Choosing a PCR Plastic Consumable—Four Main Considerations

The choice of PCR/qPCR plastic consumable for optimal handling may depend on the number of reactions to be done at one time. For low throughput applications, individual PCR tubes are generally more suitable, whereas PCR plates are preferred for experiments that require processing more samples.

PCR tubes are recommended if you are doing a few reactions per day; you can use only the number of tubes you need, and it is easy to vary the number of samples. A PCR tube strip—comprising 8 or 12 attached tubes attached linearly—is easier to handle than individual tubes, and they can be cut to suit the number of samples you need.

24-well and 48-well PCR plates give the convenience of the plate format without the need to use a whole plate. These plates have the same well dimensions and well-to-well spacing as a standard PCR tube or 96-well PCR plate to maintain standard reaction volumes but are easier to handle and seal than an equivalent number of tubes. Plates such as the Thermo Scientific Thermo-Fast 24-well PCR plate are ideal for lower-throughput thermal cyclers as well as for scientists with a 96-well thermal cycler who do not want to use a whole plate to run a moderate number of samples.

Segmented PCR plates such as the Applied Biosystems MicroAmp TriFlex 3x32 PCR plate and Thermo Scientific Thermo-Fast PCR plate can be separated into 2, 3, or 4 sections and are available skirted for stability as well as labeling.

For the ultimate in flexibility for a PCR plate, Armadillo PCR Strip Plates and VersiPlate PCR Strip Tube Plates allow users to separate the plate into any number of columns. With VersiCap segmentable cap mats or 8-cap strips, they provide a highly efficient use of PCR consumables with minimal waste.

PCR plates, workhorses of the molecular biology lab, are the way to go if you are routinely analyzing dozens of samples and controls at a time. PCR plates are available in 96- and 384-well formats; for most laboratory applications, 96-well plates provide sufficient throughput and are straightforward to set up. 384-well plates use a fraction of the reagent volume per well and support higher throughput; however, they require careful pipetting and sample tracking and so are often used in conjunction with automated liquid handlers.

Most PCR tubes and plates are compatible with both thermal cyclers and qPCR instruments. However, compatibility does not mean optimal results. Because both amplification and analysis happen in the same tube during real-time quantitative PCR, it is important to choose a qPCR tube or plate that supports both functions well.

For real-time/quantitative PCR (qPCR), consider using plates with white wells instead of the traditional clear polypropylene. White wells enhance sensitivity of the assay and minimize variability in qPCR data. White PCR plates also prevent sample crosstalk and loss of fluorescent signal due to refraction into the well sides and maximize the amount of fluorescence reaching the detector. Ultimately, these advantages contribute to improved detection and measurement of fluorescence signals in qPCR reactions.

Use of optical caps and seals is also important for qPCR. The high-clarity material effectively transmits the fluorescent signal, optimizing the amount of fluorescence reaching the detector in a qPCR instrument

Optical PCR tubes and caps are a good choice for low-throughput qPCR experiments as the features of frosted sides and optically clear caps help boost the fluorescence signal as described above for white qPCR plates.

Once you have decided among PCR tubes, tube strips, or plates, finding PCR plastic consumables that are compatible with your thermal cycler or qPCR instrument is critical for success. Here is a summary of the most relevant features that drive compatibility; to find specific consumables that fit your instrument model, use the PCR and qPCR plastic consumable selection tool.

Well volume impacts choice of both PCR plate and PCR tube. Well volumes of both 0.2 mL (“standard”) and 0.1 mL (“low profile”) are quite common. Low profile consumables have the advantage of using half the reagents per reaction but might not be as efficient at amplifying very low levels of DNA.

A key PCR tube feature that drives instrument compatibility is cap style. Thermal blocks may accept domed and/or or flat-capped tubes, but it is better to use a consumable that best fits the block. For example, using flat-capped tubes in a thermal cycler that accepts domed caps is not ideal because there is no direct contact between the lid and the thermal block.

Among the myriad options for PCR plates, a primary driver of instrument compatibility is skirt type. The skirt describes the vertical edge material at the periphery of a PCR plate. The design of your PCR instrument determines whether it accepts full skirt, semi-skirt, and/or no skirt PCR plates.
 

When looking for an automation-compatible PCR plate, consider the plate skirt as discussed above. While both semi- and fully skirted plates are compatible with robotic handling, fully skirted plates provide greater mechanical strength as well as stackability.

The PCR plate materials are also important for automated workflows—look for plates with polycarbonate frames for strength and polypropylene wells for optimal heat transfer. Thermo Scientific Armadillo PCR plates feature polycarbonate frames for excellent thermal and mechanical stability and are available barcoded, making them excellent for automated workflows.

Spotlight article: Four key features for high-throughput PCR plates

In conclusion, as a critical component in the setup of PCR, plastic consumables play an important role in the success of the experiments and data collection. Taking some time to consider your specific needs can accelerate your ramp up to optimal PCR and qPCR results.