Electrophoresis permits assessment of RNA by size and amount. However, in native gels RNA electrophoretic mobility will depend on not only the size of the RNA but also its secondary structure.
The procedure for running a native RNA gel is very similar to that for running a DNA agarose gel. Here are a few things to note.
- At least some protocols discuss using TBE buffer (89 mM Tris-HCl pH 7.8, 89 mM borate, 2 mM EDTA). However, TAE buffer should be sufficient?
- The samples can be loaded directly without heating.
- An aliquot of intact RNA should always be run as a positive control to rule out unusual results due to gel artifacts.
- Run the gel at low voltage (reports of 5-6 V/cm or 8V/cm are common as measured between the electrodes).
- These are run at low voltages - 8V/cm - and 1 x TBE to prevent denaturation of small fragments of RNA by the heat generated in the gel during electrophoresis. The rate of migration is approximately inversely proportional to log10 of their size. However, the base sequence composition can alter the electrophoretic mobility of RNAs such that two RNAs of the same size may show up to a 10% difference in electrophoretic mobility. 
- Native agarose gel electrophoresis may be sufficient to judge the integrity and overall quality of a total RNA preparation by inspection of the 28S and 18S rRNA bands. The secondary structure of RNA alters its migration pattern in native gels so that it will not migrate according to its true size. Bands are generally not as sharp as in denaturating gels, and a single RNA species may migrate as multiple bands representing different structures.