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Polyacrylamide gels

Polyacrylamide gels are a widely-used analytical tool in biochemistry and molecular biology.
These versatile gel matrices are employed for the separation and characterization of proteins, nucleic acids, and other biomolecules.
Optimizing reproducibility with polyacrylamide gels is crucial for consistent research results.
PubCompare.ai's AI-driven platform can help streamline this process by identifying the most effective protocols from literature, pre-prints, and patents.
Their AI-powered analysis pinpoints the best methods and products to achieve reliable, consistent outcomes.
Leveraging PubCompare.ai can help researchers optimizie their polyacrylamidie gel workflows and streamline their studies.

Most cited protocols related to «Polyacrylamide gels»

1
CRISPR Efficiency Measurement by SURVEYOR Assay
293FT and HUES9 cells were transfected with DNA as described above. Cells were incubated at 37 °C for 72 h post-transfection before genomic DNA extraction. Genomic DNA was extracted using the QuickExtract DNA Extraction Solution (Epicentre) following the manufacturer's protocol. Briefly, pelleted cells were resuspended in QuickExtract solution and incubated at 65 °C for 15 min, 68 °C for 15 min, and 98 °C for 10 min.
The genomic region flanking the CRISPR target site for each gene was PCR amplified (target sites and primers listed in Supplementary Tables 1 and 2), and products were purified using QiaQuick Spin Column (Qiagen) following the manufacturer's protocol. 400 ng total of the purified PCR products were mixed with 2 μl 10× Taq DNA Polymerase PCR buffer (Enzymatics) and ultrapure water to a final volume of 20 μl, and subjected to a re-annealing process to enable heteroduplex formation: 95 °C for 10 min, 95 °C to 85 °C ramping at −2 °C/s, 85 °C to 25 °C at −0.25 °C/s, and 25 °C hold for 1 min. After re-annealing, products were treated with SURVEYOR nuclease and SURVEYOR enhancer S (Transgenomics) following the manufacturer's recommended protocol, and analyzed on 4–20% Novex TBE polyacrylamide gels (Life Technologies). Gels were stained with SYBR Gold DNA stain (Life Technologies) for 30 min and imaged with a Gel Doc gel imaging system (Bio-rad). Quantification was based on relative band intensities. Indel percentage was determined by the formula, 100 × (1 − (1 − (b + c)/(a + b + c))1/2), where a is the integrated intensity of the undigested PCR product, and b and c are the integrated intensities of each cleavage product.
Hsu P.D., Scott D.A., Weinstein J.A., Ran F.A., Konermann S., Agarwala V., Li Y., Fine E.J., Wu X., Shalem O., Cradick T.J., Marraffini L.A., Bao G, & Zhang F. (2013). DNA targeting specificity of RNA-guided Cas9 nucleases. Nature biotechnology, 31(9), 827-832.
Publication 2013
Buffers Cells Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Genes Genome Gold H-DNA INDEL Mutation Oligonucleotide Primers polyacrylamide gels Stains Taq Polymerase Transfection
2
Electrophoretic Separation and Blotting of RNA
All RNA samples were separated by electrophoresis using either 10 or 15% polyacrylamide (19:1) gels cast in 7 M urea and buffered with 20 mM MOPS/NaOH (pH 7) using a Protean II rig (Bio-Rad). Tris-based buffers were avoided as it was anticipated that these might interfere with the EDC-mediated cross-linking step. The electrophoresis buffer was 20 mM MOPS/NaOH (pH 7). RNA markers were 32γP-end-labelled Decade® RNA markers (Ambion) prepared according to the manufacturer's instructions. After gel electrophoresis, gels were stained with ethidium bromide (EtBr) or SybrGold® (Molecular Probes) and imaged on a FLA-5000 system (Fuji) with Aida Image Analyser software to visualize and record the amount and distribution of the RNA.
For blotting, gels were placed over a sheet of nylon hybridization membrane (Hybond-NX®, Amersham/Pharmacia) that had been pre-wetted in distilled water. This was then sandwiched between pieces of 3MM® Whatman filter paper (three layers on each side), also pre-wetted in distilled water and placed in a ‘semidry’ electroblotter (SciPlas). Excess liquid and air bubbles were squeezed from the sandwich by rolling the surface with a clean pipette. Electrophoretic transfer of RNA from the gel to the membrane was carried out at 20 V at 4°C for 30–60 min.
