I am having problem on how DNA is quantified by using optical density. Can anyone help me with the procedure? Most of protocols online suggest to use nanodrops. I do not have nanodrop machine. Only have spectrophotometer. Thanks
Muhammad: You need a relatively concentrated DNA sample to be measured with a regular spectro(photo)meter or a plate reader. We usually use 5 microliters of mini-prep DNA sample and diluted to 300 microliters (60x) and read at A260 and A280 with a microcuvette of 1.0 cm light pah to get ODs and their ratio for purity (good DNA has 1.8-2.0 of A260/280). After that, you simply calculate with C = A x 60 (dilution factor)/50 (microgram per ml for double stranded DNA). Good luck.
However, I will say that you also need to look at the 260/230 ratio as well as the 260/280 ratio if you can: 260/230 < 1.0 indicates salt contamination of your DNA and/or phenol or Trizol if you have extracted your DNA the old fashioned way
What is more absorption at 260nM is not specific to DNA: It will also detect RNA and indeed any organic, e.g. phenol/Trizol with an aromatic ring (in fact @ 260nM you are inducing resonance of your delocalised pi electrons in your aromatic ring)
Thus specs or Nano drops @ 260nM can over estimate the amount of DNA
To elaborate, if your 260/280 ratio is > 2.2 (up to 2.2 is actually OK) and your 260/230 ratio is < 1.0 then you might have trizol contamination of your DNA (if used to extract) where as a 260/280 ratio < 2.0 with a 260/230 ratio < 1.0 implies salt contamination
Finally, remember for UV absorption (DNA/RNA) to use a quartz and not a plastic cuvette