Hello,
I am using the QIAamp Fast DNA Stool Mini Kit for DNA isolation from mouse fecal samples. My results are showing both low DNA concentration and a low A260/230 ratio. This seems unusual, since in previous isolations from the same fecal samples I obtained much higher concentrations.
Is it normal to occasionally get such low yields with this kit, or could this indicate a problem with the extraction process? What would you recommend to improve the concentration and purity in this situation?
Hello Hazal
Some variability with stool is expected, but low yield plus low A260/230 usually means inhibitor carryover or overloading. I’d standardize the input and homogenization, follow the kit’s exact lysis temperature/time, and ensure accuracy with the InhibitEX/debris-pellet step.
Add an extra AW1/AW2 wash and a 1–2 min dry spin, then elute with pre-warmed buffer (smaller volume, 5 min incubation). If purity remains low, perform a quick post-extraction clean-up and quantify using Qubit. These tweaks usually fix both yield and A260/230.
One way is to add phosphate buffered saline to the original sample and vortex thoroughly and use a certain amount of the solution prepared for extraction, which in addition to reducing inhibitors allows for better lysis and better passage of materials through the binding column in subsequent steps. Also, increase the washing and also centrifuge the column empty one step before adding the release buffer to completely empty the washing solution materials. And this can help the quality of the extracted DNA.
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