I am having minimal luck using Qiagen Stool and Plant DNeasy kits for extraction from herbarium specimens that are 20-60 years old. I use a bead beater with MP Bio Matrix A to break up my samples. The yields are low and I have trouble with contaminates when it comes time for PCR. I am trying to amplify chloroplast and nuclear regions that are 1000 bp or shorter.
Super hard to get enough DNA from herbarium samples, especially poace with high silicate concentration! . what is the sample vol/weight are we talking about? The front-end sample processing steps are very important to get better DNA yield. I suggest that you should use liquid nitrogen for crushing the sample and increase the incubation time in buffer that has atleast 1mM EDTA. You could also think of using Cellulase (Aspergillus niger, available through Sigma) to digest and help release DNA from dry samples.. These are fairly active at pH8, 37deg C ( I believe). In that case, you should follow it with Phenol: CHCl3 extraction protocol (Also try to use Phenol that is not cold.. may be at 37deg C)
Hope it helps. Good luck!
Saeidi, S., McKain, M. R., Kellogg, E. A. Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens. J. Vis. Exp. (133), e56837, doi:10.3791/56837 (2018).
I suggest maybe you should use liquid nitrogen for tissue dissociation (grinding), in my experience, I usually increased incubation time on lysis step (sometimes overnight) and increase vortex frequency. Sometimes add some enzymes,depend on what kind of contamination...
Good luck!
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