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View additional product information for Novex™ Tricine Welcome Pack, 10-20% - FAQs (EC6625A, EC6625B, EC6625C)
118 product FAQs found
Coupling of chromophores to proteins affects the apparent molecular weight of proteins in SDS-PAGE relative to unstained standards. The apparent molecular weight of prestained protein standards is calibrated in the classical TRIS glycine-SDS Laemmli system, however prestained proteins may have different mobility in other electrophoresis buffer and gel systems. It should also be noted that the sizing of proteins by gel electrophoresis does not give an exact value and depends on the protein sequence and post-modification.
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The upper bands of the ladder may be degraded by proteases. Ladder, gel, buffer, pipettes, pipette tips, or equipment can be contaminated by proteases during usage. A general recommendation would be to avoid working with proteases in the same room. We would recommend preparing fresh solutions, cleaning the equipment, and using clean pipettes and tips. If the ladder itself is contaminated, please use a new tube of the ladder.
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No, proteins in Thermo Scientific protein ladders are not His tagged. However, non-specific interaction between the ladder proteins and primary or secondary antibodies is possible and some His-Tag detection systems, such as Thermo Scientific 6xHis Protein Tag Stain Reagent Kit, show non-specific interaction. The protein ladder bands are more readily detected when using high antibody concentrations. The non-specific cross-reactivity is difficult to predict, it often has a different pattern dependent on the antibodies used in each individual experiment. The most general way to handle this problem would be to use lower concentrations of antibodies and to use lower amount of protein ladders. It may also be useful to leave one empty well between the ladder and the sample to overcome a possible leakage of the signal to the nearby sample lane.
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PageRuler Unstained protein ladders can be detected directly on Western blots by using Strep-Tactin conjugates or an antibody against the Strep-tag II sequence. All PageRuler and Spectra ladder proteins contain an integral Strep-tag II sequence, however the prestained ladders cannot be detected by Strep-Tactin conjugates.
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All PageRuler and Spectra ladder bands are recombinant prokaryotic proteins purified from E. coli cells. None of them are related to eukaryotic proteins, however this cannot exclude the possibility that the ladder proteins may possess an epitope that is cross-reactive with the antibody used.
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Protein ladder bands can sometimes be detected with chemiluminescent techniques due to non-specific interactions of ladder proteins with either primary or secondary antibodies (or with both). The ladder bands are only rarely detected by chromogenic substrates. The extremely high sensitivity of the chemiluminescent assays is needed to see the bands, so the actual degree of cross-reactivity is low. The non-specific cross-reactivity is difficult to predict, it often has a different pattern depending on the antibodies used. If antibodies recognize a linear epitope, the cross-reactivity may be due to sequence homology. If antibodies react with a denaturation-resistant conformational epitope it could be impossible to identify the exact reason for detected cross-reactivity. The most general way to handle this problem would be to use lower concentrations of antibodies.
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No. Thermo Scientific protein ladders contain a mix of recombinant prokaryotic proteins purified from E. coli cells. E. coli does not have native glycosylation pathways, so none of the ladder proteins are glycosylated.
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Thermo Scientific ladders are not designed for protein quantification. For quantification, we would recommend to use a protein of known concentration as a reference.
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Yes, PageRuler Prestained NIR Protein Ladder (Cat. No. 26635) contains proteins that are blue-stained and fluor-labeled for near-IR fluorescent visualization and protein sizing following electrophoresis.
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Protein ladders can be run on lower percentage gels than we recommend, however it should be expected that several bands of lower molecular weight proteins will run out of the gel if the gel is run until the dye front reaches the bottom of the gel. In case of shorter electrophoresis time it is also possible that some lower bands will not separate and will be covered by the dye front. In addition, lower molecular weight protein bands may look diffused. The lower percentage gels can be used in cases when the customer is interested in visualization of large proteins only.
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Most of the common gel running buffers are composed of Tris-glycine or Tris-tricine. Tris-glycine buffer systems are useful for separation of proteins over a wide range of molecular weights (5-300 kDa) and are compatible with denaturing or non-denaturing conditions. Tris-tricine buffer is generally recommended for the electrophoresis of low molecular weight proteins and peptides (<10 kDa) that need to be reduced and denatured prior to loading. Tris-acetate buffer system is used for separation of larger proteins (>200 kDa).
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Prestained ladders/markers are recommended for approximate determination of molecular weight and for monitoring the progress of the electrophoresis run and the efficiency of protein transfer to membranes during Western blotting procedures. Unstained ladders/markers are used for precise determination of molecular weights in any denaturing buffer system.
We do not provide the exact or approximate concentration of proteins in Thermo Scientific protein ladders, and they are not meant to be used for quantifying the protein concentration of a band. For densitometry assessment, we recommend loading a known amount of a protein standard and determining the linear range according to the gel or membrane stain used.
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DTT is not stable, so it must be added and the reduction performed just prior to loading your samples.
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Precipitation of the LDS or SDS at 4 degrees C is normal. Bring the buffer to room temperature and mix until the LDS/SDS goes into solution. If you do not want to wait for it to dissolve, you can store the sample buffer at room temperature.
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While they are both Bis-Tris based gels, the chemistries are very different since Bolt gels are optimized for western blotting. Another key difference is the wedge well design of the Bolt gels, which allows larger sample volumes to be loaded.
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The neutral operating pH of the NuPAGE Gels and buffers provides following advantages over the Laemmli system:
-Longer shelf life of 8-12 months due to improved gel stability
-Improved protein stability during electrophoresis at neutral pH resulting in sharper band resolution and accurate results (Moos et al, 1998)
-Complete reduction of disulfides under mild heating conditions (70 degrees C for 10 min) and absence of cleavage of asp-pro bonds using the NuPAGE LDS Sample buffer (pH > 7.0 at 70 degrees C)
-Reduced state of the proteins maintained during electrophoresis and blotting of the proteins by the NuPAGE Antioxidant
Please refer to the following paper: Moos M Jr, Nguyen NY, Liu TY (1988) Reproducible High Yield Sequencing of Proteins Electrophoretically Separated and Transferred to an Inert Support. J Biol Chem 263:6005-6008.
