I have extracted DNA from desert soil using a commercial Qiagen kit. When I check my DNA on Qubit and Nanodrop I consistently get very low readings (
How big are the DNA bands.
The low OD260/230 is probably caused by guanidinium salts not washing off the column. Try loading less sample or doing 2 washes to get rid of the chaotrophic salts...they absorb at 230 so give a low 260/230 ratio. A low reading from Qubit may be that it relies on an intercalating dye and if most of your purified sample is rna not dna then you will get a low reading for dna
Paul Rutland the DNA bands are >10kbp. There is no visible trace of RNA or DNA degradation on the gel. I use 2ul of DNA for both the Nanodrop and Qubit respectively.
I already do two washes, and I also did an extra on-column wash with 70% EtOH (this had no extra effect). I also washed the soil with PBS twice before the extraction and tried both EtOH only and NaOAc + EtOH precipitation after the extraction - still the Nanodrop readings were low for 260/230.
That is very thorough Miranda Procter and I do not have much else to suggest although it still looks like humic substances co purifying with the dna and causing both low 260 readings and low 260/230. I can only suggest looking into removal of more of the humics from the soil sample before the purification step. Something like below
https://www.sciencedirect.com/science/article/abs/pii/S0167701205003507#:~:text=Here%20we%20report%20an%20effective%20pr
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