Polyacrylamide Gel

A sparse sheet of polyacrylamide gel serves as an elastic base for anchoring rigid islands of SU-8 photoresist, such that translocation of the islands is adamant by the rigidity of polyacrylamide, the size of the islands, and forces applied by cells to the adhesive islands.

From: Methods in Prison cell Biology , 2014

Technologies to Engineer Cell Substrate Mechanics in Hydrogels

Makoto Funaki , Paul A. Janmey , in Biological science and Technology of Stem Cell Niches, 2017

8.1 Polyacrylamide Gels

Polyacrylamide gels have served equally an important tool to investigate the effect of substrate stiffness on cellular functions in various cell types since Pelham et al. reported that prison cell move and focal adhesion in fibroblasts are regulated by the stiffness of collagen-coated polyacrylamide gels. 62 One of the advantages of polyacrylamide gels is that they are biologically inert. Equally a result, tuning the stiffness of polyacrylamide gels by adjusting the concentrations of acrylamide and bisacrylamide, which affects the density of the polyacrylamide network, does not influence the biochemical holding of the gels. Thus, it is possible to assume that whatever departure in cellular functions observed betwixt cells seeded on polyacrylamide gels with different stiffness is attributable to the difference in the stiffness of gels. Past varying the concentrations of acrylamide and bisacrylamide, the range of stiffness can embrace that of nearly soft tissues (Fig. 23.two). 63 Still, this biological inertness of polyacrylamide prevents binding of cell surface receptors and adhesion molecules nowadays in the medium. Thus, to appoint in cells, adhesive molecules demand to be covalently linked to the gel by using cross-linkers, which take two functional groups; one binds to polyacrylamide and another binds to adherence molecules, such as collagen and fibronectin. half-dozen,64 One disadvantage of polyacrylamide gels is its limitation to 2-D civilization considering acrylamide is highly toxic before polymerization.

Figure 23.2. Mechanical properties of polyacrylamide substrates.

The shear modulus of polyacrylamide gels with a range of acrylamide (indicated as percents near data lines) to bis-acrylamide (indicated equally cross-linker) proportions was measured. The shear modulus (Thou), expressed in Pascal, increases at constant polymer mass with increasing cross-linker. Increasing the concentration of acrylamide from 3% to 12% besides creates a large stiffness range from 10 to 50,000   Pa. The solid line denotes the theoretical stiffness of a rubberlike network if every cross-link was elastically effective.

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Tissue Engineering science and Regenerative Medicine: Fundamentals

L. Vincent , A.J. Engler , in Comprehensive Biomaterials Two, 2017

5.5.3.two.ane Polyacrylamide

PA gels are inert, constructed hydrogels most normally used for poly peptide separation in gel electrophoresis. As PA gels are like shooting fish in a barrel to fabricate, accept widely tunable mechanical properties, and are easily functionalized with adhesive ligands, these substrates are besides well suited to report the effects of substrate modulus on a diversity of cellular functions detailed in Section 5.5.four. Polymerization of PA hydrogels occurs through a gratis radical-driven reaction where acrylamide and bis-acrylamide solutions in varying concentrations are mixed with a free radical source, nigh commonly ammonium persulfate. 74 The mechanical properties of the synthesized gels vary from ~0.ane to 100   kPa (Fig. 2), 18,75 where moduli values are based on mutual principles of condensed matter physics 76,77 ; college concentrations of acrylamide monomer yield stiffer gels (insets iii and four) due to increased chain entanglement. Increasing cross-linker concentration, on the other hand, generates more than physical tethers between the polymer backbone, thereby reducing individual chain flexibility and increasing the Immature׳s modulus of the textile (insets ii and iv). Uniform distribution of the gratis radical source or fifty-fifty mixing of the monomer and cross-linker generates static gels, 9 which are most commonly used for cell civilisation as they generate a roughly even cell response, making them suitable for many biochemical assays. However, PA gels can also be micropatterned with step or smoothen gradients of Young׳southward modulus made past polymerizing next gels of different moduli (Fig. 3(a)) 10,78 or by photoactivation of the gratis radical initiator Irgacure 2959 via gradients of UV initiation (Fig. 3(bi)) 79,80 or cross-linker concentration established in microchannels (Fig. 3(bii)), 57 respectively. Ultimately, these gradients study a prison cell׳south power to undergo durotaxis ('duro' being latin for hard), that is, the characteristic movement of a cell along a stiffness gradient, and each of these techniques yields different gradient strengths, which has recently been shown to be of import for cell behavior. 81 However, one of the main drawbacks to using PA substrates is acrylamide and initiator cytotoxicity. Gels must oft be soaked in buffer earlier use to allow unreacted species to diffuse out of the substrates, thus limiting these polymers to 2D in vitro studies.

