weak band during denature agarose gel electrophoresis of RNA - RNA denature agarose gel electrophoresis (Nov/07/2006 )

I ran agarose gel electrophoresis today to check whether or not there is degradation during RNA isolation. But the picture of elestrophoresis is very unclear. I prepare the sample without EtBr during electrophoresis but add a dye step after electrophoresis. I added 5ul of 10mg/ml EtBr into 100 DEPC water for dying step. After one hour dying step. the band is still very unclear as it shown in attachment. I want to know what are the possible reason for the unclear band. The marker is also unclear (indeed, it is DNA marker not RNA marker. In the 2nd well from left hand). Sample is in the 4th well.
Thank you.

Someone suggest me check it by nature gel electrophoresis. So I did it and the result is shown as the attachment.
Sorry for the bad quality of gel.

Did you destain the top gel after staining? The formaldehyde background often masks the bands so you need to get the excess formaldehyde out of the gel

I would suggest staining for 20 mins then destaining for the same length of time in water. I used to include the EtBr in the gel as I poured it

Have a look at my protocol here

http://molecularbiology.forums.biotechniqu...pic.php?t=10217

Thank you very much. And now I know, it should be called "stain" not "dye".
I think our protocol are similar. I will have a try the destaining step.