Hydroxyamine will react with citosyne and guanine in RNA and DNA. You should estimate amount of RNA/ DNA in your sample and adjust amount to your reaction.
Why do you want the RNA contaminant appear in your mutagenesis work. Remove all RNA by simple RNAse and then carry out the mutagenesis. Why do you want to invite trouble unnecessarily?
@ Jai: Actually what happened was in one of the sets RNA was not removed by mistake, so i just wanna know to what extent RNA would effect the experiment..