Fig. ii. Rubberband modulus of range of polyacrylamide gels. Elastic modulus of polyacrylamide substrates for gels with different concentrations of acrylamide monomer and bis-acrylamide cross-linker. Substrates polymerized in solutions with college concentrations of acrylamide monomer yield stiffer gels (insets iii and 4) due to increased chain entanglement and nonspecific interactions between polymer chains. Adding increasing amounts of cantankerous-linker in the polymerization mixture generates more concrete tethers between the backbone of polymers and increases the Young׳s modulus of the material (insets two and iv).

Fig. 3. Methods to generate stiffness gradients. Several photolithographic methods accept been used in synthetic systems to generate spatial gradients of stiffness, including (a) using sequential polymerization to generate footstep gradients and (b) photoactivatable methods where gradients are formed either by spatially controlling solution exposure to UV (i) or by employing microfluidic mixing to have cantankerous-linker gradients with uniform activation (ii). Each of the latter cases can yield moduli of different ranges, which is critical for cell sensing.

To facilitate jail cell attachment to the nonadhesive PA, proteins are usually covalently attached to the PA gel surface. Incubation with Northward-sulfosuccinimidyl-6-(4′-azido-2′-nitrophenylamino) hexanoate (sulfo-SANPAH), a UV-activatable cross-linker, 4 or hydrazine hydrate 82 allows for covalent tethering of ECM proteins such as fibronectin, 83 collagen, 84 or combinations of proteins 85 onto PA gels. In addition, spatial distribution of proteins has been achieved on PA gels using micropatterning 86,87 and microcontact printing. 85 Varying the concentration of solubilized protein added to these synthetic matrices allows for more than or fewer cell attachment sites, assuasive investigators to control the adhesion strength of cells on these matrices. eight

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Ribonucleases - Function A

A.D.J. Scadden , Sorem Naaby-Hansen , in Methods in Enzymology, 2001

Materials

SDS–PAGE apparatus: We apply gels of approximately 17cm × 12cm × 0.8 mm. Drinking glass gel plates are baked at 200° for iv–6 h prior to assembly and Teflon spacers and combs are done thoroughly with ii% SDS before use.

Polyacrylamide gel mixes: Ensure acrylamide is of high quality and deionised before utilise (this is important for recovery of enzyme action after electrophoresis):

Resolving gel:

12.5%: 12.five% acrylamide (A), 0.1% bisacrylamide(B); fifteen%: fifteen% A, 0.087% B; 20%: twenty% A, 0.066% B. 375 gM Tris-HCl, pH 8.eight; 50 μl 10% (v/v) ammonium persulfate and five μl TEMED are added per ten ml gel mix.

Stacking gel:

v% acrylamide, 0.13% bisacrylamide, 125 mThou Tris-HCl, pH six.8; 50 μl ten% (v/v) ammonium persulfate and five μfifty TEMED are added per 5 ml gel mix.

2 × poly peptide sample buffer: 4% SDS, 160 mG Tris-HCl, pH half dozen.8, 20% (5/five) glycerol, 0.05% bromphenol blue. A reducing agent such as 2-mercaptoethanol [x% (v/v)] may exist added (see note i).

Prestained protein molecular weight markers (Bill; broad range)

Poly peptide molecular weight markers: Our standard molecular weight markers contain the following components: β-galactosidase (116 kDa), phosphorylase b (97 kDa), bovine serum albumin (BSA) (68.5 kDa), catalase (57.5 kDa), glutamate dehydrogenase (55.5 kDa), creatine kinase (43 kDa), glyceraldehyde-3-phosphate dehydrogenase (36 kDa), carbonic anhydrase (29 kDa), and RNase A (13.7 kDa). Molecular weight markers are prepared in the presence of a reducing agent such as 2-mercaptoethanol.

