Scientists in fields ranging from basic research to clinical diagnostics rely on qPCR to assess gene expression, pathology (infectious disease and oncology in particular), genetic modification in organisms, and microbiologic ecology – to name just a few critical examples. This popularity has given rise to a vast array of qPCR protocols, reagents, kits, and products. Many components are optimized for specific uses, systems, and instrumentation. All of this diversity is great for science, but it can complicate the execution of everyday experiments.

While most users focus on assembling the PCR reaction solutions and collecting template nucleic acids, it’s important to think about where the action happens: the PCR plate. Making sure you have the right plate for the job really shouldn’t be an afterthought as the wrong choice can impact the quality and consistency of your results.

To help make an informed plate choice, take a look at the key plate questions and considerations below. 

A good place to start is to determine whether you need a 96-well plate, 384-well plate format, or both. This will depend on the scale of your experimentation (number of required reactions) as well as what your qPCR machine can handle. If your qPCR machine can read either format, it might be a good idea to have both on hand.

While 24- and 48-well plates are also available, they aren’t used very often, compared with 96- and 384-well plates. For some, these formats are selected for experiments that don’t require 96 wells. As an alternative to this, users could select a plate format that is designed to segment. These plates can be used as full 96-well plates or broken up into 32, 24, or 8 well segments. Plate segmentation reduces plastic waste and cost, while also maximizing flexibility. 

Not all plates fit all thermocyclers, qPCR instruments, robotic arms, and samplers. PCR plate compatibility is based on four main plate design features: The skirt, deck, well rim, and notch.

The skirt describes the peripheral panel that surrounds the plate wells. Its core function is to provide structural stability for handling and pipetting. While non-skirted plates can be used with a variety of thermocyclers and qPCR instruments, they aren’t suitable for robotic handling.

Skirted plates can be separated into semi- or full skirt categories. While both provide additional structural support and are compatible with robotic handling, full skirted plates are designed for instruments with raised blocks and provide greater mechanical strength. For these reason, fully skirted plates are the best choice for automated workflows, since robotic arms can bend or warp other plate formats more easily.

To see examples of these skirts and their matching instruments in action watch films watch Learn how to choose a PCR Plate video. 

The deck is a portion of plastic on the top of the plate. Generally, flat deck plates can be used in more instruments and can be readily sealed, raised decks, though less common, are required for optimal fit and performance in certain instruments as they help balance lid pressure during experiments. Some plates also have well rims, which are raised lips surrounding each well. These rims can help secure film seals and reduce sample evaporation.A notch is a plate corner that is not a right angle. While not all plates have notches, users can select plates with a notch at either the A12, H1, or H12 (96-well count) corners. Essentially, the only detail that matters here is matching the notch position to the PCR block.

If you’re using high-throughput systems, it is strongly recommended that you purchase plates that fit the ANSI/SBS footprint, set forth by American National Standards Institute (ANSI) and the Society for Biomolecular Sciences (SBS). The ANSI/SBS footprint was designed to enable cross-compatibility of PCR plates between various robotic handling systems.

For qPCR reactions, users should opt for white wells rather than the traditional clear versions. White wells increase assay sensitivity and reduce variability in qPCR data by preventing fluorescence transmission into the thermal block and by minimizing refraction of the fluorescence signal. Both of the aforementioned benefits result in more fluorescence getting back to the detector. 

With a plate that fits both your experiments and instruments, you can go for gold and confidently collect high-quality qPCR data with minimal headache. Remember that PCR is largely about carefully assembling and combining the right materials and that includes the plate itself!

For more help finding a plate that works with your existing qPCR instrument, check out our qPCR and PCR Plastics Selection Tool.