What type of analytical agarose gel do I need for my RNA samples?
Since RNA is a single-stranded nucleic acid and tends to form secondary structures, a standard agarose gel will not give an accurate size separation of your total RNA or mRNA sample. Therefore a denaturing agent like formaldehyde must to be added to the agarose gel and the RNA to ensure the molecules remain single-stranded. Because of the single-stranded nature of the molecule, RNA tends not to incorporate stains like ethidium bromide as well as DNA. We recommend including ethidium bromide in both the loading buffer and the gel to give better staining and visualization of the RNA. The following is a basic protocol for pouring a denaturing MOPS buffer/formaldehyde gel and performing electrophoresis of RNA samples to visually assess the quality of the purified RNA (1). • Prepare a 1% agarose/formaldehyde gel containing 0.5µg/ml ethidium bromide as follows: Components Volume 5X MOPS buffer (see recipe below) 20ml DEPC-treated or Nuclease-Free Water (Cat.# P1193) 72ml Agarose, molecular bi
