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Best Practices to Improve PCR/qPCR Data (Vol. 1)

Side by side comparison of a white tube with transparent optical cap and a transparent tube with transparent optical cap.

Polymerase chain reaction or PCR is a vital process for researchers and a variety of genetic technologies. In an effort to get results faster, many labs are overspending on consumables or have even grown accustomed to using products that are not well suited for their work. The old cliché “this is what we have always used” gets thrown around far too often!

It is easy to understand this common pitfall. There isn’t a Consumer Report on which plate(s) are best for PCR and sales reps may not always be versed in the technical and scientific benefits. While it is always best to sample and test products before purchasing, these tips will help improve your PCR and qPCR data.

3 Ways to Improve Your Lab’s PCR Process:

PRO TIP #1: Know when to use white, colored and transparent products.

Side by side comparison of a white tube with transparent optical cap and a transparent tube with transparent optical cap.Use white plates for qPCR. Clear also works — but never use colored plates.

White plates work best because the light source is above the well shooting downward. White refracts the light back into the reader, but anything with color will absorb the light. Transparent plates allow the light to be absorbed by the metal of the qPCR machine.

Left: White tube with transparent optical cap. High S/N ratios. Right: Transparent tube with transparent optical cap. Poor S/N ratios.

PRO TIP #2: Stabilize the denaturation process.

If you don’t have a full block, put an empty tube in each corner to help stabilize the heated lid. This helps limit evaporation and the likelihood of crushing tubes. Please note, this will only be effective with the same tubes that are being used in the rest of the block. You will also need to replace the corner tubes every so often, as they will melt over time.

To test for evaporation:

  1. Look for one tube with a significantly different volume than other tubes. Evaporation can change the pH. If this happens, you may be experiencing issues during denaturation.

  2. Use a pipettor. If you are using a 30-microliter reaction, be on the lookout for bubbles in the tip when drawn out. If you put 30 in and get bubbles out, then you have evaporation.

PRO TIP #3: Use quality products from a trusted vendor.

Parts and informaton about a PCR plate

No two products are created equally. When making the switch from one supplier to another, ask yourself the following questions:

  • “Is this a company I can trust?”

    Bio-Rad, Fisher, VWR, MIDSCI and many others have worked hard to earn the trust of our clients and build a solid reputation. If you don’t know or have never heard of the company you are considering a purchase from, exercise caution. There are some extremely cheap plastics on the market that just do not work. 
  • “Are they offering samples and/or a money-back guarantee?”

    Ask for a sample or a money-back guarantee. In most cases, a plate for an ABI 7700 that looks just like the plate you use in your ABI 7700 will work just fine. Which brings us to our final question . . . 
  • “Does each plate/strip/tube look the same?”

    Consistent results cannot be achieved without consistently high-quality materials. If the products you see don’t look the same, ask to see more pictures and/or product samples.

    Will something that looks different work? Maybe. But if they look identical the odds are even better.

Save Money on PCR Products & Equipment with MIDSCI

MIDSCI is a dealer for a wide range of PCR and qPCR manufacturers in the United States and is uniquely qualified to help improve your lab’s processes. From PCR machines and plastics to Taq polymerase, dNTP solution and more, MIDSCI can stock your laboratory with the best equipment and research supplies. Our sales are backed by a professional customer service team that is always available to answer your questions.

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Don’t fall into the trap of buying the same old thing over and over again. If you are ready to improve your PCR processes, submit a request online, call us toll-free at 1 (800) 227-9997 or send an email to

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