Verifying the Quality and Quantity of your ChIP DNA

The guide reports on experiments undertaken to compare the performance of the Thermo Scientific NanoDrop 2000™, the Life Technologies Qubit 2.0® fluorimeter and the Agilent Bioanalyzer 2100© for qualitative and quantitative analysis of double stranded immunoprecipitated DNA. The advantages and limitations of detection sensitivity, reproducibility and automated analysis of each instrument are discussed. The compatibility of each method with downstream applications including next generation sequencing is also examined.

The fields of epigenetics, molecular biology and biochemical research continue to evolve at a rapid pace and the modern lab user must be considerate of the time and cost of performing basic laboratory techniques. One of the most common and often laborious measurements in bioscience labs is that of DNA quantification and characterisation. Researchers may wish to quantify DNA for a variety of applications including next generation sequencing (NGS), PCR amplification and plasmid transfection. However, the accuracy of DNA quantification very much depends on the technology being used and whether it is the most appropriate for the sample type being quantified.

The guide concludes that for accurate quantification of DNA, which is critical for downstream processes, it is highly recommended that a fluorometric method is used. The advantages of the Qubit 2.0® and Bioanalyzer 2100© are clear with respect to sensitivity and the sizing capability of the latter. The NanoDrop 2000© does have the potential to be a cheap and reliable way of determining the crude quantity of DNA or RNA in your sample. But, for applications that require the greatest accuracy when quantifying DNA, such as NGS, it is essential to use fluorescence-based quantification as standard.