Nucleic acid staining and PCR - Query onthe effect of nucleic acid stains on PCR (May/05/2009 )

Can anybody tell me if DNA stained with nucleic acid stains (in this case SYTO 9 - Invitrogen), will have an effect on its amplification by PCR, or indeed its purification using a spin column technique?

The effect on PCR is hard to judge unless you know the how the stain works (i.e. chemical or physical interaction?). Stains such as EtBr which interact physically without affecting the chemical structure should have little affect at low concentrations, and should be able to be washed away before PCR. A substance that actually chemically alters the DNA will probably affect the PCR more, especially as it may well sterically hinder the polymerase from traveling along the DNA.