Why is the DNA concentration you measured lower than measured by nanodrop?
• We use a fluorometer coupled with Hoechst 33342 dye to measure DNA concentration. Because Hoechst 33342 only binds to double strand DNA, not protein, RNA or other contaminants, the DNA concentration measured with this technique is more accurately measured. In comparison, nanodrop is based on absorption peak at 260/280 nm wavelength. Many contaminants in the DNA solution could affect the OD reading. We found if the DNA concentration measured by fluorometer is significantly lower than the client’s concentration measured by spectrophotometer (such as nanodrop) the sequencing reactions tends to fail due to the contaminants present in the DNA samples.
