Hi everyone
I am trying to extract DNA from soil, 260/280 ratio is 1.8 in nanodrop, concentration is 587 ng/ul.
but I can not see the band in gel agarose.
Thank you in advance
Please let me get understood your procedure for making agarose gels.
OD260/280 is a ratio so measures the purity of dna from protein contamination. It does not measure the length of the dna and also it will measure RNA and nucleotides. It is possible that either you have some RNA and quite a lot of degraded DNA which will run as a smear spreading the dna over the whole length of the gel track so that amounts that you can see in a tight band will not be visible when spread over most of a gel lane. A picture of the gel would help. Lack of a band of dna does not mean that you cannot pcr out of your DNA as pcr template is often in amounts invisible on agarose gels
The ratio of the purity has nothing to do with the migration of DNA. This ratio allow you to use the DNA. Actually, you have a good yield and pure DNA. Try to check the electrophoresis, the buffers and the reagents.
Dear Sang-Min Paik, Paul Rutland, Ines Hosni
Thanks a lot for the quick answers and your valuable explanations
I use safe stain in gel agarose, the ladder was observed, and uses 1x loading dye.
Dear Paul, I do not even see a smear in the gel!!
If your dna is high molecular weight then it may be stuck in the well which is normal for long dna. Another possibility is that Nanodrop is very sensitive to the dna solvent. You must zero the nanodrop with exactly the same buffer/water that the dna is dissolved in to get a good result and the optics of the machine must be clean. If your dna was eluted off a column then blank/zero your nanodrop with the elution buffer. It may just be that you have less dna than you think so it is not very visible. Try also running a pcr with dna dilutions to get a feel for how much of your sample you need to use to get a good pcr product. Perhaps try 1ul of 1:2 dna dilution and 1:4, 1:8 and 1:16 dilutions with a set of primers that usually work well
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