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The formulations of buffers for our precast protein gels can be found at this link: https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-gel-electrophoresis/protein-electrophoresis-buffers-reagents.html
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The Tricine gel system, first described by Schagger and von Jagow in 1987, is a modification of the Laemmli Tris-Glycine system to allow for better resolution of smaller proteins and peptides. In the Laemmli system, the proteins are "stacked" in the porous top portion of the gel (stacking gel) between a highly mobile "leading" chloride ion present in the gel buffer and the slower "trailing" glycine ion supplied by the running buffer. These concentrated, thin bands of protein undergo sieving once they reach the resolving gel, which separates them by size.
The resolution of smaller proteins (under 5 kDa) is hindered by the continuous accumulation of free dodecyl-sulfate (DS) ions (from the SDS sample and running buffers) in the stack. This build-up of DS leads to convective mixing of the DS ions with the smaller proteins, causing fuzzy bands and decreased resolution. The mixing of the DS ions with the small proteins will also interfere with the fixing and staining process later. To solve this problem, Schagger and von Jagow replaced the trailing glycine ion with a faster moving Tricine trailing ion. Many small proteins which run with the stacked DS in the Tris Glycine system will separate from DS in the Tricine gel system, resulting in sharper, cleaner bands and better resolution.
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Either BME or DTT can be used in the NuPAGE LDS Sample Buffer.
Make sure that a fresh solution of BME is used. FINAL concentration:
DTT 50-100 mM
BME 2-5%
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There may be too much beta-mercaptoethanol (BME), sample buffer salts, or dithiothreitol (DTT) in your samples. If the proteins are over-reduced, they can be negatively charged and actually repel each other across the lanes causing the bands to get narrower as they progress down the gel.
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Barbell-shaped bands are a result of loading too large a sample volume.
When a large sample volume is loaded, part of the sample tends to diffuse to the sides of the wells. When the run begins and the sample moves through the stacking portion of the gel, the sample will stack incompletely, causing a slight retardation of the portion of the sample that diffused to the sides of the wells.
This effect may be intensified in larger proteins, whose migration is more impeded in the low concentration acrylamide of the stacking gel.
To alleviate the problem, concentrate the protein and load a smaller volume. This gives a "thinner" starting zone.
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Some potential causes are:
1) Re-oxidation of protein during run
2) Protein has highly hydrophobic regions where protein can exclude SDS.
Steps you can take to improve results:
1) Reduce samples right before loading, and add antioxidant to running buffer. Do not use samples that have been stored in reducing agent.
2) Load sample with 2X sample buffer instead of 1X.
3) Add SDS to upper chamber buffer: try 0.1, 0.2, 0.3, and 0.4% (don't go any higher than 0.4%)
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Yes. All detergents and even phospholipids in cell extracts will form mixed micelles with SDS and migrate down into the gel.
They can also interfere with the SDS:protein binding equilibrium. Most of the nonionic detergents significantly interfere with SDS-PAGE.
We recommend that you keep the ratio of SDS to lipid or other detergent at 10:1 (or greater) to minimize these effects.
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There shouldn't be any negative effects unless the percentage of acetonitrile reaches 40% or 50% of the sample volume.
At these concentrations, there is the possibility of the acetonitrile affecting the binding of SDS to the protein, which, in turns, affects the migration of the protein.
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There is no SDS in the gels. Denaturing conditions are created by using sample buffers and running buffers that contain SDS.
The benefit of not having SDS in the gels is that the gel can be used for both native and denaturing conditions.
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Invitrogen gels are packaged in Packaging Buffer: Tris HCl, pH 8.65, with 0.02% sodium azide (expect that residual acrylamide monomer is also present). Wear gloves at all times when handling gels.
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A temperature increase to 35°C to 40°C during electrophoresis is not uncommon for Tricine gels. If you want to run the gels at a cooler temperature, the lower (outer) buffer chamber can be filled higher or they can be run at a lower voltage, for example 100 V.
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For non-sequencing applications, any transfer buffer used with Tris-Glycine gels can be used with Tricine gels including Tris-Glycine transfer buffer. For sequencing applications, the buffer should be chemically compatible with sequencing protocols. Non-glycine based transfer buffers such as the NuPAGE Transfer buffer, 1/2X TBE Transfer buffer, or CAPS Buffer can be used for N-terminal sequencing . Generally, a pH which is close to neutral is desirable to maintain gel and protein stability. High current should be avoided because it can lead to heat generation and instability.
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If the Tricine gel is run with Tris-Glycine sample buffer, the bands will behave abnormally and resolve poorly. If the Tricine gel is accidentally run with Tris-Glycine running buffer, the gel will take longer to run and the resolution, especially for smaller proteins, will be worse than when the proteins are run on a Tris-Glycine gel with Tris-Glycine buffers. This is due to a combination of increase in stack area size (glycine is a slower ion than Tricine) and the higher ionic strength of the Tricine gel.
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Protein samples are possibly reoxidizing before the run is complete in the Tricine gel system. Since Tricine is a glycine derivative, the running pH ranges of the two systems are different. As a consequence, reduced samples tend to oxidize more in the Tricine system. Adding more reducing agent will not solve the problem.
One option is to alkylate the sample by reducing with 20 mM DTT at 70°C for 30 min, followed by 50 mM iodoacetic acid to alkylate.
Another method which inhibits oxidation is the addition of thioglycolic acid (TGA) to the running buffer. The reference to this is described by Hunkapiller et al, Methods of Enzymology, (91), 399, 1983.
Caution should be taken when using this method since this compound is both toxic and expensive. In addition, the TGA must be fresh as it tends to become oxidized itself over time. Oxidized TGA will actually promote sample re-oxidation.
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TCEP, Tris Carboxy Ethyl Phosphene is an alternative sulfhydryl reducing agent for protein samples. It is an extremely potent and effective reducing agent for particularly ‘difficult' proteins. It is compatible with the Tris-Glycine gels and NuPAGE gels. It should be added to the sample buffer for these systems. 20 mM final (maximum) concentration is sufficient for samples. You may add alkylating agents, e.g. Iodine (50 mM Iodoacetic acid), to prevent re-forming of S-S bonds but it is not necessary. Do not heat because this will hydrolyze much of your sample. Instead let the sample sit for several minutes at RT and then load.
