What is the best way to determine the concentration of my DNA sample?
By agarose gel verification: Verify the concentration of your sample on an agarose gel along with a mass standard to get a fairly good idea of the concentration of your DNA. By fluorimeter: Fluorimetry readings will give a more accurate concentration of your DNA sample. However, they will not discriminate between any contamination and true products such as non-specific PCR product, genomic DNA, some salts (which can elevate or depress fluorescence readings), etc. In some cases, the contaminants can add to or even mask the true concentration of your sample. By spectrophotometer: This method is probably the least reliable of the three, as it measures concentration by comparing the OD 260 / OD 280 ratio of your sample, and does not directly measure the DNA concentration or give you an idea of what may be contained in the sample. Any other contaminants in a DNA preparation that show fluorescence at this wavelength can change the result, giving an incorrect quantification. We can quantitate