Pall G.S., Codony-Servat C., Byrne J., Ritchie L, & Hamilton A. (2007). Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Research, 35(8), e60.
Publication 2007
Buffers CD3EAP protein, human Crossbreeding Edema Electrophoresis Ethidium Bromide Molecular Probes morpholinopropane sulfonic acid Nylons polyacrylamide Tissue, Membrane Transfer RNA Urea
3
CRISPR Target Sequence Analysis Protocol
Genomic DNA of HEK293T cells or zebrafish embryos was extracted at 50 hpf using a genome DNA extraction kit (Tiangen) following the manufacturer's protocol. In brief, cells or embryos were resuspended in cell lysis solution and incubated at 65 °C for 15 min and 95 °C for 10 min. The genomic region surrounding the CRISPR target site for each gene was PCR amplified and cloned into the pEASY vector (Transgen), which was used for Sanger sequencing (Biomed, Beijing). A total of 200-400 ng PCR products (TakaRa) were subjected to a re-annealing process to enable heteroduplex formation: 95 °C for 10 min, 95 °C to 85 °C ramping at 2 °C/s, 85 °C to 25 °C at 0.3 °C/s and holding at 25 °C for 1 min. After re-annealing, products were treated with SURVEYOR nuclease and SURVEYOR enhancer S (Transgenomic), following the manufacturer's recommended protocol, and analyzed on 10% polyacrylamide gels. Gels were stained with 0.5 μg/ml EtBr in 1× TBE for 20 min, washed in water for 20 min and imaged with a gel-imaging system (Tanon). Quantification was based on relative band intensity.
Chang N., Sun C., Gao L., Zhu D., Xu X., Zhu X., Xiong J.W, & Xi J.J. (2013). Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos. Cell Research, 23(4), 465-472.
Publication 2013
Cells Cloning Vectors Clustered Regularly Interspaced Short Palindromic Repeats EDNRB protein, human Embryo Genes Genome MMP2 protein, human polyacrylamide gels Zebrafish
4
Collection and Characterization of Nanoparticulate Matter
nPM collection and transfer into aqueous suspension. We collected nPM with a high-volume ultrafine particle (HVUP) sampler (Misra et al. 2002 ) at 400 L/min flow in Los Angeles City near the CA-110 Freeway. These aerosols represent a mix of fresh ambient PM mostly from vehicular traffic nearby this freeway (Ning et al. 2007 (link)). The HVUP sampler consists of an ultrafine particle slit impactor, followed by an after-filter holder. The nPM (diameter < 200 nm) was collected on pretreated Teflon filters (20 × 25.4 cm, polytetrafluoroethylene, 2 μm pore; Pall Life Sciences, Covina, CA). We transferred the collected nPM into aqueous suspension by 30 min soaking of nPM-loaded filters in Milli-Q deionized water (resistivity, 18.2 MW; total organic compounds < 10 ppb; particle free; bacteria levels < 1 endotoxin units/mL; endotoxin-free glass vials), followed by vortexing (5 min) and sonication (30 min). As a control for in vitro experiments with resuspended nPM, fresh sterile filters were sham extracted. Aqueous nPM suspensions were pooled and frozen as a stock at –20°C, which retains chemical stability for ≥ 3 months (Li N et al. 2003; Li R et al. 2009). For in vitro experiments, nPM suspensions were diluted in culture medium, vortexed, and added directly to cultures.