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If the Antioxidant is omitted from the running buffer, it is possible to resolve reduced and non-reduced samples on the same gel, although the resolution may be lower. Furthermore, it is not recommended that the reduced and non-reduced samples be run side-by-side in adjacent lanes.
However, because of the neutral pH of the NuPAGE gels, the reducing agent (beta-mercaptoethanol or DTT) will not migrate through the gel with the protein the way it does in the basic environment of the Tris-Glycine gels. Instead, the reducing agent tends to remain at the top of the gel. For this reason, the NuPAGE Antioxidant is incorporated into the buffer in the upper buffer chamber. The antioxidant is able to migrate fully with the proteins and keep them reduced. As a result, it is possible that proteins prepared as non-reduced samples could become somewhat reduced during the electrophoresis run. This would result in smearing of the samples.
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Here are possible causes and solutions:
- Not enough volume of ladder loaded on the gel: Load an appropriate volume of the ladder onto the gel. Here are our recommendations:
--- Mini-gel: 5 µL per well (0.75-1.0 mm thick) or 10 µL per well (1.5 mm thick)
--- Large gel: 10 µL per well (0.75-1.0 mm thick) or 20 µL per well (1.5 mm thick)
- Incomplete or poor transfer: Optimize transfer conditions
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Here are possible causes and solutions:
Here are possible causes and solutions:
- Ladder was boiled: Discard boiled aliquot.
- Too much volume of ladder used: Add less volume or dilute the ladder in protein loading buffer prior to use.
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The fading is most likely due to detergent in the western blocking/washing solutions that can remove some of the proteins from the membrane. The dye itself will not wash off of the proteins because it is covalently bound. We have found that smaller pore size membranes retain the proteins better during blocking and wash procedures, and hence recommend use of 0.2 µm instead of 0.45 µm membranes for best resolution and protein retention. After transfer, it is a good idea to circle the pre-stained bands with a pencil on the membrane, so band positions can be identified after blocking and processing.
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- Decrease voltage, current or length of transfer time
- Make sure that the methanol concentration in the transfer buffer is proper; use a methanol concentration of 10-20% methanol removes the SDS from SDS-protein complexes and improves the binding of protein to the membrane.
- Make sure that the SDS concentration (if added) in the transfer buffer is proper, don't use more than 0.02-0.04% SDS. Using too much SDS can prevent binding of proteins to the membrane.
- Check the pore size of the membrane and the size of the target protein. Proteins smaller than 10 kDa will easily pass through a 0.45 µm pore size membrane. If proteins smaller than 10 kDa are of interest, it would be better to use a 0.2 µm pore size membrane.
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- Increase voltage, current or length of time for transfer
- SDS in the gel and in the SDS-protein complexes promotes elution of the protein from the gels but inhibits binding of the protein to membranes. This inhibition is higher for nitrocellulose than for PVDF. For proteins that are difficult to elute from the gel such as large molecular weight proteins, a small amount of SDS may be added to the transfer buffer to improve transfer. We recommend pre-equilibrating the gel in 2X Transfer buffer (without methanol) containing 0.02-0.04% SDS for 10 minutes before assembling the sandwich and then transferring using 1X transfer buffer containing 10% methanol and 0.01%SDS.
- Methanol removes the SDS from SDS-protein complexes and improves the binding of protein to the membrane, but has some negative effects on the gel itself, leading to a decrease in transfer efficiency. It may cause a reduction in pore size, precipitation of some proteins, and some basic proteins to become positively charged or neutral. Make sure that the methanol concentration in the transfer buffer is not more than 10-20% and that high-quality, analytical grade methanol is used.
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Pre-stained standards have a dye that is covalently bound to each protein that will result in the standard migrating differently in different buffer systems (i.e., different gels). As a result, using a pre-stained standard for molecular weight estimation will only give the apparent molecular weight of the protein. Pre-stained standards may be used for molecular weight approximation, confirming gel migration and estimating blotting efficiency but for accurate molecular weight estimation, an unstained standard should be used.
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- While loading, take care to make sure that there is no cross-contamination from adjacent sample lanes.
- Make sure that the correct amount of standard is loaded per lane. Loading too much protein can result in extra bands and this is a problem especially with silver-stained gels.
- Improper storage of the standard or repeated freeze/thawing can result in protein degradation.
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Here are some suggestions:
- Make sure that the correct amount of standard is loaded per lane. Loading too much protein can cause smearing and this is a problem especially with silver stained gels.
- Bands will not be as well resolved in low percentage gels. Try using a higher percentage gel.
- If the bands look smeary and non-distinct after a western transfer/detection, this may be due to the antibody being too concentrated. Follow the manufacturer's recommended dilution or determine the optimal antibody concentration by dot-blotting.
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Here are some suggestions:
- Check the gel type/percentage of the gel that was used. Depending on the gel type and/or percentage, all the bands may not be seen. For example, the smallest bands of the protein standard may not resolve on a very low percentage gel whereas the higher molecular weight bands may not resolve on a high percentage gel.
- Check the expiration date on the protein standard. Expired lots may result in faded or missing bands due to protein degradation.
- Check the storage conditions for the protein standard. Improper storage conditions will compromise the stability of the proteins in the standard.
- Make sure that the protein standard was not heated/boiled prior to loading on the gel. Our protein standards are ready to load and we do not recommend heating/boiling them as this may cause degradation of proteins in the standard.
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The Spectra Protein Ladders contain recombinant prokaryotic proteins and do not contain any animal-derived proteins.
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The Spectra Multicolor Low Range Protein Ladder is a prestained mixture of six recombinant proteins (1.7 to 40 kDa) for use in gel electrophoresis and western blotting. Three different chromophores are bound to the proteins, producing a brightly colored ladder.
