I have been doing RNA EMSA and UV-crosslinking studies for a while. My UV-crosslinking used to work beautifully until I had to change my RNase T1, since then I have been getting a lot of background and my complexes are not nearly as strong as they used to be. One thing that baffles me in particular is that when I run just my RNA probe on 10% SDS gel with or without UV crosslinking, I see a smear that runs along the entire length of my running gel; my stacking gel, however, is clean. Does anyone have any experience with this? Could you please tell me what is causing this smear?
RNA EMSA help
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