Animals and exposure conditions. The nPM suspensions were reaerosolized by a VORTRAN nebulizer (Vortran Medical Technology 1 Inc., Sacramento, CA) using compressed particle-free filtered air [see Supplemental Material, Figure S1 (doi:10.​1289/ehp.1002973)]. Particles were diffusion dried by passing through silica gel; static charges were removed by passing over polonium-210 neutralizers. Particle sizes and concentrations were continuously monitored during exposure at 0.3 L/min by a scanning mobility particle sizer (SMPS model 3080; TSI Inc., Shoreview, MN). The nPM mass concentration was determined by pre- and postweighing the filters under controlled temperature and relative humidity. Inorganic ions [ammonium (NH4+), nitrate (NO3–), sulfate (SO42–)] were analyzed by ion chromatography. PM-bound metals and trace elements were assayed by magnetic-sector inductively coupled plasma mass spectroscopy. Water-soluble organic carbon was assayed by a GE-Sievers liquid analyzer (GE-Sievers, Boulder, CO). Analytic details for nPM-bound species are given by Li R et al. (2009). Samples of the reaerosolized nPM were collected on parallel Teflon filters for electron paramagnetic resonance (EPR) analysis.
Mice (C57BL/6J males, 3 months of age) were maintained under standard conditions with ad libitum Purina Lab Chow (Newco Purina, Rancho Cucamonga, CA) and sterile water. Just before nPM exposure, mice were transferred from home cages to exposure chambers that allowed free movement. Temperature and airflow were controlled for adequate ventilation and to minimize buildup of animal-generated contaminants [skin dander, carbon dioxide (CO2), ammonia]. Reaerosolized nPM or ambient air (control) was delivered to the sealed exposure chambers for 5 hr/day, 3 days/week, for 10 weeks. Mice did not lose weight or show signs of respiratory distress. Mice were euthanized after isoflurane anesthesia, and tissue was collected and stored at –80°C. All rodents were treated humanely and with regard for alleviation of suffering; all procedures were approved by the University of Southern California Institutional Animal Care and Use Committee.
EPR spectroscopy of nPM. The reaerosolized nPM was collected on filters (described above), which were inserted directly in the EPR quartz tube (Bruker EPR spectrometer; Bruker, Rheinstetten, Germany); spectra were measured at 22°C. The g-value was determined following calibration of the EPR instrument using DPPH (2,2-diphenyl-1-picrylhydrazyl) as a standard. The EPR signal for DPPH was measured and the corresponding g-value was calculated. The difference from the known g-value of 2.0036 for DPPH was then used to adjust the observed g-value for the sample.
Cell culture and nPM exposure. Hippocampal slices from postnatal day 10–12 rats were cultured 2 weeks in a humidified incubator (35°C/5% CO2) (Jourdi et al. 2005 (link)) with nPM suspensions added for 24–72 hr of exposure. Primary neurons from embryonic day 18 rat cerebral cortex were plated at 20,000 neurons/cm2 on cover slips coated with poly-d-lysine/laminin and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with B27, at 37°C in 5% CO2 atmosphere (Rozovsky et al. 2005 (link)). Primary glial cultures from cerebral cortex of neonatal day 3 rats (F344) were plated at 200,000 cells/cm2 in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% l-glutamine and incubated as described above (Rozovsky et al. 1998 (link)). For conditioned medium experiments, glial cultures were treated with 10 mg nPM/mL; after 24 hr, media were transferred by pipette to neuron cultures.
Neurite outgrowth and toxicity assays. After treatments, neurons were fixed in 4% paraformaldehyde and immunostained with anti–β-III-tubulin (1:1,000, rabbit; Sigma Chemical Co., St. Louis, MO); F-actin was stained by rhodamine phalloidin (1:40; Molecular Probes, Carlsbad, CA). A neurite was defined as a process extending from the cell soma of the neuron that was immunopositive for both β-III-tubulin (green) and F-actin (red). The length of neurites was measured using NeuronJ software (Meijering et al. 2004 (link)). Growth cones were defined by the presence of actin-rich filopodia and lamellipodia (Kapfhammer et al. 2007 ). Collapsed growth cones were defined as actin-rich neuritic endings in which filopodia and lamellipodia were indistinguishable. In neurite outgrowth and growth cone collapse assays, individual neurons were selected from two cover slips per condition; n is the total number of neurons analyzed per treatment. Cytotoxicity in slice cultures was assayed by lactate dehydrogenase (LDH) release to media and by cellular uptake of propidium iodide (PI) (Jourdi et al. 2005 (link)). Neuronal viability was assayed by Live/Dead Cytotoxicity Kit (Invitrogen, Carlsbad, CA) by computer-assisted image analysis of fluorescent images. Mitochondrial reductase was assayed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) at 585 nm in undifferentiated PC12 cells (Mosmann 1983 (link)). For viability assays, n is the total number of hippocampal slices analyzed (LDH release and PI uptake) or the total number of cell culture wells analyzed per condition.
