I understood that you need to have completely denatured RNA. Then you should mix the sample with good quality loading dye solution that contains formamide (like Fermentas 2X RNA Loading Dye Solution (#R0641)), heat at 70ºC for 10min, chill on ice for 3 minutes and load onto the gel.
Best would be to use denaturing formaldehyde agarose gel in MOPS buffer according to the below protocol:
• Freshly prepare 10X MOPS buffer:
0.4M MOPS (pH 7.0),
0.1M Sodium acetate,
0.01M EDTA (pH 8.0).
• Prepare 1% gel as follows:
-Stir 1g of agarose powder in 72ml of deionized water
-Melt the agarose, and then add 10ml of 10X MOPS buffer and mix.
-When the agarose solution cools to 60°C, add 18ml of fresh formaldehyde (37%) in a fume hood and mix thoroughly.
- Pour the gel.
• Place the gel into an electrophoresis apparatus containing 1x MOPS buffer
• Heat the RNA samples and ladder at 70°C for 10min, and then chill on ice for 3 minutes. Load onto the gel.
Try, I believe this will work