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What test to perform on DNA?

What test to perform on DNA? - DNA Techniques

What test to perform on DNA? - Post questions and discuss DNA techniques and protocols such as DNA extraction, PCR, and the study of DNA-binding proteins.


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Old 09-13-2011, 09:20 PM
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Default What test to perform on DNA?



Hi all,

First off, what is more stable, DNA, or proteins (and how did you arrive at that conclusion)? The part in parentheses is somewhat important, as our lab is deciding on tests to run on 5 year old samples, and we need to think about what to do with our very limited quantity of sample.

My boss thinks that DNA is more stable, and my coworker thinks that protein is more stable.

Presuming that DNA is more stable, what sort of tests can we run on our samples (between knockout and wildtype) that might be able to show some interesting information? My boss has suggested EMSA. Anything else you can think of?

Thanks!
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Old 09-14-2011, 01:27 AM
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Default Re: What test to perform on DNA?

Well its impossible to compare unless they are both extremely clean and stored at the same temperature. Lyophilized proteins store extremely well, even better if its recombinant protein - possibly even better than genomic DNA that is isolated from cells or bacteria.

However generally protein samples are usually more "dirty" meaning they are not isolated by column to exclude anything else - so DNA, RNA (and proteinases are present but usually inhibited) - so they usually degrade very quickly especially when at -20C. Depends what you want to do with the protein, if you want to test activity forget it! If you want to isolate a protein I would start again. Only probably good western blot or ELISA if stored properly.

DNA samples if stored on filter paper or -80C are usually tough enough if isolated well. EMSA usually requires quite fresh DNA well isolated DNA as you will get a smudge if there is any degradation but it would be a waste of DNA (kind of point-less to do EMSA) as you can even just PCR those fragments for EMSA.

If you are using that protein for EMSA binding assays on DNA, forget it you need fresh well folded, active protein.

Last edited by admin; 09-14-2011 at 01:34 AM.
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Old 09-14-2011, 03:04 PM
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Default Re: What test to perform on DNA?

Thank you very much for the reply. I forgot to add, the samples are stored as tissue samples. So for instance, hippocampus, neocortex, brainstem, etc. So the DNA and proteins are mixed together, and stored in the -80 for 5 years.
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Old 03-24-2012, 03:48 AM
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Default Re: What test to perform on DNA?

DNA tests observe three major stages. The first stage refers to the act of obtaining DNA samples. It could be a piece of a hair, a dried body fluid on a cloth or any other material, a layer of skin, samples of blood and other forms of body fluids, a mouth swab or any fragment of the body that can be traced back to the person being searched or tested.
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