Immunoblotting. Mouse hippocampi were homogenized using a glass homogenizer in cold lysis buffer as described by Jourdi et al. (2005) (link). After sample preparation, 20 μg protein was electrophoresed on 10% sodium dodecyl sulfate polyacrylamide gels, followed by transfer to polyvinylidene fluoride (PVDF) membranes. The PVDF membranes were blocked with 5% bovine serum albumin for 1 hr and probed with primary antibodies overnight at 4°C: anti-GluA1 (glutamate receptor subunit 1; 1:3,000, rabbit; Abcam, Cambridge, MA), anti-GluA2 (1:2,000, rabbit; Millipore, Billerica, MA), anti-PSD95 (1:1,000, mouse; Abcam), anti-synaptophysin (1:5,000, mouse; Stressgene; Enzo, Plymouth Meeting, PA), and anti-β-III tubulin (loading control; 1:15,000, rabbit; Sigma), followed by incubation with secondary antibodies (1:10,000) conjugated with IRDye 680 (rabbit, LI-COR Biosciences, Lincoln, NE) and IRDye 800 (mouse, LI-COR). Immunofluorescence was detected by infrared imaging (Odyssey, LI-COR).
Quantitative polymerase chain reaction (qPCR). Total cellular RNA was extracted from cerebral cortex of nPM-exposed mice and rat primary glia (Tri Reagent; Sigma), and cDNA (2 μg RNA; Superscript III kit; Invitrogen) was analyzed by qPCR, with primers appropriate for mouse (in vivo) or rat (in vitro). Genes examined by qPCR were CD14, CD68, CD11b, CD11c, GFAP (glial fibrillary acidic protein), IFN-γ (interferon-γ), IL-1α, IL-1, IL-6, and TNFα. Data were normalized to β-actin.
Statistical analysis. Data are expressed as mean ± SE. The numbers of individual measurements (n) are described above and listed in the figure legends. Single and multiple comparisons used Student’s t-test (unpaired) and one-way analysis of variance (ANOVA)/Tukey’s honestly significant difference, with statistical significance defined as p < 0.05.
Morgan T.E., Davis D.A., Iwata N., Tanner J.A., Snyder D., Ning Z., Kam W., Hsu Y.T., Winkler J.W., Chen J.C., Petasis N.A., Baudry M., Sioutas C, & Finch C.E. (2011). Glutamatergic Neurons in Rodent Models Respond to Nanoscale Particulate Urban Air Pollutants in Vivo and in Vitro. Environmental Health Perspectives, 119(7), 1003-1009.
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Publication 2011
5
CRISPR-Cpf1 Genome Editing Protocol

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Publication 2015
Buffers Cells Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Genes Genome Gold H-DNA INDEL Mutation Plasmids polyacrylamide gels RNA, CRISPR Guide Stains Taq Polymerase Transfection

Most recents protocols related to «Polyacrylamide gels»

1
Polyacrylamide Gel Functionalization for Cell Adhesion
Not available on PMC !
We prepared polyacrylamide gels with a stiffness of 18kPa according to a previously established protocol and functionalized them with Sulpho-SANPAH (Thermo Fisher Scientific) 72 . For the gels we prepared a solution of 0.16% bis-acrylamide and 7.5% acrylamide, 0.01% v/v 200-nm-diameter dark-red fluorescence carboxylate-modified beads (Fluospheres, Thermo Fisher Scientific), 0.5% v/v ammonium persulfate (Sigma Aldrich) and 0.05% tetramethylethylenediamine (Sigma Aldrich), in PBS. We placed a 22ul drop of unpolymerized gel on a glass-bottom MatTek 35 mm dish and immediately covered it with an 18mm circular coverslip. The gels were then allowed to polymerize at room temperature for 1 hour and then covered with PBS before removing the circular coverslip. Functionalization of the gel surface was achieved by incubation with a solution of 2 mg/ml Sulpho-SANPAH under ultraviolet light for 7 minutes (wavelength of 365 nm at a distance of 5 cm). Then, two washes of PBS were performed for 2.5 minutes under mild agitation to remove excess Sulpho-SANPAH. The gels were then immediately used for microcontact printing of fibronectin lines.
