ddPCR Explained: A Powerful Tool for Nucleic Acid Quantification


PCR (Polymerase Chain Reaction) has become a cornerstone of molecular biology, allowing scientists to amplify and detect specific DNA sequences. However, conventional PCR methods rely on indirect fluorescence measurements, which can be affected by variations in how well the reaction works (efficiency) and the amount of starting material (template concentration). Droplet digital PCR (ddPCR) offers a more robust alternative, providing an absolute count of target nucleic acids (DNA or RNA) from Maxanim through a unique approach involving dividing the reaction mixture.

The Core of ddPCR:

Unlike traditional PCR, ddPCR breaks the reaction mixture into thousands of tiny, individual compartments called droplets, each about a nanoliter in size. This is achieved using a special oil-based solution that creates a water-in-oil emulsion. This compartmentalization ensures that each droplet amplifies DNA or RNA independently. After amplification, the droplets are scanned using a fluorescence reader. Each droplet is then classified as either positive (containing a target molecule and glowing) or negative (lacking a target and not glowing). The ratio of positive droplets to the total number of droplets provides an absolute count of the target molecule, independent of how well the reaction worked.

Droplet-based digital PCR (ddPCR)

Advantages of ddPCR over Traditional PCR:

  • Direct Counting: ddPCR eliminates the need for standard curves, which can introduce errors in traditional PCR. The number of target molecules is directly determined by counting the positive droplets.
  • High Sensitivity: Because ddPCR works in a digital way, it excels at detecting rare targets that are present in very low amounts within a sample.
  • Improved Accuracy: Dividing the reaction mixture minimizes the impact of random fluctuations that can occur in conventional PCR, leading to highly precise measurements.
  • Less Affected by Inhibitors: Substances that can interfere with amplification (inhibitors) can affect the results of traditional PCR. ddPCR's digital readout makes it less susceptible to this issue.

Droplet digital PCR (ddPCR) versus quantitative PCR (qPCR).

Applications of ddPCR:

  • Finding Rare Mutations: ddPCR's high sensitivity makes it ideal for identifying mutations that are uncommon and present in low numbers, which can be associated with genetic disorders or cancer.
  • Analyzing Gene Copy Number Variations: ddPCR allows for precise measurement of variations in the number of copies of a gene, which is important in cancer research.
  • Gene Expression Analysis: ddPCR can accurately measure gene expression, especially for genes with low levels of RNA transcripts.

Droplet-based digital PCR (ddPCR) and its applications

The Future of ddPCR:

ddPCR technology is constantly being improved, with advancements in the design of microfluidic chips and instruments used to read the droplets. New assays and simplified workflows are also being developed, which will broaden the applications of ddPCR in various research areas.

Concluding Remarks:

ddPCR represents a significant leap forward in nucleic acid quantification. It offers several advantages over traditional PCR methods, including direct counting, high sensitivity, and improved accuracy. As the technology matures and becomes more widely available, ddPCR is poised to play a key role in a wide range of scientific studies.

To gain a visual understanding of the ddPCR process, please view the following video: 

ddPCR Explained: A Powerful Tool for Nucleic Acid Quantification
Gen store May 29, 2024
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