|MadSci Network: Molecular Biology|
Hello you, I must say that this is a question that I have never asked myself. I have thought a lot about it and I finally did a trial gel just to UV shadow some DNA but I couldn't see because of the thickness of the gel (even if I had taken care of that). I think that there is no problem with the migration. We should say that both the acrylamide and agarose gels are based on a matrix that acts as a sieve in an electrical field. So, no worries about the basic principles. However, I have to say that you should try to make your gel as thin as possible in your agarose tray because it could potentially be a problem for the staining and/or observation of your gel afterwards. Finally, if you don't own one and have some money to spare, the ideal way to go is to get a MINI-PROTEAN II (or III) system from BIORAD (or something similar). These apparatus are designed to do protein stuff but I use them for nucleic acid work. They are small (about 6X6 cm) and can do quite thin gels. I typically use ten times less acrylamide to do the same job. Of course, the more resolution you need, the longer your gel should be. Nevertheless, these gels can do a good job in some situations. Hope this helps, Daniel
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