FAQ: Which measurement system is best used for assessing the concentration of HMW DNA?

In our experience, and in contrast to common belief, measuring the concentration of HMW DNA by Qubit® is not the most accurate approach. OD measurements provide more accurate concentration values, but because of the viscosity of HMW DNA samples, several replicates are required. Qubit readings will typically underestimate the amount of HMW DNA; for genomic DNA isolated with silica spin columns (usually 20-80 kb), Qubit provides DNA concentration readings 10-15% lower than those obtained by spectrophotometer. The ability of the intercalating dye to stain the DNA decreases with increasing DNA fragment length, resulting in an even larger difference between Qubit and OD values when working with HMW DNA. Differences can be as large as 35%, or even higher in some cases, resulting in a significant underestimation of DNA concentration.