I need to do troubleshooting for getting proper RNA bands in the gel. So any method or way of troubleshooting is welcome. And my samples are either getting stuck in wells of the gel or are getting smeared. How to take care of this?
Your RNA are getting stucked because maybe your UREA-PAGE concentration is higher than it is supposed to be, allowing the polymerization of polyacrilamide and then this polymer is blocking the flow of your analysis because is denser than the buffer impeding the sample migration to the gel.
Understood what you said, so how I should go about troubleshooting?
1 way of troubleshooting that I did was treating the samples with formalin and SDS and then loading in gel which did result in movement from the wells.