Are GelRed® and GelGreen® compatible with downstream applications such as cloning, ligation and sequencing?

Yes. We recommend Qiagen or Zymoclean™ gel extraction kits or phenol-chloroform extraction to remove the dye from DNA. Some users have reported performing PCR on DNA in the presence of GelRed® with no purification step, for example by incubating GelRed®-stained gel slices in TE buffer to extract DNA by passive diffusion for use in PCR, or by using a few microliters of molten agarose from GelRed®-stained gel slices containing DNA for PCR.