If the concentration of ethidium bromide is very high, what will have effects on visibility of bonds production on agarose gel.
What is the best alternative for ethidium bromide?
If you're trying to remove contaminating RNA in your preps, a simple RNase treatment should suffice, I think. Run two lanes on your gel, with and without RNase treatment and see if there are any changes in smearing/dodgey bands.
if it's low levels of RNA that you're trying to visualise, your best bet is to use SYBR Gold. It's more sensitive to single-stranded oligos than ethidium and has a very short staining time (5-30min). Adding too much ethidium on your gel can cause a lot of background fluorescence when visualising as well. Note that the SYBR Gold emission spectra is different from Ethidium Bromide as well so you might need a different filter on your imaging dock to see SYBR Gold-stained samples.
The best alternative for ethidium bromide is GelRed - fluorescent nucleic acid gel stains with high sensitivity and exceptional stability.
If you have too much EtBr, it could increase the background levels to make it hard to see your band of interest. I agree the both SYBR gold and GelRed are good alternatives to EtBr for RNA.
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