Make sure that RNase A is added into PD1 (or PM1) Buffer. Store the PD1 (or PM1) Buffer at 4ºC. If RNase A-added PD1 (PM1) Buffer is not properly stored at 4ºC or has been stored for a long time (e.g. more than 6 months) RNase A activity may have been reduced, thus not being able to degrade RNA completely. In this case, fresh RNase A has to be added into PD1 (PM1) Buffer with a final concentration of 50 mg/ml. Again, store the buffer at 4ºC.
Why do we get eluted plasmid contaminated with RNA? "