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Can I use AccuBlue®, AccuClear®, or AccuGreen™ kits to quantify short dsDNA?

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The AccuClear®, AccuBlue®, & AccuGreen™ DNA quantitation kits use a high MW dsDNA standard, and are most accurate at quantifying high MW DNA.  While all of the DNA quantitation assays are sensitive to DNA length to some extent, some assays are more accurate with short dsDNA fragments than others.

For quantitation of fragments between 25 and 500 bp:

  • AccuBlue® High Sensitivity assay is the most accurate; fluorescence with fragments was ~ 80% of the fluorescence of genomic DNA, and consistent across length and concentration.
  • AccuBlue® Broad Range assay is also consistent across length and concentration, with ~ 60% of the fluorescence of genomic DNA.
  • AccuGreen™ High Sensitivity assay gives a consistent signal of ~ 80% of the fluorescence of genomic DNA with fragments of 100 bp and higher, but only in the range of 10-100 ng of DNA. Below that, small DNA fragments were inconsistently quantified.
  • AccuClear® assay is more variable based on DNA fragment length and concentration. Therefore we do not recommend using this assay with short dsDNA fragments.

To quantify short dsDNA fragments we recommend:

  • Use the AccuBlue® High Sensitivity DNA Quantitation assay
  • Use sample concentrations well above the stated lower detection limit of the assay (for example, if the stated linear detection range is 0.2-100 ng, for a small fragment you should aim for an amount greater than 2 ng).
  • (For best results) Provide your own dsDNA standard of a similar length as your samples.

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