Rossetti L., Grosser S., Abenza J.F., Valon L., Roca‐Cusachs P., Alert R., & Trepat X. (2024). Optogenetic generation of leader cells reveals a force-velocity relation for collective cell migration.
Publication 2024
2
Protein Profiling of Dehydrated Seeds
The densitometry and the concentration of proteins in seeds dehydrated by TSD and DEMI-LP were determined.
With the protein extracts obtained, the 12% PAGE-SDS polyacrylamide gels were made (Acrylamide-Bis Acrylamide 30:08, tris–HCl 1.5 M pH 8.8, SDS 10%) by conventional methods, and 60 mg of protein per lane was used. These samples were denatured for 5 min with a denaturing buffer (2.5 mL Tris–HCl 0.5 M pH 6.8,1 mL Bis-mercaptoethanol 5%, 4.5 mL distilled H2O, 4 mL 10% SDS, 20 μL or 0.0002 g bromophenol blue 1%, 8 mL Glycerol 10%) consisting in tubes placed over boiling water in a hot dish. The gels were run for 30 min at 80 V and then for 120 min at 100 V. Once the shift was over, the gels were stained with Coomassie blue G-250 (C47 H48 N3 O7 S2 Na ) in an aqueous acetic acid solution (10%).
Ortiz-Hernandez A.A., Araiza-Esquivel M.A., Delgadillo-Ruiz L., Espinosa-Vega L.I., Olvera-Olvera C.A., Lopez-Martinez A., Vega-Carrillo H.R, & Ortega-Sigala J.J. (2024). Comparison of dehydration systems in quality and chemical effects on sunflower seeds. Scientific Reports, 14, 12014.
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Publication 2024
3
Olive Pomace SOD Isoenzyme Analysis
Olive pomace LMW samples were subjected to native-polyacrylamide gel electrophoresis (PAGE) in 4–20% gradient precast polyacrylamide gels (Mini-Protean TGX Stain-Free gels, Biorad®, Hercules, CA, USA) containing trihalo (2,2,2-Trichloroethanol) [50 (link)]. During electrophoresis, trihalo covalently modifies tryptophan residues in the protein, generating a fluorescence signal which can be observed with UV light. Peptide bands were visualised in a UV transilluminator. For the detection of superoxide dismutase (SOD) activity in gels, peptide samples were first separated by native-PAGE on 10% acrylamide gels. SOD activity was detected by a photochemical method using nitrobluetetrazolium [51 (link)]. A freshly prepared Olea europaea extract [24 (link)] containing the isoenzymes Mn-, Cu,Zn-, and Fe-SOD was used as a control.
López-Huertas E., Rubí-Villegas J., Sánchez-Moreno L, & Nieto R. (2024). Olive Pomace Extract Contains Low Molecular Weight Peptides and Possesses ACE Inhibitory Activity. International Journal of Molecular Sciences, 25(7), 3962.
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Publication 2024
4
Polyacrylamide Gel Fabrication and Functionalization
Not available on PMC !
The preparation of PA gels followed the methodology outlined in a previous study 76 (link) . In brief, a mixture of 40% acrylamide solution (BIORAD, #1610140), 2% Bis-Acrylamide solution (BIORAD, #1610142), and distilled water was blended and adjusted to manufacture PA gels with varying rigidity. This PA gel solution was degassed for 15 minutes (min) to expedite polymerization and enhance gel uniformity. Subsequently, the gel solution was mixed with 10% ammonium persulfate (Sigma-Aldrich, #A3678) and TEMED (Sigma-Aldrich, #T9281), and promptly polymerized onto coverslip glass. To immobilize extracellular matrix proteins onto the surface of the PA gel, a hetero-bifunctional crosslinker, 0.5 mg/mL Sulfo-SANPAH (Sigma-Aldrich, #80332), was applied to the gels, followed by exposure to UV light. The gels were then coated with 0.05 mg/mL fibronectin (Sigma-Aldrich, #F0895) and incubated at 37 °C overnight to facilitate crosslinking.
