We quantify NGS libraries all the time and qPCR works brilliantly, but nucleic acids need to be handled differently. We don't actually run that much quantifiaction on DNA and RNA as most of our users have already done this; we asked them to do it so we could more efficiently run larger batches of library prep to keep costs down and turnaround times as short as possible. Over the last few years we've been running the Nextera exome preps and DNA quant has become more important than ever before, in fact we started running a secondary quant just to be certain about DNA concentration.
Most of the time DNA and RNA quant works well and we've favoured the fluorescent Qubit assay recommended by Illumina in their protocols. A nanodrop or plate reading spec at 260:280nM measures total nucleic acid and is confounded by ssDNA, RNA, and oligos so can give inaccurate results. We run the Qubit dsDNA BR Assay from Molecular Probes on the PHERAstar fluorescent plate reader (here's their handy protocol). We have only been using 1ul of DNA (Illumina suggest 2) for each sample but we run triplicate assays to get a high-quality quantitation.
Problems with the Qubit assay: Recently some users have reported problems with the accuracy of the QuBit assay on our plate reader and the manager of our Research Instrumentation Core helped us to get to the bottom of the issues and some excellent results. The main problem turned out to be addition of DNA into the working dye solution, it was the DNA coating the outside of the tips that appeared to be making the results so flaky. Changing the protocol to add DNA to the plate first fixed it and the results are looking great.
It ca also be very important to be certain which assay you should use; BR (Broad range) or HS (High Sensitivity). If you are working with low concentration nucleic acids then the HS assay is probably the one to use. For really accurate quant we'd suggest a quick QT check first, then normalisation of samples to about twice what you need; a second triplicate and robust quant will allow you to dilute the samples to the perfect working concentration.
It ca also be very important to be certain which assay you should use; BR (Broad range) or HS (High Sensitivity). If you are working with low concentration nucleic acids then the HS assay is probably the one to use. For really accurate quant we'd suggest a quick QT check first, then normalisation of samples to about twice what you need; a second triplicate and robust quant will allow you to dilute the samples to the perfect working concentration.
- Add DNA to the measurement plate/tubes before anything else
- Use a repeat pipette to make sure each well gets the same/right amount of dye solution
- Shake the tubes/plate in the dark for at least 10 minutes (quant will be inaccurate if the dye has not intercalated properly, you can check your standard curve replicates to verify if this is an issue)
- The triplicates really are worth the effort - especially if you're doing a Nextera prep
