We have been cleaning genomic DNA after a WGA step with the Zymo kit and the samples showed nice clean bands of high molecular weight on an agarose gel immediately after the DNA cleaning. We then kept the samples 2 days in the fridge before storing them at -20C. One week later, we rechecked the samples on agarose gel for selection of candidates for NGS and all samples were degraded - showing a smear instead of the earlier nice clean bands of high molecular weight. The only explanation we can see is that the Elution buffer was contaminated with a DNase (the eppendorf we are using are RNAse and DNase free).
Any recommendations for alternative kits that will not destroy my extremely valuable DNA?
Dear Joelle,
I think you are right, your elution buffer might be contaminated wiht a DNase and destroyed your DNA. Have you try to directly freeze your DNA at -20C after cleaning it and defreeze your sample only when you need?
To clean my gDNA after WGA, is used the SigmaSpin Post-reaction Clean-up column (Sigma-Aldrich) [http://www.sigmaaldrich.com/life-science/molecular-biology/automated-sequencing/sigmaspin.html].
This works very well to get clean and intact DNA for library preparation for Illumina sequencing. The good thing with this column is you don't need to add buffer, so you decrease the risk to get contamination with a DNase for example.
I hope this will help you and good luck with your experiments!
Winka
Joelle
Try freezing them immediately. Also check your freezer isnt a frost free freezer that runs a regular defrost cycle as freeze thawing your DNA will degrade it quicker. What is the buffer your DNA ends up in?
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