Shin S.J., Bayarkhangai B., Tsogtbaataar K., Yuxuan M., Kim S., Kim Y., Kim D., Kim D., Lee J., Hyun J., & Kim H. (2024). Matrix-rigidity cooperates with biochemical cues in M2 macrophage activation through increased nuclear deformation and chromatin accessibility.
Publication 2024
5
Fabrication of p(AAm-co-AA) Microspheres
Not available on PMC !
The p(AAm-co-AA) microspheres in this study were fabricated according to methods in recent reports [33] . Briefly, the compositions of the aqueous prepolymer solutions were 15% (w/v) AAm, 1% to 4% (w/v) AAc, 0.05% to 1% (w/v) Bis, and the composition of the wetting fluid was 99% (v/v) hexadecane and 1% (v/v) Darocur 1173 photoinitiator. As shown in Figure 1-a, the prepolymer solution was placed into a micropatterned PDMS mold, which was formed with Sylgard 184 containing 10% (w/w) curing agent following overnight incubation at 65 °C on a silicon master template. Bubbles in the microwells were removed by rubbing the surface of the mold with a disposable pipet tip. Excess prepolymer solution was removed via pipetting, and the wetting fluid was then placed on top of the mold in order to lead to surface tension-induced droplet formation. For beads with a diameter greater than 300 𝜇m, applying manually pressure around the hexagonal mold helps droplet formation. The mold was then carefully placed on an aluminum mirror (Thorlabs, Newton, NJ) and exposed to low-intensity 365 nm UV light with an 8 W hand-held UV lamp (Spectronics Corp., Westbury, NY) for 15 min to initiate radical chain polymerization. The microspheres were collected via pipetting, transferred to a microcentrifuge tube, and rinsed to remove any wetting fluid and unreacted chemicals as follows: mixing the microspheres in 2-propanol by pipetting, allowing them to settle to the bottom, and removing the supernatant. After rinsing at least three times with 2-propanol, the rinsing procedure was repeated at least three times with deionized water containing 0.05% (v/v) Tween 20 and at least twice with 20 mM MES buffer (adjusted to pH 6 with 1 M NaOH) containing 0.05% (v/v) Tween 20 or deionized water.
Blanc B., Zhang Z., Liu E., Zhou N., Dellatolas I., Aghvami A., Yi H, & Fraden S. (2024). Active Pulsatile Gels: From a Chemical Microreactor to a Polymeric Actuator. Langmuir : the ACS journal of surfaces and colloids, 40(13).
Publication 2024

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1
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β-actin is a protein that is found in all eukaryotic cells and is involved in the structure and function of the cytoskeleton. It is a key component of the actin filaments that make up the cytoskeleton and plays a critical role in cell motility, cell division, and other cellular processes.

More about "Polyacrylamide gels"

Polyacrylamide gels are a versatile and widely-used analytical tool in biochemistry and molecular biology.
These gel matrices are employed for the separation, characterization, and identification of proteins, nucleic acids, and other biomolecules.
Optimizing the reproducibility and consistency of polyacrylamide gel experiments is crucial for obtaining reliable research results.
PubCompare.ai's AI-driven platform can help streamline the process of identifying the most effective protocols for polyacrylamide gel workflows.
Their platform analyzes research literature, pre-prints, and patents to pinpoint the best methods and products to achieve reliable, consistent outcomes.
This includes not only polyacrylamide gels, but also related techniques like PVDF membranes, nitrocellulose membranes, and polyvinylidene difluoride membranes, which are often used in conjunction with gel electrophoresis.
By leveraging PubCompare.ai's AI-powered analysis, researchers can optimize their polyacrylamide gel protocols and streamline their studies.
This can involve identifying the optimal reagents, such as protease inhibitor cocktails and BCA protein assay kits, as well as the most effective imaging systems, like the Odyssey Infrared Imaging System.
Incorporating β-actin as a loading control can also help ensure consistent results across experiments.
PubCompare.ai's platform can help researchers overcome the challenges of reproducibility and variability often encountered with polyacrylamide gels, leading to more reliable and consistent research outcomes.