An alternative method to assess DNA and RNA concentration is to tag the sample with a Fluorescent tag, which is a fluorescent dye used to measure the intensity of the dyes that bind to nucleic acids and selectively fluoresce when bound (e.g. Ethidium bromide). This method is useful for cases where concentration is too low to accurately assess with spectrophotometry and in cases where contaminants absorbing at 260 nm make accurate quantitation by that method impossible. The benefit of fluorescence quantitation of DNA and RNA is the improved sensitivity over spectrophotometric analysis. Although, that increase in sensitivity comes at the cost of a higher price per sample and a lengthier sample preparation process.
There are two main ways to approach this. "Spotting" involves placing a sample directly onto an agarose gel or plastic wrap. The fluorescent dye is either present in the agarose gel, or is added in appropriate concentrations to the samples on the plastic film. A set of samples with known concentrations are spotted alongside the sample. The concentration of the unknown sample is then estimated by comparison with the fluorescence of these known concentrations. Alternatively, one may run the sample through an agarose or polyacrylamide gel, alongside some samples of known concentration. As with the spot test, concentration is estimated through comparison of fluorescent intensity with the known samples.
If the sample volumes are large enough to use microplates or cuvettes, the dye-loaded samples can also be quantified with a fluorescence photometer. Minimum sample volume starts at 0.3 μl.
To date there is no fluorescence method to determine protein contamination of a DNA sample that is similar to the 260 nm/280 nm spectrophotometric version.