Applied Color Theory

When it comes to choosing a PCR (polymerase chain reaction) plate for your lab, it’s not just about aesthetics. For standard PCR, the color of the well doesn’t matter all that much since the plates are only used as a vessel for amplification and samples are transferred to a gel for analysis. In qPCR (quantitative PCR), however, the type of well you choose can have a huge impact on your results.

To understand why, let’s go back to the basics. During qPCR, light of a certain wavelength excites the samples in each well, which then emit light of a different wavelength (fluorescence). This fluorescence is measured with a sensor, generally located above the plate. For the sensors to work most effectively, they need light to be reflected back at them. Standard clear-well plates are the least effective at reflecting light, which can cause a high level of variance between readings. White wells, on the other hand, have been proven to improve the reflection of fluorescence. This means that your readings will have less noise, and yield higher sensitivity and consistency in your results.

Unfortunately, not all PCR plates are created equal. Many variables in plate manufacturing can impact your results. Factors such as wall thickness, contaminants, and incomplete mixing of polymers can all lead to inconsistent, and therefore inferior, plate performance. Variable molding conditions can yield inconsistencies in wall thickness within a single well, as well as across all the wells on a plate. Thicker wells, or sections of wells, will reflect more light and cause inconsistent readings. Contaminants can also affect the efficiency of a reaction, or may give off some levels of autofluorescence which can obfuscate your results. Insufficient mixing of the plate polymer with any color pigments will create variabilities in well wall color, and therefore your results.

Here at Arvensis, we offer two types of white well plates that are compatible with different sensors. Both are manufactured with the most advanced and precise methods of polymer blending and molding to yield consistent, even well shape and color. Our standard plate is designed to reflect the appropriate level of fluorescence for the vast majority of instruments. Some, however, require an even stronger signal. For these instruments, we have designed a plate for enhanced sensitivity that reflects even more fluorescence than our standard plate.

In short, your PCR plate should never be a variable in your experiment design. To that end, the importance of using a reliable plate from a trusted manufacturer cannot be overstated. When you are relying on qPCR to quantify the amount of DNA in your sample, using anything but white wells means you are compromising on sensitivity and that means you are compromising on accuracy.