Substrate RNA is transcribed from a suitable plasmid using T3, T7, or SP6 RNA polymerase. RNAs are internally labeled using whatever [α-32P]NTP (3000 Ci/mmol, 10 Ci/μ50; Amersham); we normally apply [α-32P]UTP. RNA substrates are labeled to a specific activity of approximately one × 106 cpm/pmol. This is accomplished by using x μCi [α32P]UTP and 0.25 chiliadM unlabeled UTP in a 10 μfifty transcription reaction. The terminal RNA concentration used for the in-gel assays is 0.v μg/ml (this is equivalent to v pmol/ml for a 300 nt RNA substrate, as used to assay p29). Inosine-containing RNA (I-RNA), generated past substituting GTP with ITP in the transcription reaction, was generally used to assay p29. Other modifications to the RNA may be made if necessary for assaying particular ribonucleases.

Glass dish (approximately 14 cm × xx cm; baked at 200° for 4–6 h). A glass plate larger than the dish should be used as a chapeau to shield radioactive decay.

Assay buffer every bit appropriate for assaying enzyme of interest (20 mM HEPES–KOH, pH vii.9, v thouM MgCl2 for p29).

Analysis buffer plus 20% (v/v) 2-propanol.

Rocking platform or shaker.

Perspex (Plexiglas) screen (at least 1 cm thick) to shield beta emission. All steps preceding and post-obit electrophoresis should be performed behind this screen.

Benchkote (squares of approximately l cm × 50 cm). All manipulations of the gel should be performed on squares of Benchkote. Any radioactive contamination is thus contained and may be disposed of immediately.

Geiger–Müller radioactivity monitor. All piece of work areas should be closely monitored for radioactivity earlier and after apply.

Fuji Film, standard autoradiography, and/or phosphorimaging apparatus.

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Protein | Determination and Characterization

D. Otter , in Encyclopedia of Food Sciences and Nutrition (2nd Edition), 2003

Polyacrylamide gel electrophoresis

Polyacrylamide gels are iii-dimensional networks of acrylamide reacted with the bifunctional reagent N,N'-methylene-bis-acrylamide (abbreviated as Bis) via a free-radical initiated vinyl polymerization mechanism. The pore size of the gel is very reproducible and is direct related to the ratio of acrylamide to Bis. The resulting gels are described in terms of %T, the concentration (w/five) of acrylamide and Bis, and %C, the weight percentage of the cantankerous-linker in T. For proteins, %T values of 5–10% result in gels with relative molecular mass (G r) ranges of 20 000–200 000 Da. Separation of proteins in complex samples based on size, net charge, and hydrophobicity is possible using different polyacrylamide gel electrophoresis (PAGE) formats.

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Separation and Sequencing of Heparin and Heparan Sulphate Saccharides

Mark A. Skidmore , Jeremy E. Turnbull , in Chemistry and Biology of Heparin and Heparan Sulfate, 2005

1 Polyacrylamide Gel Electrophoresis

Polyacrylamide gels are created by the polymerization of acrylamide monomers with the N,N-methlylenebisacrylamide cross-linker. The pore size, formed inside the gel, is dependent on the amount of cross-linking and the lengths of the polymer chains. Ammonium persulphate is usually used as the complimentary radical initiator while Due north,Due north,N',N'-tetramethylenediamine (TEMED) stabilizes the polymerization chain reaction. The chain reaction is inhibited by molecular oxygen so the polymerization is conventionally carried out betwixt two thin glass plates with the elevation of the gel solution covered with water-saturated butanol. Gels used for sequencing, etc. [such as in integral glycan sequencing (IGS)] are more often than not run on a vertical platform apparatus.

For the analysis of oligosaccharides derived from heparin and heparan sulphate a 33% polyacrylamide gel (with nineteen:1 acrylamide:bisacrylamide cross-linker) has been found to give practiced separation. The concentration of the acrylamide solution can however be adapted though to give more tailored average pore sizes and hence separation ranges. Slope gels can be used, just these are difficult to bandage and reproducibility poses a serious trouble. Unlike protein electrophoresis, carbohydrate gels are in the native form and hence the carbohydrate conformation (and thus mobility) will depend on the verbal oligosaccharide structures present within. Therefore, a simple directly migration distance to size relationship cannot be achieved.

