High-Throughput PCR and qPCR Plates: Four Key Attributes

First and foremost, automated plate handling in high-throughput PCR applications necessitates the use of skirted PCR plates. The outer plastic skirt or frame provides stability when robotic paddles grip the plate, helping prevent damage and distortion as the plates are transferred from station to station in the workflow.

Semi-skirted plates typically require a support rack on each key location of the robot deck. Since some thermal cyclers and qPCR instruments need semi-skirted plates, it’s best to check with your automation supplier to help ensure you obtain compatible supports.

Learn more about PCR plate skirt types

Many traditional PCR plates are made entirely from polypropylene. This plastic offers exceptional heat transfer properties, facilitating accurate temperature manipulation in PCR reactions. However, because polypropylene is pliable, robotic arm grippers (Figure 1A) can bend or distort it during the handling process. 

The best high-throughput PCR plates use polycarbonate frames. Polycarbonate plastic offers greater structural strength and a higher melting point. Importantly, these PCR plates still use polypropylene wells to maintain optimum heat transfer (Figure 1B).

Low profile PCR plates are beneficial for automated and high-throughput PCR applications because they:

1. Use less reagent per reaction
2. Have faster run times
3. Have a lower stacking height than standard PCR plates

Low-profile PCR plates are shorter than standard plates and have a smaller well capacity (0.1 mL vs 0.2 mL for standard PCR wells). Low-profile PCR plates and compatible instruments are often called “fast” because the smaller reaction volume takes less time to reach the target temperature than standard PCR reactions, which allows for shorter run times.

PCR/qPCR plates with raised well rims facilitate effective sealing to help prevent evaporation and contamination during the amplification process. With large numbers of plates to process and the resulting potential for wait times during workflows, limiting evaporation is even more important for high-throughput qPCR and PCR applications.

Learn more about plate sealing

The rest of the plate deck should be below the height of the well rims, so nothing interferes with the plate seal. Indented alphanumeric grid reference lettering helps provide durability of visual markings while maintaining the plate deck height.

The PCR plate frame must be designed to ANSI/SLAS 1-2004: Microplates Footprint Dimensions  and related standards to be compatible with robotic systems.

Finally, frames of multiple colors can help with organization and visual monitoring of batches in a high-throughput setting.

High-throughput qPCR workflows can process large numbers of samples and generate many data points. Use of barcoded PCR plates is essential to manage this information and track plate-specific data. Choose barcode labels that are scratch- and chemically resistant and able to withstand both the high temperatures in the thermal block and low temperatures for storage (e.g., –196°C to 120°C).

Whereas most plate barcode labels must be applied in the correct position to be read by your automated thermal cycler or qPCR instrument, robotic systems can usually rotate a plate to align it with a barcode reader. First-rate vendors offer pre-barcoded PCR plates and can place the barcode in the required position; customized barcoded PCR plates are also available.

Although the above should help narrow down the plate type you need for an automated PCR or qPCR workflow, there are still hundreds of PCR plates to choose from. Take advantage of Thermo Fisher Scientific’s PCR and qPCR plastics selection tool to select a plate that will fit in your instrument regardless of brand, based on thermal cycler/qPCR instrument model, number of wells and other factors.

If you have additional requirements that cannot be met with a catalog item, consider working with Thermo Fisher Scientific to design custom PCR or qPCR plates for your specific application.