Hi, I am developing an assay based around seeing yoyo stained DNA after a one hour treatment with 1M HCl. The DNA is "naked" (ie, stripped of all proteins) and stretched on a PDMS gel. Does anyone have any insight into the potential for the harsh pH to effect the fluorescence of DNA prestained with yoyo?
Hi Nicholas,
Yoyo is a dye based on an oxazole group. I've joined its synthesis scheme. The oxazole group is a bit similar to a substituted aldehyde and therefore, in theory, highly susceptible to acid pHs!!! But in the case of YOYO, there is a loooong extensive delocalization of double bonds (hence fluorescence). The longer teh delocalization, the higher the decrease in reactivity of the oxazole and the higher its stability to acidic conditions. To my opinion, YOYO should be stable in acidic conditions.
Best wishes
Philippe
Thanks Philippe, as it turns out you are correct.I got the results today. no diminished fluorescence. if anything I saw lower background.
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