A mutual method for visualization of unlabeled oligosaccharides is the blue dye Azure A. Staining occurs due to ionic interactions with the highly negative accuse sulphate and carboxylic acid groups nowadays in this class of carbohydrate. Background staining can easily be removed by washing with double-distilled water. The limit of detection is in the order of a few micrograms (13). Detection of oligosaccharides separated on gels can too be achieved using radiolabels (19) or fluorescent tags (twenty) and preparative scale purification of saccharides is as well possible (21).

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Techniques for Protein Analysis

Gülay Büyükköroğlu , ... Candan Hızel , in Omics Technologies and Bio-Engineering, 2018

xv.1.three.1 Polyacrylamide Gel Electrophoresis

Polyacrylamide gels are based on the free radical polymerization principle of acrylamide and cross-linking N,N′-methylene-bis-acrylamide. This material is physically very stable and stiff. Information technology is peculiarly used for the electrophoretic separation of small or medium sized (upwards to about ane×10half dozen  Da) proteins. Its interaction with the migrating molecules is at the lowest level. The separating power of this gel depends on the dimension of the molecule to exist separated too as the concentration of acrylamide and bis-acrylamide. Depression concentration acrylamide and bis-acrylamide polymerization is preferred to prepare gels with larger pores for high molecular weight samples. The difference of polyacrylamide gel electrophoresis (Page) from gel permeation chromatography is that pocket-size molecules move faster in polyacrylamide gels in comparison with larger molecules (Sadeghi et al., 2006). A standard gel used for the separation of proteins generally contains well-nigh vii.5% polyacrylamide.

Pore size in polyacrylamide gels is determined with the values of %T [full polyacrylamide percent (w/v)] and %C bis [the ratio of bis to monomer (w/w)] using the following formulae:

% T = Acrylamide ( g ) + Bis ( g ) Volume ( mL ) × 100

% C bis = Bis ( g ) Acrylamide ( g ) + Bis ( 1000 ) × 100

Page is given different names according to the blazon of gel (tube and slab gel electrophoresis or continuous and discontinuous gel electrophoresis), the position of the gel (vertical and horizontal gel electrophoresis), the chemical composition of the gel (native and sodiumdodecylsulfate (SDS), gel electrophoresis), and the pore distribution of the gel (homogeneous and slope gel electrophoresis) (Wenk and Fernandis, 2007).

In tube PAGE, glass tubes (ten   cm×6   mm) are used and the gel textile is filled into these tubes and polymerization is attained. Gel tube is placed vertically between 2 different buffer stocks. Cathode is generally located in the upper stock, whereas anode is located in the lower stock. Since most of the biologic materials are negatively charged, they move toward the anode. Hence, the sample to be analyzed is applied on the upper section of the gel with a tracking dye and electrical current is passed through the arrangement. Since the tracking dye moves faster than the compounds in the sample, the current is stopped when it reaches the end of the gel, the gel is taken out of the tube and dyed.

Slab gels are used more in comparison with the columns since they enable the analysis of many samples in the same back up surround (at the same conditions). Polyacrylamide gel is prepared betwixt two drinking glass plates (Fig. 15.2). A plastic comb placed on the top of the gel during polymerization enables the formation of minor wells in the gel. The comb is removed afterwards polymerization, the wells are done with the buffer in club to remove the salts and unpolymerized acrylamide. The gel cassette is placed between two buffers; samples are placed within the wells and current is passed. The gel is painted appropriately at the cease of the electrophoresis for imaging.

Figure 15.2. Schematic diagram of polyacrylamide gel electrophoresis.

SDS anionic detergent is used in SDS-PAGE in club to denaturate the proteins surrounding the main skeleton of the polypeptides also as to give a negative charge to the molecules (Černý et al., 2013). The motility rate of the polypeptides in this method depends on molecular weight too as internal electrical loads. Thus, it is a method that is oft used for determining the molecular weights of the practical samples. A protein sample with unknown molecular weight is applied side by side with a protein of known molecular weight on the same gel and then is separated electrophoretically in different lines. The comparison of the bands on the gel after painting gives an idea about the molecular weight of the poly peptide. In addition, it is besides possible to determine the molecular weight by evaluating the results of this separation mathematically (Righetti et al., 2001).