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We recommend storing the Spectra Protein Ladders at -20 degrees C where they are stable for a year. The Spectra Multicolor Broad Range Protein Ladder and Spectra Multicolor High Range Protein Ladder are stable for up to 3 months at 4 degrees C. The Spectra Multicolor Low Range Protein Ladder is stable for up to 2 months at 4 degrees C.
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Zymogram gels are essentially Tris-Glycine gels containing the substrate. Protein standards run based solely on the percentage of acrylamide and hence should run the same in both kinds of gels. It is quite possible though that if the standard is prestained, the proteins will appear a different color because of the staining (or pre-staining) of the Zymogram gels.
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Our protein standards are not designed for protein quantitation.
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We do not recommend using our prestained standards for native gel electrophoresis since they are already denatured (in SDS sample buffer) and pre-reduced (by a proprietary method), and will not resolve well in under native conditions.
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We recommend using unstained protein ladders for molecular weight estimation applications as prestained ladders have a dye that is covalently bound to each protein that will result in the ladder migrating differently in different buffer systems (i.e., different gels). As a result, using a prestained ladder for molecular weight estimation will only give the apparent molecular weight of the protein. Prestained ladders may be used for molecular weight approximation, confirming gel migration and estimating blotting efficiency but for accurate molecular weight estimation, an unstained ladder should be used.
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Please find this information in the respective manuals for the individual protein standards.
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Our protein standards are ready to load. We do not recommend heating them as this may cause protein degradation.
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Except for our NativeMark Unstained Protein Standard (designed for native electrophoresis), all of the other unstained and prestained standards we offer (Invitrogen Sharp, SeeBlue, SeeBlue Plus2, BenchMark, HiMark) have been pre-reduced (by a proprietary method). Hence, you do not need to add reducing agent.
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The Mini Blot Module is designed exclusively for the Mini Gel Tank. It will also fit in the Bolt Mini Gel Tank (discontinued as of December 31, 2014) but will not fit in the XCell SureLock Mini Cell or other vendors' electrophoresis tanks.
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Due to the universal electrode design, the Mini Blot Module fits on either side of the Mini Gel Tank.
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Yes, we offer the Mini Blot Module (Cat. No. B1000), designed to be used with the Mini Gel Tank. This blot module will also work with the Bolt Mini Gel Tank (discontinued as of December 31, 2014). Please note that the Bolt Mini Blot Module (discontinued as of December 31, 2014) is also compatible with both the Bolt Mini Gel Tank and the Mini Gel Tank.
Bolt Bis-Tris Plus gels can also be transferred using the XCell SureLock Mini Cell, iBlot Dry transfer system, or using the Invitrogen Semi-Dry Blotter.
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Chlorobutanol is used as a preservative in the NuPAGE transfer buffer and is not necessary for efficient transfer of proteins. You may prepare the buffer without chlorobutanol but keep in mind that the buffer will not be stable for long periods. We recommend using it within 2 weeks.
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We do not recommend using Carbonate or CAPS transfer buffers to transfer NuPAGE gels as the transfer efficiency will be badly compromised. Further, the high pH environment (>pH 9) of these buffers will make the NuPAGE Antioxidant non-functional.
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To increase efficiency of transfer of high molecular weight proteins from NuPAGE gels, we recommend pre-equilibrating the gel in 2x NuPAGE Transfer buffer (without methanol) containing 0.02-0.04% SDS for 10 minutes before assembling the sandwich and then transferring using 1x NuPAGE transfer buffer containing methanol and 0.01% SDS.
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We recommend marking the cassette at the bottom of the wells with a marker pen prior to placing the cassette in the electrophoresis tank.
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Here are possible causes and solutions:
- Tape left on the bottom of the cassette. Remove tape from bottom of cassette.
- Connection to power supply not complete. Check all connections with a voltmeter for conductance.
- Insufficient buffer level. Make sure there is sufficient buffer in the electrophoresis tank to cover the wells of the gel.
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Here are possible causes and solutions:
- Buffers are too concentrated or incorrect. Check buffer recipe; dilute or re-make if necessary.
- Current is set at a higher limit. Decrease current to recommended running conditions (see Page 8 of the manual).
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Here are possible causes and solutions:
- Buffers are too dilute. Check buffer recipe; remake if necessary.
- Buffer chamber is leaking. Make sure the cassette clamp is firmly seated, the gaskets are in place and the cassette clamp is locked.
- Current is set too low. Set correct current.
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Here are the replacement parts we offer for the Mini Gel Tank:
Replacement part - Cat. No.
Gel Runner Tank - B4478641
Mini Gel Tank Lid - A25944
Mini Gel Tank Base - A25950
Cassette Clamp, left - A25946
Cassette Clamp, right - A25945
Cassette Clamp Cam Handle Set - A26732
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Here are our recommendations:
- When electrophoresis is complete, dispose of the buffer appropriately. Rinse the tank with water to remove residual buffer.
- Clean the surface of the Mini Gel Tank with a soft non-abrasive, lint-free cloth dampened with water.
- Do not use harsh detergents or solvents to clean the unit.
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The Mini Gel Tank is not compatible with chlorinated hydrocarbons (e.g., chloroform), aromatic hydrocarbons (e.g., toluene, benzene) or acetone.
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The Precise Tris-HEPES gels are compatible with the XCell SureLock Mini Cell or Mini Gel Tank when used with adaptor plates.
Note: Two adaptor plates are required when running just one gel and one adaptor plate is required when running two gels using the XCell SureLock Mini Cell or Mini Gel Tank.
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Our Original Bolt Bis-Tris Plus Mini gels (Cat. No. BGxxxxxBOX, discontinued as of December 31, 2014) can only be run in the Bolt Mini Gel Tank (discontinued as of December 31, 2014, and will be offered until inventory is depleted).
