DNA vs Protein Stains - Are there any that don't stain BOTH? (Apr/16/2009 )

Hi folks - I do a lot of gel-shift assays that result in both proteins and DNA being included on the same gel, and in the same lanes. It's vital to be able to tell, after staining, which bands are proteins and which bands are DNA. Do any of you have experience with stains that ONLY stain DNA and not protein or vice versa? I've tried: SYBR Green, Flamingo, GelStar, Eth. Bromide, and SYBR Ruby, all of which have carryover (i.e. when you image it, regardless of whether your scanning at the Nucleic Acid or Protein wavelengths, both DNA and protein bands show up.

Any ideas? p.s. Please stick to stains - I don't want to get too crazy with fluorescent oligo labels or DIG labels or anything like that.

Thanks folks,

Chris

In my experience with EMSA, DIG probes are commonly used. I know it is expensive, but it will save you time and cross-staining issues. I suppose the other way to do it, would be to find something that stains only proteins, and then bind that along with another dye that will stain both DNA and protein, then do a subtraction of the regions that stain for protein only.