Analysis of a commercial surfactant for digital PCR assay

Digital PCR assay represents an example of the power of PCR and provides unprecedented opportunities for molecular genetic analysis in cancer.
The technique is to amplify a single DNA template from minimally diluted samples, therefore generating amplicons that are exclusively derived from one template and can be detected with different fluorophores or sequencing to discriminate different allele.

Digital PCR assay has been applied in quantification of mutant alleles and detection of allelic imbalance in clinical specimens, providing a promising molecular diagnostic tool for cancer detection.

In this application note we are investigating the usability of the commercially available surfactant dSurf for an exemplary digital PCR-assay.

We kindly thank of Photonic Leibniz Institute Technology for this collaboration, and for sharing the results obtained with their system. For information about Photonic Leibniz Institute Technology :

Introduction to digital PCR

Analysis of a commercial surfactant for digital PCR assay

Digital droplet-based assays offer promising opportunities for the absolute quantitation of low concentration analytic species. During the last decade digital-PCR assay (dPCR) became one of the most prominent assays for this class of analytical methods. For performing the assay, the sample volume is split into multiple droplets in such a way that each droplet contains either one or none of the target DNA molecules. Due to the small droplet volume, the PCR reaction runs very efficiently even from a single molecule.

During amplification, a fluorescent dye is formed or activated. The positive droplets become fluorescent. Absolute quantitation of the number of target molecules is simplified to the count of fluorescence active droplets in the generated droplet collection. Not regarding the simplicity of the approach, its technical implementation is challenged by stabilizing the droplets collected over the complete assay avoiding unwanted droplet coalescence or crosstalk between the droplet ingredients. This has been solved by utilizing perfluorinated mineral oils as the carrier oil in combination with advanced perfluorinated surfactants, which stabilize the emulsion and avoid crosstalk and DNA exchange between the individual droplets.

In this application note we are investigating the usability of the commercially available surfactant dSurf for an exemplary digital PCR assay.

Digital PCR Assay: Materials and methods

droplet generation method for digital pcr assay
Microfluidic workstation utilized for droplet generation with quality monitoring by video microscopy
Table analysis of a commercial surfactant for digital pcr assay

Droplets were generated at a working pressure of 240 mbar for the dSurf and 140 mbar for the PCR-Mix. The chip was connected with PEEK 1/32” tubing OD x .010” and 2x sleeves 1/16” OD x .033” ID x 1.6”, tubing length: 200 mm. Generated droplets were collected into a 0.2 ml PCR vial. Amplification was performed in a conventional thermocycler with the settings displayed on the right. For readout, the amplified droplet collection was transferred into a cell counting capillary slit chamber for subsequent brightfield and fluorescence image acquisition.

Digital PCR Assay: Partial results

Droplet generating process for digital pcr assay
Figure 2: Droplet generating process. The droplet generator operating in transition mode between dripping and jetting. No significant differences in the mode of operation as in the droplet sizes and size uniformity can be recognized. The middle circle above the droplet channel has a diameter of 50µm
digital pcr assay evaluation procedure
Figure 4: Evaluation procedure for the dPCR. Starting point are brightfield and fluorescence images of the generated droplets. The processing is done by a self developed software to detect and evaluate the intensity of the droplets. The parameters for detecting the droplet contours are defined in advance. Only droplets of a valid size are included in the result.


The experiments have shown that the dSurf surfactant is suitable for scientific as well as routine digital PCR applications. The generated droplets were homogeneous in shape and size. Superior droplet stability of the dSurf surfactant system was observed during the amplification process. A few droplets have dissipated during the experiments, but this can be neglected. The reproducibility of the experiments was also confirmed. Droplet generation with identical parameters leads to identical droplet size and quality. Summarily, dSurf can be employed as a surfactant composition for digital droplet-based assays, and therefore, for digital PCR assay.


1. Pohl, G. and I.-M. Shih, Principle and applications of digital PCR. Expert review of molecular diagnostics, 2004. 4(1): p. 41-47.
2. Huggett, J.F., S. Cowen, and C.A. Foy, Considerations for digital PCR as an accurate molecular diagnostic tool. Clinical chemistry, 2015. 61(1): p. 79-88.
3. Quan, P.-L., M. Sauzade, and E. Brouzes, dPCR: a technology review. Sensors, 2018. 18(4): p. 1271.

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