EMSA probe - (Mar/02/2007 )
What is the longest probe that you have used in an EMSA? I typically use 30bp, but I would like to use something much longer.
I have used probe up to 700bp long, it was working OK for me, 4% gel.
700 for EMSA? why?
I do not understand how you can ensure specificity? it only takes a handful of bases to be recognized by the TF. a 700bp probe could potentially bind a very large number of TFs. the only advantage I see, is that if very extensive secondary structure as well as a large number of TFs are the subject of your study..but wouldn't it still be hard to make sense of your data?