Performing Polymerase Chain Reaction (PCR) is a fundamental technique in molecular biology. It allows scientists to amplify DNA fragments for various applications, such as DNA sequencing, cloning, and gene expression analysis. While PCR is traditionally carried out in tubes or microplates, a question often arises: Can you do PCR in a 96-well plate Filler? In this article, we will explore the possibilities and advantages of using a 96-deep well plate for PCR and provide insights into how this technique can be beneficial for your research.

Understanding PCR

What is PCR?

PCR, or Polymerase Chain Reaction, is a molecular biology technique used to amplify DNA sequences. It involves a series of temperature-controlled steps that replicate DNA, making it possible to obtain millions of copies from a single template DNA strand. PCR is a versatile tool used in various fields, from genetics to forensics.

Traditional PCR Tubes and Microplates

In conventional PCR, scientists use small tubes or microplates to carry out the reactions. Each tube or well typically holds a single reaction, which can be limiting when dealing with numerous samples or high-throughput experiments.

Advantages of Using a 96-deep Well Plate

Increased Throughput

Using a 96-deep well plate for PCR significantly increases throughput. With 96 individual wells, you can simultaneously process multiple samples, making it a time-efficient choice for laboratories handling large volumes of experiments.

Reduced Contamination

Deep well plates are designed to minimize the risk of contamination. Their deep, conical wells help prevent cross-contamination between samples, ensuring the integrity of your results.


Using deep well plates can be more cost-effective than traditional tubes or microplates. You can save on consumables, reduce reagent usage, and increase the overall efficiency of your PCR experiments.

PCR in a 96-deep Well Plate: Step-by-Step

Step 1: Sample Preparation

Start by preparing your DNA samples, primers, and reaction mix. Load each well with the necessary components.

Step 2: Thermal Cycling

Perform the thermal cycling process by subjecting the 96-deep well plate to a PCR machine. This will involve denaturation, annealing, and extension cycles to amplify the DNA.

Step 3: Analysis

After the PCR is complete, analyze the results. You can use various techniques, such as gel electrophoresis or real-time PCR, to evaluate the success of your reactions.

Applications of PCR in 96 Deep Well Plates

High-Throughput Screening

96-deep well plates are invaluable for high-throughput screening, allowing scientists to process a large number of samples simultaneously.


Researchers often use deep well plates for genotyping studies. The increased throughput and reduced contamination risk make it an ideal choice for such applications.

Drug Discovery

Pharmaceutical and biotech companies utilize deep well plates for drug discovery, where multiple compounds and reactions need to be tested rapidly and accurately.


In conclusion, performing PCR in a 96-well plate Filler is not only possible but offers several advantages for researchers. This approach can increase throughput, reduce the risk of contamination, and save costs in the long run. When it comes to high-throughput experiments, genotyping, or drug discovery, a 96-deep well plate can be a valuable tool in your molecular biology arsenal.

Frequently Asked Questions (FAQs)

1. Can you use any type of 96-deep well plate for PCR?

You should use PCR-grade, sterile 96-deep well plates to ensure accurate and contamination-free results.

2. What are the recommended PCR conditions for a 96-deep well plate?

The PCR conditions depend on your specific experiment, but they typically include denaturation, annealing, and extension steps.

3. Are there any limitations to using a 96-deep well plate for PCR?

While it offers many advantages, one limitation is that you need a compatible thermal cycler that can accommodate the plate.

4. Can I adapt my existing PCR protocol for a 96-deep well plate?

Yes, most PCR protocols can be adapted for a 96-deep well plate with minor adjustments to reagent volumes and thermal cycling conditions.

5. Where can I purchase 96 deep well plates for PCR?

You can find PCR-grade 96 deep well plates at scientific supply companies, laboratory equipment suppliers, or online.

In this article, we’ve explored the advantages of using a 96-deep well plate for PCR and provided step-by-step guidance on how to perform PCR in this format. Whether you’re in research, genotyping, or drug discovery, considering a 96-deep well plate for your PCR experiments can enhance efficiency and accuracy.