Nanodrop result of my DNA samples extracted from fresh finger millet leaves showed 260/280 ratio ranged from 1.7-2.2 whereas 260/230 ratio ranged from 1.1-2.2. How can I assess the quality of such DNA samples? Are all these samples good enough for SSR work?
For SSR you will be doing PCR, so if PCR works well, then it should be fine to proceed with your desired analysis.
I think checking whether wave of peaks is clear is important. If one clear peak represent, DNA quality is good. But if the peak is not clear, the DNA quality is not good if 260/280 ratio is appropriate value.
That is excellent DNA quality. You only need 1ng/ul to get a good reaction. I would add 1.2M betaine to the PCR if you can to break down secondary structures and help GC content.
Your results look good for some samples and not so good for others. There should be a 260/280 ratio of ~ 2.0 for DNA. The 260/230 degree of purity is a second measure of DNA purity with the values of a "pure" nucleic acid generally in the range of 1.8-2.2. I suggest repeating the DNA extraction process for samples that showed values below 1.7. Quantification on agarose gel is also quite effective. Some lab analysts even prefer it.
Though for information sake we use nanodrop/spectrophotometer for quantification of DNA, load 1uL of DNA on gel based on those readings quantify visually then you know DNA quality also (whether degraded or intact) then make dilutions 10 or 50 ng/uL use them for your PCRs. 10 ng/uL is sufficient for SSR amplification.
I always quantify DNA visually by loading 1uL on gel then make dilutions. I answered many questions with gel pictures. If you have patience can check my question answers link since 2011.
Good Luck!!
Please I have a question is it possible to use the nanodrop spectrophotometer to measure the amount of annealed double stranded oligonucleotides around 25 nucleotides per strand so in total around 50 nucleotides? if no, is there any suggestion to determine their amount per microlitters?
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