I am working on a project trying to isolate intracellular DNA (iDNA) from a soil sample. I have been trying different approaches to mute or block the amplification on extracellular DNA (eDNA), and I am now trying to wash the sample to free up any eDNA fragments that may be adsorb to soil particles before the treatments that I am applying. I have read one paper that used SDS at 0.1% concentration to (what I assume) wash off or desorb the DNA from the particles. I am still very new to molecular research and throwing soil chemistry on top of it is a little challenging, although exciting to learn. does this seam reasonable, using low conc. SDS as a detergent, or is there a better solvent?
Hello!
I suggest that first you need to use some cell wall degrading enzymes or treatment to allow SDS to show it best effect, by which ultimately you can recover the intracellular eDNA.
All the best.
Jagat
the question of the research is what percentage of of the genomic data that we get from high throughput sequencing comes from live cells vs dead cells or eDNA. I would be worried about any real high conc of SDS because of cell lysis. I want to try and free up any eDNA and bind it using specific chemicals, prior to extracting the DNA from the soil. this should cause a reduction in sequencing but I want to be careful as to not lyse any living cells.
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