods to separate mucin macromolecules by electrophoresis using an agarose gel, transfer protein into nitrocellulose membrane, and detect signal with mucin-specific antibodies as well as infrared fluorescent gel reader. These techniques are widely applicable to determine mucin quantitation, multimerization and to test the effects of pharmacological compounds on mucins.

Mucins are high-molecular-weight glycoconjugates, with size ranging from 0.2 to 200 megadalton (MDa). As a result of their size, mucins do not penetrate conventional polyacrylamide gels and require larger pores for separation. We provide a detailed protocol for mucin agarose gel electrophoresis to assess relative quantification and study polymer assembly.

Mucina Agarosio elettroforesi su gel: Western Blotting per glicoproteine ​​ad alto peso molecolare


Mucins, the heavily-glycosylated proteins lining mucosal surfaces, have evolved as a key component of innate defense by protecting the epithelium against ...

Analysis of Mitochondrial Respiratory Chain Complexes in Cultured Human Cells using Blue Native Polyacrylamide Gel Electrophoresis and Immunoblotting

Mitochondrial respiration is performed by oxidative phosphorylation (OXPHOS) complexes within mitochondria. Internal and environmental factors can perturb the assembly and stability of OXPHOS complexes. This protocol describes the analysis of mitochondrial respiratory chain complexes by blue native polyacrylamide gel electrophoresis (BN-PAGE) in application to cultured human cells. First, mitochondria are extracted from the cells using digitonin, then using lauryl maltoside, the intact OXPHOS complexes are isolated from the mitochondrial membranes. The OXPHOS complexes are then resolved by gradient gel electrophoresis in the presence of the negatively charged dye, Coomassie blue, which prevents protein aggregation and ensures electrophoretic mobility of protein complexes towards the cathode. Finally, the OXPHOS complexes are detected by standard immunoblotting. Thus, BN-PAGE is a convenient and inexpensive technique that can be used to evaluate the assembly of entire OXPHOS complexes, in contrast to the basic SDS-PAGE allowing the study of only individual OXPHOS complex subunits.

This protocol demonstrates the analysis of mitochondrial respiratory chain complexes by blue native polyacrylamide gel electrophoresis. Here the method applied to cultured human cells is described.

Analisi dei complessi della catena respiratoria mitocondriale in cellule umane coltivate mediante elettroforesi in Gel di poliacrilammide nativo blu e Immunoblotting

Mitochondrial respiration is performed by oxidative phosphorylation (OXPHOS) complexes within mitochondria. Internal and environmental factors can perturb ...

Detection of Glycosaminoglycans by Polyacrylamide Gel Electrophoresis and Silver Staining

Sulfated glycosaminoglycans (GAGs) such as heparan sulfate (HS) and chondroitin sulfate (CS) are ubiquitous in living organisms and play a critical role in a variety of basic biological structures and processes. As polymers, GAGs exist as a polydisperse mixture containing polysaccharide chains that can range from 4000 Da to well over 40,000 Da. Within these chains exists domains of sulfation, conferring a pattern of negative charge that facilitates interaction with positively charged residues of cognate protein ligands. Sulfated domains of GAGs must be of sufficient length to allow for these electrostatic interactions. To understand the function of GAGs in biological tissues, the investigator must be able to isolate, purify, and measure the size of GAGs. This report describes a practical and versatile polyacrylamide gel electrophoresis-based technique that can be leveraged to resolve relatively small differences in size between GAGs isolated from a variety of biological tissue types.

This report describes techniques to isolate and purify sulfated glycosaminoglycans (GAGs) from biological samples and a polyacrylamide gel electrophoresis approach to approximate their size. GAGs contribute to tissue structure and influence signaling processes via electrostatic interaction with proteins. GAG polymer length contributes to their binding affinity for cognate ligands.

Rilevazione di glicosaminoglicani mediante elettroforesi su gel di poliacrilammide e colorazione dell'argento

Sulfated glycosaminoglycans (GAGs) such as heparan sulfate (HS) and chondroitin sulfate (CS) are ubiquitous in living organisms and play a critical role ...

Dissecting, Fixing, and Visualizing the Drosophila Pupal Notum

The pupae of Drosophila melanogaster are immobile for several days during metamorphosis, during which they develop a new body with a thin transparent adult integument. Their immobility and transparency make them ideal for in vivo live imaging experiments. Many studies have focused on the dorsal epithelial monolayer of the pupal&#160;notum because of its accessibility and relatively large size. In addition to the studies of epithelial mechanics and development, the notum has been an ideal tissue to study wound healing. After an injury, the entire epithelial repair process can be captured by live imaging over 6-12 h. Despite the popularity of the notum for live imaging, very few published studies have utilized fixed notum samples. Fixation and staining are common approaches for nearly all other Drosophila tissues, taking advantage of the large repertoire of simple cellular stains and antibodies. However, the pupal notum is fragile and prone to curling and distortion after removal from the body, making it challenging to complement live imaging. This protocol offers a straightforward method for fixing and staining the pupal notum, both intact and after laser-wounding. With this technique, the ventral side of the pupa is glued down to a coverslip to immobilize the pupa, and the notum is carefully removed, fixed, and stained. The notum epithelium is mounted on a slide or between two coverslips to facilitate imaging from the tissue&#39;s dorsal or ventral side.

Dissecting, Fixing, and Visualizing the Drosophila Pupal Notum

The present protocol details the preparation and visualization of fixed tissue of the Drosophila pupal notum. It can be used for either intact or wounded tissue, and the original architecture of the tissue is preserved. The procedures for dissecting, fixing, and staining are all described in this article.

Dissezione, fissaggio e visualizzazione della Drosophila Pupal Notum

The pupae of Drosophila melanogaster are immobile for several days during metamorphosis, during which they develop a new body with a thin transparent ...

Methods Article

Denaturazione Urea elettroforesi su gel poliacrilammide (PAG Urea)