Posts Tagged ‘electrophoresis’

Brilliant yet simple method for labeling polyacrylamide gels

 :: Posted by American Biotechnologist on 03-24-2011

Most people who have run polyacrylamide gels have at one point or another gotten confused with the gel’s orientation. This is especially true following protein transfer from the gel to a membrane for the purpose of western blotting or other downstream processing. This can be extremely frustrating and may even jeopardize your entire experiment if you are unable to tell the right side of the gel from the left or your control samples from your treatment group.

Several methods have been created to help bench scientists avoid this problem. These include the use of multicolored protein ladders and marking a predefined corner of your membrane once the protein has been transfered (I cut the bottom left corner of the membrane).

Today, Arefeh Seyedarabiclose from the Department of Structural and Molecular Biology, University College London published a new and very basic method for labeling polyacrylamide gels on the Nature Protocol Exchange website. Essentially, Arefeh suggests labeling the bottom inside corner of the long glass plate (facing the gel) with permanent marker). During electrophoresis the label will transfer from the plate to the gel, thereby permanently labeling your gel. Simple and brilliant!

To see the full method and associated figures click on A method for labeling polyacrylamide gels.

If you would like to share other great molecular biology methods, please post a comment or send us an email using the email button at the top of the page.

Arefeh Seyedarabi, A method for labeling polyacrylamide gels, Protocol Exchange (2011) doi:10.1038/protex.2011.222, Published online 24 March 2011

Interdisciplinary Approach Creates New Tools for Protein Scientists

 :: Posted by American Biotechnologist on 06-23-2010

One of my favorite pastimes is reading about situations where experts from different (and seemingly divergent) disciplines get together to discuss interdisciplinary cooperation and mutual progress. All too often scientists segregate themselves according to their area of expertise and only make use of the techniques that they are familiar with or have access to in order to answer the question at hand. While this may be a more comfortable approach to science it tends to overlook the benefits that can be achieved by incorporating techniques from other disciplines into one’s research methodology.

Now for a personal disclosure statement: I am a molecular biologist. I too am guilty of focusing on what I know and ignoring techniques that seem foreign to me. So when I came across a paper that had the term synchotron x-ray fluorescence, my mind froze and I thought that I had accidentally surfed into an area that I was not allowed to enter (but it got through my firewall anyway). My google alert is set to receive articles on protein electrophoresis so I can stay abreast of the latest developments in my field. How did x-ray fluorescence sneak in there? Nonetheless, after overcoming my initial uncertainly, I clicked through to the article which I am glad to report will make an interesting blog post.

In a recent issue of ACS Chemical Biology, Lydia Finney and her team from the Argonne National Laboratory in Argonne, Illinois presented a new use for two relatively old and well-established technologies in the study of protein-metal ion interaction. What I found particularly interesting about this study was its synthesis of analytical techniques common to chemistry and biology. Essentially they ran protein samples on a nondenaturing PAGE, immobilized them on a membrane and performed XRF mapping. While both electroblotting and XRF imaging are common in their respective fields, this is the first time that they have been used in concert to solve a scientific problem. The result is an eloquent technique for analyzing the complex mechanisms that regulate metal toxicity and metalloproteomics.

In a commentary to the article written in the same issue of ACS Chemical Biology, Nathan Zahler notes that the fusion of these techniques opens up the road for several other interesting studies such as assessing the interrelationships in the regulation of different transition metals, the study of post-translational modifications that incorporate non-metallic elements and 2D electrophoretic separations for increased protein resolution and mass spectroscopic identification of metal binding proteins.

Whatever the case may be, this study is a prime example of what can be accomplished by out of the box thinking and networking among like-minded individuals from diverse scientific backgrounds.

How has your research been impacted by incorporating techniques from other disciplines? I’ve heard that there are several scientific societies dedicated to interdisciplinary research. Have you come across groups that are worth investigating?

Finney, L., Chishti, Y., Khare, T., Giometti, C., Levina, A., Lay, P., & Vogt, S. (2010). Imaging Metals in Proteins by Combining Electrophoresis with Rapid X-ray Fluorescence Mapping ACS Chemical Biology, 5 (6), 577-587 DOI: 10.1021/cb1000263

A gel worthy of high-impact publication

 :: Posted by American Biotechnologist on 03-02-2010

Yes…SDS PAGE is boring. But it’s an indispensable part of our bench research. We put tons of time into designing experiments, sample prep and playing video games (oops…Freudian slip). It is therefore absolute torture when we load our precious sample into a gel, run it for 30 to 60 minutes only to discover that the quality of the gel has significantly compromised what promised to be an award winning figure worthy of publication in the likes of Nature or Science (would you even think of publishing anywhere else?).

For as long as I can remember, Bio-Rad has been at the forefront of electrophoresis technology. There is hardly a graduate student out there who has not come across a green MP3 or MP tetra electrophoresis unit during the course of their graduate work. Now Bio-Rad has released a new SDS Polyacrylamide Gel that provides high resolution separation regardless of the origin or complexity of the sample. Moreover, whether you are a 2-D researcher, a “stainer” or a run of the mill 1D separation type of scientist, the new TGX gels will help you produce results that your reviewers will be proud of! See the tech note for more details.

When Separation is Critical…

 :: Posted by American Biotechnologist on 02-22-2010

Molecular biology has always included an element of separation. Whether it be by chromatography for proteins or electrophoresis for the “Big 3″ (proteins, DNA and RNA), separating complex biological mixtures into well defined components is a cornerstone of molecular bench work. Over the last decade, these separation techniques have become more fine-tuned culminating with the advent of electrophoretic microchip platforms in the 1990s. Automated electrophoresis systems have helped speed up sample run times on the order of hundreds of seconds resulting in the ability to resolve many more samples with higher resolution in a shorter period of time.

In this technical note, Bio-Rad describes the performance of a number of assays available with the Experion automated electrophoresis system compared to another system on the market. The article shows that the Experion is a powerful tool for automated electrophoresis and can be an invaluable tool for your molecular research.