Hi Vanessa It is better to get rid of traces of residual acrylamide that may contaminate your final purified and refolded RNA. It is usual to have contaminations with monomeric acrylamide. NMR spectroscopists studying RNA can usually detect its presence on their spectra. If you can dialyze your purified product to try to get rid of it it would be the best. Traces (sometimes it is not a negligible amount) are not good because you may not be able to reproduce your results and optimize eventual crystals. And for RNA this can be an excruciating pain. When we transcribe RNA, we usually run the preparative acrylamide-urea gels and elute the RNA out of the gel (most of the time by electroelution). The RNA usually contains urea and acrylamide so I either precipitate using the salt/ethanol technique and then resuspend the pellet and dialyze/refold or I further purifiy on an ion exchange (Q type column) to try to clean it up.
If you have an NMR spectroscopist friend around, try to look at the presence of acrylamide before and after these steps and see what works the best for you. Hope this helps Pascal Egea, PhD University of California San Francisco Department of Biochemistry and Biophysics