Our New Bolt Bis-Tris Plus Mini gels (Cat. No. NWxxxxxBOX), as well as our Invitrogen Mini gels and NuPAGE Mini gels can be run using the Mini Gel Tank, or XCell SureLock Mini-Cell. To run these gels using the Bolt Mini Gel Tank (discontinued as of December 31, 2014), upgrading of the tank is necessary by replacing the black 10.5 cm cassette clamp cam handles with gray 10 cm cassette clamp cam handles (Cat. No. A26732, Cassette Clamp Cam Handle Set). Instructions for replacement of the cam handles can be found here (https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-gel-electrophoresis/protein-gel-electrophoresis-chamber-systems/mini-gel-tank/resources-upgrading-bolt-mini-gel-tank.html).
Our Midi gels can be run using the XCell4 SureLock Midi-Cell.
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Here are possible causes and solutions:
- Membrane blotting pads are dirty or contaminated. Soak pads with detergent and rinse thoroughly with purified water before use. Replace pads when they become worn or discolored.
- Blocking was uneven. The incubation dish must be sufficiently big to allow thorough coverage of membrane. Shake or agitate during each step.
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Here are possible causes and solutions:
- Membrane contaminated by fingerprints or keratin proteins: Wear clean gloves at all times and use forceps when handling membranes. Always handle membranes around the edges.
- Concentrated secondary antibody used: Make sure the secondary antibody is diluted as recommended. If the background remains high, but with strong band intensity, decrease the concentration of the secondary antibody.
- Concentrated Primary antibody used: Decrease the concentration of the primary antibody.
- Affinity of the primary antibody for the protein standards: Check with the protein standard manufacturer for homologies with primary antibody.
- Insufficient removal of SDS or weakly bound proteins from membrane after blotting: Follow instructions for membrane preparation before immunodetection.
- Short blocking time or long washing time: Make sure that each step is performed for the specified amount of time.
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Here are possible causes and solutions:
- Insufficient blocking or non-specific binding: We suggest trying our WesternBreeze Blocker/Diluent (Cat. No. WB7050).
- Membrane is contaminated: Use only clean, new membranes. Wear clean gloves at all times and use forceps when handling membranes.
- Higher intrinsic background with PVDF membranes: Switch to nitrocellulose membranes.
- Nitrocellulose membrane not completely wetted: Follow instructions for pre-wetting the membrane.
- Blot is overdeveloped: Follow recommended developing time and remove blot from substrate when signal - to -noise ratio is acceptable.
- Insufficient washing ; Follow recommended number of washes. In some cases, it may be necessary to increase the number or duration of washes.
- Concentrated secondary antibody used: Determine optimal antibody concentration by performing a dot blot and dilute antibody as necessary.
- Concentrated primary antibody used: Determine optimal antibody concentration by performing a dot blot and dilute antibody as necessary.
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Here are possible causes and solutions:
- The primary antibody and secondary antibody are not compatible: Use a secondary antibody that was raised against the species in which the primary antibody was raised.
- The primary antibody is too dilute: 1) Use a more concentrated antibody solution. 2) Incubate longer (e.g., overnight) at 4 degrees C. 3) Use fresh antibody and keep in mind that each time an antibody solution is used, its effective antibody concentration decreases.
- Something in your blocking buffer interferes with binding of the primary and/or secondary antibody: Try an alternate blocking buffer ± a mild surfactant like Tween-20 (0.01-0.05% v/v). There are many blocking buffer recipes available, based on non-fat dry milk, BSA, normal serum, gelatin and mixtures of these and other materials. Note that BSA (1-5%) is considered the best blocker for nitrocellulose membranes. It is easy to check the efficacy of different blocking buffers by performing dot-blots.
- The primary antibody does not recognize the protein in the species being tested: 1) Evaluate primary antibodies by dot-blotting first to how well they react with your protein. 2) Check the immunogen sequence, if provided, and determine if it is found in your protein. 3) If no immunogen sequence is available, perform a PubMed/BLAST alignment to assess the degree of homology between your target protein and the protein against which the antibody was generated. Note that many antibodies against human proteins will also recognize the non-human primate version because there is usually a high degree of amino acid identity. In contrast, many antibodies against human proteins will not recognize the corresponding proteins from rodents (and vice versa). Remember that significant homology between sequences does not guarantee that the antibody will recognize your protein. 4) Always run the recommended positive control, if available.
- Insufficient protein is bound to the membrane or the protein of interest is not abundant enough in the sample: 1) Load at least 20-30 ?g protein per lane on your gels (as a starting point), since proteins representing less than ~0.2% of the total protein are difficult to detect on western blots. 2) Use an enrichment step to increase the concentration of the target protein. For example, prepare two nuclear lysates prior to blotting nuclear proteins or perform an immunoprecipitation (IP) prior to SDS-PAGE. 3) Reduce the volume of cell extraction buffer used to lyse your cells or tissue. 4) Be sure to use freshly prepared protease inhibitors and phosphatase inhibitors, if needed, in your protein extraction buffer. 5) Run the recommended positive control, if available.
- Poor or no transfer of the proteins to the membrane 1) Check the protein transfer efficiency with a reversible protein stain like Invitrogen Reversible Membrane Protein Stain, ponceau S, amido black or use pre-stained molecular weight standards. 2) Verify that the transfer was performed with the correct electrical polarity. 3) Remember that proteins with basic pI values (e.g., histones) and high MW may not transfer well. 4) Remember that if your target protein has a low MW (≤10 kDa), it may transfer more quickly than expected. 5) If you are using PVDF membranes, make sure to pre-soak the membrane in methanol first before soaking it in transfer buffer. Note that methanol in transfer buffer increases protein binding to nitrocellulose, but omitting methanol can increase transfer efficiency of high MW proteins. 6) Low MW proteins may pass through the 0.45 µm pores in nitrocellulose membranes, so switch to NC with 0.2 or 0.1 µm pores instead.
- Excessive washing or blocking of the membrane:- 1) Avoid over-washing the membrane. Extra washing will not allow you to visualize your protein of interest if there are other problems with your blot. 2) Avoid over-blocking by using high concentrations of the blocking buffer components or long incubation times. Too much blocking can prevent your antibodies from binding to your protein. Gelatin, in particular, can mask proteins on the blot, so avoid it, if possible. Milk can also mask proteins, so instead of using 5% milk in your blocking buffer, try using it at 0.5% instead, or remove it altogether. 3) Switch to a different blocking reagent and/or block the blot for less time.
