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If I'm understanding your question correctly, make sure to add an RNAse inhibitor to your RNA sample.
Iam not sure what you trying to ask,
I have performed gel electrophoresis many times. However, i used it mainly for DNA identification by the usage of restriction enzymes. I used to get RNA contamination sometimes, but it did not migrate as DNA. RNA looked very bright in colour and they remained in the wells.
to my understanding DNA and RNA are both macromolecules, so iam not sure what you mean by ''handling".