09 February 2022 0 6K Report

I performed the RNase footprint with an 106-nt RNA. However, my hydrolysis ladder showed poor resolution from the >35-nt bands (attached figure). I used the 8M Urea gel with 10% AcrylamideBis 19:1 and a 30-cm gel casting (0.75mm thickness). I set the voltage as 500V (the current displayed as 17mA at the start and kept decreasing to 6 mA) and ran the gel until the 17-nt band reached to the end. Some denature gel protocols mentioned that the gel will be heated up to 50-55 degree during running, but my gel was quite cool.

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