How to denature RNA by using agarose gels
RNA is fractionised by running through a 1.2% Agarose, 2% formaldehyde gel (120ml gel = 1.44g agarose, 6.96ml formaldehyde, 12ml 10xMOPS, 100ml DEPC treated water; MOPS and formaldehyde added after dissolved agarose has cooled to 65°C). Samples contained 10 mg of total RNA in 20 ml RNA running buffer consisting of 50% deionised formamide, 7% formaldehyde, 0.5mg/ml ethidium bromide, 1mM EDTA, 20% glycerol, 1xMOPS buffer, 0.25%bromophenol blue.
Prior to loading, samples were heated for 10 min at 65°C. Electrophoresis was performed at 5V/cm gel for 2Hrs in a fume hood.