Comparison of Three Methods of Measuring RNA and DNA Concentrations of Individual Pacific Herring, Clupea pallasi, Larvae

Whole-body concentrations of RNA and DNA of individual Pacific herring, Clupea pallasi, larvae were measured with three methods that rely on the fluorescence of dyes bound to nucleic acids. Two methods use the dye ethidium bromide and do not purify nucleic acids, and one method uses ethidium bromide plus the DNA-specific dye bisbenzimidazole and purifies nucleic acids. Highly significant differences in RNA concentration and RNA–DNA ratios were found between the three methods. Significant differences in RNA concentration and RNA–DNA ratios were also found between yolk sac larvae and non-yolk sac larvae analyzed by one of the two ethidium bromide methods, with yolk sac larvae having the lowest ratios. These results suggest that compounds other than nucleic acids may interfere in the two ethidium bromide methods. Until a standard method for extraction and measurement of nucleic acids of larval fish is established, we recommend the use of techniques that purify nucleic acids.