Two different buffer systems, continuous and discontinuous, can be used in electrophoresis. In that location is only one separating gel in continuous organisation; the same buffer is used in the tanks and the gel. Whereas in the discontinuous organization two-sided gel preparation with dissimilar buffers is used. The "stacking" gel with its large porous structure is located at the upper side of the gel providing the social club of the applied sample in terms of its size. Whereas the "separating" gel with modest pores is located at the lower side of the gel and and then provides a more than sensitive separation of the sample. The buffers used in the preparation of the gels are dissimilar from each other. In addition, the tank buffers are prepared differently than the gel buffers so that a better separation can be attained. Slope gels are as well used to provide this feature. Acrylamide concentration is gradually increased in gradient gels as we go down from the upper department of the gel. Thus, it is ensured that the pores in the gel decrease in size gradually as we motility down. Polypeptides with similar molecular weights are separated more efficiently in this type of gel and form sharper bands (Bolt and Mahoney, 1997).

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ELECTROPHORESIS | Overview

R. Stringer , in Encyclopedia of Analytical Science (Second Edition), 2005

Polyacrylamide Gel Electrophoresis

Polyacrylamide gels are made by chemic polymerization of a mixture of acrylamide and bisacrylamide (a cross-linker) in the presence of a catalyst and an initiator of the polymerization reaction. The porosity of the gel is determined past the relative concentration of acrylamide to cross-linker and by the total percent of monomers. The final concentration of acrylamide depends on the sample under written report with loftier acrylamide concentrations giving better resolution of low molecular mass proteins, and vice versa. The gels tin be prepared with a high degree of reproducibility. It is possible to finely tailor the gel pore size, for example, by preparing gradient gels where the acrylamide concentration tin vary from 5% to 20% in the same gel, making it possible to separate a mixture of molecules with very varying molecular mass values. Past varying gel and buffer parameters it is possible to separate samples on the basis of charge, size, or a combination of charge and size. Gels tin be formed into either tubes or slabs and can be used for assay or preparatively. Polyacrylamide gel electrophoresis (Folio) is routinely used for protein analysis, and can also be used to separate nucleic acid fragments smaller than 100  bp. Nucleic acids are normally analyzed using a continuous buffer system where there is a constant buffer composition, pH, and pore size throughout the gel. Native proteins can be separated co-ordinate to differences in their charge density, so long equally the buffer in the gel is suitable for maintaining the protein in its native state. This enables enzyme preparations to exist assessed for purity and also allows their activity to exist assayed after the separation.

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Drug Discovery Technologies

G.1000.T. Bauer , Yard. Schnapp , in Comprehensive Medicinal Chemistry Ii, 2007

3.nineteen.viii.1.2 Native and isoelectric focusing polyacrylamide gel electrophoresis

Polyacrylamide gels with nondenaturated poly peptide samples deliver boosted knowledge: in the absence of SDS and β-ME or DTT, the proteins become separated according to a combination of molecular weight and overall charge: the larger the protein, the shorter the sample propagation; and the more negatively charged the poly peptide is, the faster information technology moves toward the cathode. Proteins with IP higher than the pH of the buffer organisation of the electrophoresis will not move toward the cathode. Proteins that occur with mono-, di-, or an even college aggregated country volition testify upwardly as different bands on a native gel. Separation of proteins in an electrical field under native conditions gives an approximation of the uniformity of a protein's aggregation status. The protein moves in an electrical field which, depending on whether its net charge is toward the anode or cathode, will bear upon the separation distance, depending on the size of the molecule. After staining with Coomassie, the proteins forming dimers or larger aggregates may show a ladder of bands related to the different molecular weights of the aggregates ( Effigy 5).

Isoelectric focusing gels too consist of polyacrylamide, but also contain ampholyte (bivalently charged molecules) mixtures (varieties from pH 2 to 9.5 are bachelor), to separate the proteins according to their isoelectric points (Figure v). The conclusion of the isoelectric signal of the purified protein is necessary to determine which ion commutation chromatography method to use for separation (with a cation or anion exchanger) and to analyze the posttranslational modifications of the protein of interest: phosphorylation and glycosylation can shift the IP of a protein far away from the ane originally calculated.

