Can I use ddPCR with my existing primers?

The short answer is yes!  Any primer set that works with SYBR-Green should be easily adapted for EvaGreen ddPCR.  In addition, TaqMan® probes that can be detected in the FAM or VIC/HEX channels can also be used with the QX200.

Two things to note are:

(i) The linear range of ddPCR (10-100,000 copies) is lower than for qPCR (100-10^9 copies) and it can therefore be easily overloaded.  It is recommended that you use 10-50x less cDNA template for gene expression assays than you would use in qPCR assays, especially if your template is abundant.
(ii) Genomic DNA may need to be pre-digested.  Often this can be performed in the PCR reaction buffer prior to droplet generation.

HOWEVER if you are designing a new set of primers specifically for ddPCR there are some differences between primer design for ddPCR and for qPCR.  BioRad provides some tips here: http://www.bio-rad.com/en-us/applications-technologies/planning-droplet-digital-pcr-experiments.

 

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