Posts Tagged ‘electrophoresis’

8 critical tips for western blotting analysis

 :: Posted by American Biotechnologist on 01-12-2012

So you think that protein transfer for western blotting is a piece of cake? Consider these important tips before proceeding:

  1. Use only high-quality, analytical grade methanol. Impure methanol can increase transfer buffer conductivity and yield a poor transfer.
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  3. In many cases, ethanol can be substituted for methanol in the transfer buffer with minimal impact on transfer efficiency. Check this using your samples.
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  5. Do not reuse transfer buffer since the buffer will likely lose its ability to maintain a stable pH during transfer.
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  7. Do not dilute transfer buffers below their recommended levels since this decreases their buffering capacity.
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  9. Do not adjust the pH of transfer buffers unless specifically indicated. Adjusting the pH of transfer buffers can result in increased buffer conductivity, manifested by higher initial current output and decreased resistance.
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  11. Increasing SDS in the transfer buffer increases protein transfer from the gel but decreases binding of the protein to nitrocellulose membrane. PVDF membrane can be substituted for nitrocellulose when SDS is used in the transfer buffer.
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  13. Addition of SDS increases the relative current, power, and heating during transfer, and may also affect antigenicity of some proteins.
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  15. Increasing methanol in the transfer buffer decreases protein transfer from the gel and increases binding of the protein to nitrocellulose membrane.

 

To learn more tips and tricks, download the Protein Blotting Guide from Bio-Rad Laboartories.

Analyzing Protein Bands with the Experion Automated Electrophoresis System

 :: Posted by American Biotechnologist on 12-22-2011

In this video you will learn how to analyze results from a Pro260 using the Experion Automated Electrophoresis System software by Bio-Rad Laboratories.

Proteomic Application Tips Grand Finale

 :: Posted by American Biotechnologist on 12-14-2011

In previous posts we provided you with several great tips for proteomic researchers (see five great tips for researchers working with proteins and more great proteomic applications tips). Today we will present you with the final in the series of application tips which are sure to improve the quality of your proteomic experiments.

  • To ensure proper and consistent visualization with a silver stain, use ultrapure water with all organic contaminants removed for the final rinse of your staining vessel. In addition, reserve that vessel exclusively for silver staining, and separate it from other glassware in your laboratory.
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  • Proteins must be soluble if they are to be separated and identified on 2-D gels. Protein insolubility (precipitation) leads to loss of sample spots and streaking on 2-D gels.
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  • Fractionation may improve your 2-D result by reducing sample complexity, improving the range of detection, and enriching low-abundance proteins. Fractionation can be performed according to many protein properties, including subcellular location, solubility, size, charge, and pI.
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  • Improve the resolution and reproducibility of 2-D gels by performing sample cleanup to remove salts, charged detergents, phenolics, lipids, sugars, and nucleic acids. Cleanup will also reduce disulfide bonds.
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  • NaCl increases conductivity, extends the time required for focusing, causes electroendosmosis, and results in uneven water distribution in the gel. In general, the tolerated concentrations of NaCl for proper in-gel rehydration and cup loading are 10 mM and 40 mM, respectively.
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  • Nucleic acids bind proteins through electrostatic interaction, thereby interfering with isoelectric focusing. Nucleic acids can also clog the pores of the acrylamide matrix. Remove nucleic acids with nucleases and ultracentrifugation in the presence of carrier ampholytes. In addition, benzonase can be used in a sample together with urea to remove DNA or RNA contamination.
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  • Insoluble material in a sample obstructs gel pores, resulting in poor focusing and severe streaking. Remove these materials by high-speed centrifugation (for example, 20,000 x g for 30 minutes at 20°C).
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  • To monitor the initial progress of the electrophoresis on the IPG strips, add up to 0.001% of Bromophenol Blue to both the rehydration and equilibration buffers.

For more great tips visit www.expressionproteomics.com

More great proteomic application tips

 :: Posted by American Biotechnologist on 11-28-2011

In a previous post we provided you with five great tips for researchers working with proteins. Today we will present you with five more tips which are sure to improve the quality of your proteomic experiments.

  • Negatively charged polysaccharides that contain sialic acid can produce horizontal streaks similar to those generated by nucleic acid contaminants. Ultracentrifugation is often sufficient to remove carbohydrates from samples.
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  • To prevent vertical streaking, limit the amount of protein added onto an IPG strip. Compensate for such decreases in sample load by using a more sensitive staining technique, such as silver staining.
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  • Reusing electrophoresis running buffer can result in poor separation and vertical streaking due to the depletion of ions and SDS in the running buffer. Avoid this practice, especially if vertical streaking is a persistent problem.
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  • Vertical streaking on second-dimension gels is often caused by gaps between the IPG strips and the gels. Ensure the second-dimension gel has a straight and level top edge, and that the IPG strip is in direct contact with the gel along its entire length.
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  • If some of the bands on your gel are not staining or appear faint, use silver stain as usual, then agitate it slowly in deionized water for 30 minutes and repeat. Then apply the silver stain again, starting with the silver reagent step. Proteins that did not stain on the first cycle will stain to full intensity.

For more great tips visit www.expressionproteomics.com

Efficient Electrophoresis and Protein Blotting: Aiding Advances in Cardiomyopathy Research

 :: Posted by American Biotechnologist on 11-17-2011

A native of Trinidad and Tobago, Dr Aldrin Gomes decided to specialize in the biochemical differences between normal and diseased hearts in his graduate studies at the University of the West Indies. A significant portion of his research utilized protein separation and purification techniques, making SDS-PAGE electrophoresis and protein blotting an essential tool in most of his experiments. But in a country where resources are scarce, unrelenting heat is destructive to sensitive biological materials, and slow delivery times are common for product orders, Gomes and his colleagues began to analyze the electrophoretic workflow to determine how to make the process as efficient as possible. “Because we performed a lot of electrophoresis, we published some articles whereby we looked at how we could standardize things to improve resolution in our results,” says Gomes. “We heavily researched aliquoting methods, sample buffers (methods for making them and determining actual shelf lives), whether or not buffers can be reused — even minor factors such as gel pouring techniques and plate thickness.”

Since Gomes “grew up,” scientifically speaking, in an environment where experiments must be planned far in advance and resources cannot be wasted, he cultivated the habit of designing experiments and procedures that made the best possible use of tools and time while ensuring optimal results. This followed him through his graduate work and his subsequent career, first as a research associate, then in his current role as assistant professor in the Neurobiology, Physiology and Behavior department in the College of Biological Sciences, and Physiology and Membrane Biology department in the School of Medicine at UC Davis.

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