I prepared blocking solution and RNA probe afresh but the same faint shift keeps on coming. To check whether the detection system is working I performed the detection system check with same RNA probe & there I get a nice shift. However, the problem persists when I do a gel shift with same probe. If anyone is using this technique (RNA gel shift) please share your opinions/suggestions.
There are few things you may want to check,
1. Run the gel at 4 degree C and use cold buffer.
2. Run at low voltage to reduce heating.
3. Pre-run the gel at cold for 30 min prior to your sample loading
and
4. Clean the well just before loading your sample
hope this helps,
Good luck,
Amaresh
Thank you. I usually follow all the steps you mentioned when I do gel shifts. What will pre-running the gel for 30 mins do? I do pre-run when I analyze RNA on Urea gel to make sure remaining Urea is removed from the gel.
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