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Laboratory Methods in Enzymology: Protein Part C

Krisna C. Duong-Ly , Sandra B. Gabelli , in Methods in Enzymology, 2014

8 Step four Clarify Protein Expression past SDS-Folio

8.1 Overview

A polyacrylamide gel will be run and stained to determine the amount of protein expressed (see One-dimensional SDS-Polyacrylamide Gel Electrophoresis (1D SDS-PAGE)).

viii.2 Duration

45   min

four.i

Load 10 μl of the samples generated in Steps 2 and iii onto a polyacrylamide gel and carve up proteins by SDS-Page.

4.two

Stain the gel with Coomassie blue to quantify expression (see Coomassie Bluish Staining).

four.3

Decide the distribution of the protein amid the total jail cell extract, the insoluble fraction, and the soluble fraction.

8.3 Tip

If a large corporeality of the protein is in the pellet and very picayune or none is present in the supernatant after cell lysis, in that location is a solubility problem. If in that location is no band for the desired protein, in that location may be a general expression problem (see Explanatory Chapter: Troubleshooting recombinant protein expression: general).

eight.4 Tip

Silver staining (see Silvery Staining of SDS-polyacrylamide Gel ), immunoblotting (come across Western Blotting using Chemiluminescent Substrates), and enzymatic assays can be used if the level of protein expression is below the level of detection for Coomassie blue staining.

8.5 Tip

In gel filtration chromatography (see Gel filtration chromatography (Size exclusion chromatography) of proteins ), protein species may elute at the void volume. This suggests that the poly peptide may exist equally a soluble aggregrate.

See Fig. 18.4 for the flowchart of Step iv.

Effigy 18.4. Flowchart of Footstep four.

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Micropatterning in Jail cell Biological science Part C

C.H.R. Kuo , ... E. Sivaniah , in Methods in Jail cell Biology, 2014

four.2.three Method

Polyacrylamide gel premixes of known bulk shear modulus were prepared co-ordinate to the procedures developed past Moshayedi et al. (2010). The gel template is prepared on the day of cell deposition.

1.

Use the tabular array beneath to set a 500-μl gel premix of the desired mechanical properties. For gel staining, 1% (west/v) fluorescein FDMA in DMSO is added to the gel premix. In some cases, fluorescein may amass to form insoluble precipitate in this mixture. To remove the particulates, centrifuge at 10   × g for 3   min and carefully transfer the supernatant to a new Eppendorf tube.

Shear modulus G 100   Pa 300   Pa 1000   Pa 3.3   kPa ten   kPa thirty   kPa
PBS (μl) 392.5 362.5 341 351 295 170
40% Acrylamide (μl) 62.five 62.5 94 94 150 225
two% Bis-Acrylamide (μl) 40 70 60 fifty 50 100
Stain (FDMA) (μl) v v v 5 v v
2.

Place the gel premix in a vacuum desiccator for 15   min to remove all dissolved gas.

iii.

Add ane.5   μl TEMED and 5   μl x% APS to the gel premix, mix the solution, and pipette xx–50   μl of the mixture onto the treated glass template. Avoid any intense mixing, which may innovate air into the solution. The corporeality of gel premix added will decide the final gel thickness.

4.

Gently place the RainX-treated height glass coverslip. If the desired effect is to produce gel thickness of less than ten μm, place a small weight on top of the glass coverslip and use tissue newspaper to wipe away the excess gel premix.

5.

Use the remaining gel premix in the tube to determine the extent of cantankerous-link. Depending on the ratio of monomers and cross-linkers, complete cross-linking volition take approximately 15   min.

vi.

Immerse the entire template in PBS for 30   min. And then gently slide the top coverslip off with the help of tweezers.

7.

In the hood, treat the gel template with hydrazine hydrate for 3   h.

8.

Remove the hydrazine hydrate, and treat the gel template with 5% (v/v) acerb acid in distilled water for 1   h.

9.

Move the gel template into a sterile laminar catamenia cabinet, and wash the gel 3 times in sterile PBS for ten, xx, and 30   min, respectively.

10.

To facilitate jail cell adhesion, the gels should be immersed in 100-μg/ml PDL solution and left in the incubator for at least 1   h.

eleven.

Launder the gel 3 times in PBS using the same intervals as before.

12.

Soak the gel in tissue civilization media for at least 10   min prior to cell deposition.

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