Hi I'm trying to concentrate DNA extracted from Formalin fixed paraffin embedded(FFPE) tissue. Some protocols say that you have to incubate the DNA with sodium acetate at pH 5.2 and 100% ethanol at -20ºC for 30 minutes while some say overnight. Since my DNA is fragmented due to fixation and the maximum length of fragments of genomic DNA available in this FFPE tissue range from 200-400 bp, what could be the optimum duration of incubation? Note that I also add 1 ul of Glycogen along with 100% ethanol to visualize the pellet.
There is no difference between incubating for 30 minutes vs longer (overnight). You will not see any more precipitated product in a longer incubation. However adding more glycogen will help in the precipitation of small fragments/small quantities of DNA as well as keeping the total volume of your precipitation small.
Good luck!
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