- Using the same solution of diluted primary antibody repeatedly: Use freshly-diluted antibody for each western blot because the effective concentration of a diluted antibody decreases each time it is re-used. Also, remember that dilute solutions of antibodies are less stable and may lose their activity rapidly.
- The enzyme conjugated to your secondary antibody is not working: 1) Make a fresh dilution of your secondary antibody conjugate each time you need it. Enzymes (and antibodies) may lose activity quickly in dilute solutions. 2) Omit sodium azide in buffers if you are using HRP-conjugated antibodies. 3) Avoid high heme concentrations (from blood contamination), which can interfere with HRP-based detection. 4) Avoid using phosphate in buffers with alkaline phosphatase-antibody conjugates because phosphate inhibits enzyme activity.
- Your colorimetric or other detection reagent is old and inactive: 1) Use fresh enzyme substrate for each experiment. 2) Don't use ready-to-use substrate reagents if they have changed color on their own or if they have passed their expiration date. 3) Do not dilute substrate solutions unless instructed to do so in the product manual.
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Here are some suggestions:
- Make sure that the correct amount of protein is loaded per lane; loading too much protein can cause smearing.
- Bands will not be as well resolved in low percentage gels; try using a higher percentage gel.
- This may be due to the antibody being too concentrated. We recommend following the manufacturer's recommended dilution or determining the optimal antibody concentration
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In general, background staining in Tricine gels is slightly higher than in Tris-Glycine gels. The relatively higher concentration of solutes in Tricine gels as compared to their Tris-Glycine counter parts appears to slow down the rate of solution exchange into the gel. This can be counteracted by increasing the soak time in the second sensitization step (you may leave it in overnight) as per the modified procedure, and then proceed.
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If the Tricine gel is run with Tris-Glycine sample buffer, the bands will behave abnormally and resolve poorly. If the Tricine gel is accidentally run with Tris-Glycine running buffer, the gel will take longer to run and the resolution, especially for smaller proteins, will be worse than when the proteins are run on a Tris- Glycine gel with Tris-Glycine buffers. This is due to a combination of increase in stack area size (glycine is a slower ion than tricine) and the higher ionic strength of the Tricine gel.
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One potential explanation is that the protein sample is getting re-oxidized before the run is complete. Reduced samples tend to oxidize more in the Tricine system. Adding more reducing agent will not solve the problem. One option is to alkylate the sample by reducing with 20 mM DTT at 70 degrees C for 30 minutes, followed by 50 mM iodoacetic acid. Another method which inhibits oxidation is the addition of thioglycolic acid to the running buffer. The reference to this is described by Hunkapiller et al., Methods in Enzymology, (91), 399, 1983. Caution should be taken when using this method since this compound is both toxic and expensive. In addition, the TGA must be fresh as it tends to get self-oxidized over time and will promote sample re oxidation.
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For blotting Tricine gels, we recommend using 1X Tris-Glycine Transfer Buffer with 20% methanol. The Tris-Glycine Transfer Buffer interferes with protein sequencing. Hence, if you are performing protein sequencing, we recommend using a non-glycine based transfer buffer such as 1X NuPAGE Transfer Buffer, 0.5X TBE Transfer Buffer or CAPS buffer (10 mM CAPS (3 cyclohexylamino, 1-propanesulfonic acid), 10% methanol, pH 11.0).
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The recommended sample loading volumes and protein loading amounts for the different well formats can be found at:
https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-gel-electrophoresis/protein-gels/recommended-well-loading-volumes-sample-loads.html.
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Adding urea to the sample and running buffers, in conjunction with SDS, may provide improved solubilization of the sample if denaturation by SDS does not prove to be sufficient. This must be tested empirically for the protein of interest.
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Yes. Tricine, unlike glycine, does not interfere with sequencing reagents.
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No, the Tricine is actually supplied by the running buffer.
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The Tricine gel system, first described by Schagger and von Jagow in 1987, is a modification of the Laemmli Tris-Glycine system to allow for better resolution of smaller proteins and peptides. In the Laemmli system, the proteins are "stacked" in the porous, top portion of the gel (stacking gel) between the highly mobile "leading" chloride ions, present in the gel buffer and the slower "trailing" glycine ions, supplied by the running buffer. These stacked protein bands undergo sieving once they reach the separating gel, thus resolving by size. However, the resolution of smaller proteins (under 10 kDa) is hindered by the continuous accumulation of free dodecyl-sulfate (DS) ions (from the SDS sample and running buffers) in the stacking gel. This build-up of DS leads to convective mixing of the DS ions with the smaller proteins, causing fuzzy bands and decreased resolution. The mixing of the DS ions with the small proteins also interferes with the fixing and staining process later.
To solve this problem, we offer the Invitrogen Tricine gel system that is based on the Tris-Glycine system developed by Schagger and von Jagow. This modified system uses a low pH in the gel buffer and substitutes the trailing glycine ions with faster moving tricine trailing ions. Many small proteins and peptides that migrate with the stacked DS micelles in the Tris-Glycine system are now well separated from DS ions in the Tricine gel system, resulting in sharper, cleaner bands and higher resolution.
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The ratio of acrylamide:bisacrylamide in our Tricine gels is 37.5:1 and percentage of crosslinker is 2.6%.
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Tricine gels contain a 4% stacking gel that is ~8 to 9 mm long.
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Tricine gels do not contain SDS. The Tricine system requires SDS in the sample and running buffers for best results. They are run using the Tricine SDS Sample buffer and Tricine SDS Running buffer.
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Invitrogen Tricine Gels are ideal for peptides and low molecular weight proteins (less than 10 kDa). Unlike Tris-Glycine gels, Tricine gels allow resolution of proteins with molecular weights as low as 2 kDa. Tricine, unlike glycine, will not interfere with sequencing, so Tricine gels are an excellent choice for direct sequencing after transferring to PVDF. In addition to good transfer efficiency, the Tricine system has a lower pH which minimizes unwanted protein modification. Tricine gels can only be run under denaturing conditions.
