I've used cresol red for years in routine Taq-based PCR's. I've never used it with high-fidelity systems such as Phusion. I can only find information online stating its compatibility with Taq polymerase, but what about Pfu polymerase?
The coloration is a great indicator of potential pH problems (purple=good, yellow=bad) and we tend to confirm our PCR's by electrophoresis prior to cloning and sequencing. We often run many reactions so adding a loading dye after the fact takes up a lot of time and introduces the potential for cross contamination.
Sure, adding dye after PCR reaction can take a lot of time. But for that there are PCR master mix available with dye included. So, in that case one dont need to worry about the compatibility. I can't say about the pH, since I personally have never had any problem with the pH in PCR reaction.
Thanks Abhijeet. We work with a variety of plant materials that are quite recalcitrant when it comes to extractions, so a pH check is necessary. We're not looking to adopt new systems as ours are quite optimised.
Question remains open
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