ezDNase™ Enzyme

Unfortunately, it is not possible to efficiently measure the ssDNA content in a sample that also contains dsDNA with the Qubit ssDNA Assay Kit (Cat. No. Q10212). The dye in the Qubit ssDNA Assay kit binds to both ssDNA and dsDNA.

It is possible to treat the sample with a DNase that only degrades dsDNA, such as theezDNase Enzyme (Cat. No. 11766051), and measure the ssDNA concentration afterward. However, if all dsDNA is not successfully digested, there is a risk of overestimating the ssDNA content.

The following article describes a PCR-based method to detect ssDNA in dsDNA samples:

Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

Yes, the TaqMan Cells-to-CT Express Kit includes Express ezDNase which can be added to the Express Lysis Solution for removal of gDNA during cell lysis. Express ezDNase is a double-strand specific, heat-labile DNase that will only digest gDNA, making it compatible with the downstream reverse transcription reaction. The enzyme is automatically inactivated during a heat kill step included in the reverse transcription program. To avoid the detection of gDNA, we recommend using a TaqMan Gene Expression Assay specifically designed to span an intron-exon boundary. Such assays are designated with an "_m1" suffix. More information can be found here.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Applications Support Center.

The Invitrogen ezDNase Enzyme is a novel DNase that is highly specific for double-stranded DNA. It has no activity on single-stranded DNA in RT reactions (primers or probes), or on RNA. The enzyme is also thermolabile—it is inactivated quickly at temperatures typical for the SuperScript IV RT reaction (e.g., 50 degrees C). The additional inactivation step is therefore not required for most RT-qPCR applications. If the RNA sample is to be used for RT-PCR of fragments ≥3 kb, incubate the sample for 5 minutes at 55 degrees C in the presence of 10 mM DTT to inactivate the enzyme.

Find additional tips, troubleshooting help, and resources within our PCR and cDNA Synthesis Support Center.

For RT-qPCR applications we recommend using the Invitrogen SuperScript IV VILO Master Mix (Cat. No. 11756050). The cDNA synthesis reaction setup with this master mix requires fewer pipetting steps and therefore reduces variation in the data. SuperScript IV RT, as a component of the master mix, offers the highest efficiency of cDNA synthesis step compared to competitors’ products.

Find additional tips, troubleshooting help, and resources within our PCR and cDNA Synthesis Support Center.

The only difference is that the incubation time for the reverse transcription reaction has been reduced to 10 minutes and inactivation time has been reduced to 5 minutes at 85 degrees C.