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The recommended storage temperature for Invitrogen Tricine gels is 4 degrees C where the shelf life varies from 4-8 weeks depending upon the gel percentage. The higher the percentage, the shorter is the shelf life.
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Here are some causes and solutions for wavy dye fronts:
1) Difference in buffer level between the inner and outer buffer chambers: Both buffer chambers must be filled up to the electrode with wells completely covered. This will not only prevent leaks from the inside to the outside but will also act a heat sink and prevent wavy dye fronts.
2) Using running buffer that was diluted more than 1X: We recommend using 1X running buffer.
3) Using old running buffer: Make sure that the running buffer is fresh and don't reuse the running buffer.
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It is likely that the Bolt gel cassette was inserted backwards into the unit (large plate facing the front and the wells facing the back) even though this is pretty difficult to do. When the gel is inserted backwards, the current flows from the bottom of the gel to the top, resulting in the samples running in the opposite direction. Reversing of the leads will switch the direction of the gel run, however, this will cause the current to flow from the anode to the cathode. The cathode electrode is made of stainless steel with platinum coating, and the anode electrode is made of platinum wire. Flow of electrons from the anode to the cathode will result in rusting of the steel core. On the other hand, when the leads are connected properly, the electrons flow from the cathode to the anode and the recipient of the electrons is the platinum wire that does not rust.
Note: When the Bolt gel cassette is inserted properly into the Bolt Mini Gel Tank or Mini Gel Tank, the lettering (gel type, SKU and expiration date) printed on the gel cassette reads from left to right (please see Page 11 of the manual (https://tools.thermofisher.com/content/sfs/manuals/mini_gel_tank_man.pdf).
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Here are possible causes and solutions:
1) Buffers are too concentrated or incorrect: Check buffer recipe; dilute or remake if necessary
2) Current is set at a higher limit: Decrease current to recommended running conditions.
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Here are possible causes and solutions:
1) Tape left on the bottom of the cassette: Remove tape from bottom of cassette.
2) Connection to power supply not complete: Check all connections with a voltmeter for conductance.
3) Insufficient buffer level: Make sure there is sufficient buffer in the electrophoresis tank to cover the wells of the gel.
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This could be due to:
*Debris in the well
*High salt in the sample (make sure that the salt concentration does not exceed 50-100 mM)
*Running buffer issue
*Gel casting error
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This could be due to a gel polymerization issue combined with incorrect sample preparation (final sample dilution less than 1X). Please try a different lot of the same gel and make sure that the sample is correctly prepared.
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Possible cause:
*Excess reducing agent (beta-mercaptoethanol)
*Skin protein contaminants (keratin)
Remedy:
*The addition of iodoacetamide to the equilibration buffer just before applying the sample to the gel has been shown to eliminate these artifact bands.
*Use new electrophoretic solutions and wear gloves when handling and loading the gel. This issue is more common when highly sensitive stains are used.
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Possible cause:
*Carry-over contamination of sample from one well into neighboring wells due to loading error
*Contaminated running buffer
*Gel casting error: malformed wells
Remedy:
*Use a gel loading tip to load wells
*Reduce the sample volume
*Do not delay while loading wells
*Do not delay after the run, as proteins can diffuse horizontally; a full well left next to an empty well would eventually contaminate the empty well over time.
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Possible cause:
*Poor polymerization around sample wells
*High salt concentration in sample
*Uneven gel interface
*Excessive pressure applied to the gel plates when the gel is placed into the clamp assembly
*Uneven heating of the gel
*Insoluble material in the gel or inconsistent pore size throughout the gel
*Air bubble during the run
Remedy:
*Remove excess salt/other material by dialysis, Sephadex G-25 or any other desalting column or using an Amicon concentrator.
*Either use a cooled apparatus or reduce the current at which electrophoresis is performed.
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A portion of the protein sample may have re-oxidized during the run, or may not have been fully reduced prior to the run. We recommend preparing fresh sample solution using fresh beta-mercaptoethanol or dithiothreitol (DTT). For NuPAGE gels, we recommend adding antioxidant to the running buffer.
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Gel lifting off the cassette can be caused by:
*Expired gels that are degrading
*Improper storage of gels
*Too much heat accumulating during the electrophoresis run due to excessive current
*Insufficient polymerization of the polyacrylamide
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Ghost bands are usually attributed to a slight lifting of the gel from the cassette, which results in the trickling down of some sample beyond its normal migration point. It then accumulates and appears as a faint second band.
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"Smiling" bands may be the result of the acrylamide in the gel breaking down, leaving less of a matrix for the proteins to migrate. We recommend checking to ensure that the gels have not been used past their expiration date.
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Barbell shaped bands are a result of loading too large of a sample volume. When a large sample volume is loaded, part of the sample tends to diffuse to the sides of the wells. When the run begins and the sample moves through the stacking portion of the gel, the sample will incompletely stack causing a slight retardation of the portion of the sample that diffused to the sides of the wells. This effect may be intensified for larger proteins, whose migration is more impeded in the low concentration acrylamide of the stacking gel. To alleviate the problem, we recommend concentrating the protein and loading a smaller volume. This gives a "thinner" starting zone.
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Here are possible causes and solutions:
1) Sample overload: Do not overload samples
2) Addition of reducing agent that is not fresh: Reduce samples right before loading and do not use samples that have been stored in reducing agent
3)Re-oxidation of the protein during the run: Add antioxidant to the running buffer if you are running NuPAGE gels
4) Presence of highly hydrophobic regions where the protein can exclude SDS: Load the sample with 2X sample buffer instead of 1X sample buffer
5) Excess salt in the sample: Precipitate and reconstitute in lower salt buffer
6) Not enough SDS in the sample: Add SDS to the upper buffer chamber (try 0.1%, 0.2%, 0.3% and 0.4% SDS)
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Although we recommend using the NuPAGE Sample Reducing agent for stability reasons, fresh, neat beta-mercaptoethanol can be substituted for the NuPAGE Sample Reducing Agent, with equivalent results. A final concentration of 2-5% beta-mercaptoethanol is usually sufficient to reduce the sample.
