I am using the MEGAscript RNAi Kit for synthesizing dsRNA for RNAi. I ran my reaction product on a denaturing gel and got a smear. Can you offer some advice?
If the RNA appears degraded (e.g., smeared), remove residual RNase from the DNA template preparation before in vitro transcription. Do this by digesting the DNA prep with proteinase K (100-200 µg/mL) in the presence of 0.5% SDS for 30 min at 50°C, and follow this with phenol/chloroform extraction. The RNase Inhibitor that is present in the transcription reaction can only inactivate trace RNase contamination. Large amounts of RNase contamination will compromise the size and amount of transcription products.
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Find additional tips, troubleshooting help, and resources within our RNAi Support Center.