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No. It is not efficient at the higher pH values of the other gel systems.
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Midi gels can be transferred using:
*iBlot Dry Blotting System in conjunction with Transfer Stacks
*Invitrogen Semi-Dry Blotter for simultaneous transfer of up to 2 Midi-gels
*Thermo Scientific Power Blotter for simultaneous transfer of up to 2 Midi gels
*Thermo Scientific G2 Fast Blotter (will be discontinued as soon as we exhaust current inventory).
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All detergents, or even phospholipids in cell extracts, will form mixed micelles with SDS and migrate down into the gel. They can also interfere with the SDS:protein binding equilibrium. Most of the non-ionic detergents, including NP-40, are the worst at interfering with SDS-PAGE. The rule of thumb is to keep the ratio of SDS to lipid or other detergent at 10:1 or greater to minimize these effects.
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All Invitrogen protein gels contain sucrose as a density-adjusting agent to facilitate pouring of the gel. Protein samples run on Invitrogen gels would be contaminated with large amounts of sucrose. Thus, Invitrogen gels are not recommended for this application.
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The cassettes are made of a styrene copolymer.
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We do not recommend recycling our plastic cassettes because they have a chemical coating on them that may produce toxic fumes when melted and potentially cause contamination.
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Midi gels are wider than Mini gels and hence have a larger number of wells to accommodate additional samples in one gel. An experiment from a Mini gel can be easily scaled-up to a Midi gel of the same gel chemistry.
Midi gels:
*NuPAGE Bis-Tris, NuPAGE Tris-Acetate, & Invitrogen Tris-Glycine: Gel dimensions are 13cm x 8.3cm and Cassette dimensions are 15cm x 10.3cm.
Mini gels:
*NuPAGE Bis-Tris, NuPAGE Tris-Acetate, & Invitrogen Tris-Glycine: Gel dimensions are 8cm x 8cm and Cassette dimensions are 10cm x 10cm.
*New Bolt Bis-Tris Plus (Cat. No. NWxxxxxBOX): Gel dimensions are 8cm x 8.3cm and Cassette Dimensions are 10cm x10cm.
*Original Bolt Bis-Tris Plus (Cat. No. BGxxxxxBOX): Gel dimensions are 8cm x 8.3cm and Cassette Dimensions are 10cm x 10.5cm.
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All of our Invitrogen precast protein gels (NuPAGE gels, Bolt Bis-Tris Plus gels, and Novex gels) are available in Mini format. Our Mini gel dimensions are 8 cm x 8 cm and the cassette dimensions are 10 cm x 10 cm.
Our NuPAGE Bis-Tris, NuPAGE Tris-Acetate, and Novex Tris-Glycine Plus gels are also available in the wider Midi format. Our Midi gel dimensions are 8 cm x 13 cm and the cassette dimensions are 10 cm x 15 cm.
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All our Invitrogen protein gels are available in Mini format. Certain gel chemistries (NuPAGE Bis-Tris, NuPAGE Tris-Acetate, and Invitrogen Tris-Glycine gels) are also available in the wide Midi format.
Note that Bolt Bis-Tris gels are not available in the Midi format and our Thermo Scientific Precise precast gels are only available in Mini format.
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If you are running the gels at constant voltage, you do not need to increase the voltage regardless of the number of gels. However, the resulting current and wattage observed will multiply linearly with the number of gels. Keep in mind that the expected total current for your gels should not exceed the current limit of the power supply, or else the current will plateau and the run will slow down. (For example: Recommended constant voltage for running a NuPAGE Bis-Tris gel with MES Buffer is 200 V, with a starting current of 110-125 mA/gel and end current of 70-80 mA/gel. If the power supply has a current limit of 500 mA, the maximum number of NuPAGE Bis-Tris gels that can be run at one time with full power is 500 mA/125 mA = 4 gels. Any additional gels will decrease the current per gel and increase the run time.
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We do not recommend running reduced and non-reduced protein samples on the same gel, especially in adjacent lanes, since the reducing agent may have a carry-over effect on the non-reduced samples if they are in close proximity.
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We do not recommend storing reduced protein samples for long periods of time even if they are frozen because reoxidation of the sample may happen during storage, causing inconsistent results.
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*Tris-Glycine gels (except 4% Tris-Glycine gels) have a 34.5:1 Acrylamide:bisacrylamide and 2.6% Crosslinker.
*4% Tris-Glycine gels have a 76:1 ratio Acrylamide:bisacrylamide and 1.3% Crosslinker.
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The percentage of the stacking gel is 4% in most of our gels including the Bolt Bis-Tris Plus gels. The NuPAGE Tris-Acetate gels contain a 3.2% stacking gel.
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Our Invitrogen precast protein gels contain a stacking gel that is ~8 to 9 mm long (it ends right above the first ridge on the cassette). The manufacturing method used results in an interface between the stacking and resolving gels that is not visually detectable.
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*Tris-Glycine and Invitrogen Tricine Mini gels: see here (http://tools.thermofisher.com/content/sfs/manuals/electrophoresisguide_man.pdf), Page 8
*NuPAGE Tris-Acetate and NuPAGE Bis-Tris Mini gels: see here (http://tools.thermofisher.com/content/sfs/manuals/nupage_tech_man.pdf), Page 10
*Bolt Bis-Tris Plus Mini gels: see here (http://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-gel-electrophoresis/protein-gels/bolt-bis-tris-gels.html)
*Thermo Scientific Precise Tris-HEPES gels: see here (https://tools.thermofisher.com/content/sfs/manuals/MAN0011499_Precise_Protein_Gels_UG.pdf), Page 1
*Midi gels (Invitrogen Tris-Glycine, NuPAGE Bis-Tris and NuPAGE Tris-Acetate): see here (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/novex_midigel_man.pdf), Page 4
*Thermo Scientific Precise Tris-Glycine gels: see here (https://tools.thermofisher.com/content/sfs/manuals/D25MAN0011814_Precise_TrisGlycine_Gels_UG.pdf), Page 1
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