Guest blogger: Alia Qatarneh on miniPCR

Alia Qatarneh (reproduced from
Alia works at the Division of Life Sciences at Harvard University

Alia Qatarneh is the lead research assistant at Harvard University’s Life Sciences Outreach Program, which works with high school teachers and students from across New England. Alia authored the post we reproduce below on her blog on 9/2/2014..


I had the pleasure of meeting Zeke and Sebastian over one year ago. It started when Tara asked if I could join her in a meeting with two guys who made some sort of small PCR machine. Typically the words small and PCR machine aren’t in the same sentence. Unless, that is, you are referring to your frustration of opening small 0.2mL strip tubes.

In regards to our work with Zeke and Sebastian, they found us first. Part of the Life Sciences Outreach Program at Harvard runs in conjunction with the Amgen Biotech Experience Program where we, as well as other sites across the globe, work to incorporate true and useful biotechnology procedures and techniques into high school classrooms.

One of those “got to know” procedures is the use of PCR. Polymerase Chain Reaction is one of those terms that any AP biology student will know. Students get what PCR is, in theory, but rarely have the opportunity to run a PCR reaction themselves from start to finish.

Zeke and Sebastian’s miniPCR machine allows for many things. It’s incredibly affordable, allows for students to have direct hands on experience, and takes away part of the mysterious black box effect that tends to overshadow the science of PCR.

Marie Szaniszlo, Staff Writer for the Boston Herald asked me to explain this black box effect while interviewing me for an article on Zeke and Sebastian’s cross-disciplinary work. What is it? And how does it involve miniPCR?

The black box effect generally refers to the idea of putting something in a box -> something happens inside the box -> then something different comes out of the box. The problem is, we don’t know what’s actually happening inside.

miniPCR at Harvard LSO

With general PCR machines, students put their tubes in, set up the reaction, and walk away, without actually knowing what’s happening inside. However with the miniPCR and the corresponding software, students get to see that there are 3 temperature cycles and that each temperature cycle changes or affects the DNA in their tubes in a different way (denature, anneal, and extend). This process is repeated for numerous cycles, thus resulting in a large bulk of target DNA copies. By having the students program their own miniPCR machines using the software, they quickly learn that temperature and time is important to the success of a PCR reaction.

We implemented the full use of miniPCRs during this past Spring Program. Over 200 students successfully used these miniPCR machines, hailing from various school across the New England area: Revere High School, Austin Preparatory School, Danvers High School, Arlington High School, Timberlane Regional High School, Manchester School of Technology, Pembroke High School, Quabbin Regional High School. At the end of their PCR laboratory experience, they were asked to fill out a survey. The miniPCR made quite an impression on these young scientists.

In 3 years when you look back on this experience what will you remember?

  • Using the miniPCRs (for the first time) to amplify our own genes from the cheek swabs
  • The new technology my high school hasn’t gotten yet, such as mini PCRs and better quality pipets.
    programming the pcr
  • I will remember running our dna in the gel electropherisis and actually getting to do the whole experiment with the unique pcr machine
  • programming the pcr
  • I would remember how the program of the PCR looks like a heart beat
  • I will remember the basic procedure of performing PCR, and I will also remember how amazing it was to work in a lab of such interesting quality.
  • Probably the setting up of the PCR program
  • The new use of mini PCR machines.

If you are a high school or higher-ed educator, a graduate student, a medical technician- there is something the miniPCR can give you. It could be its attractive efficiency, its ability to run PCR in remote locations, or its independent character. Regardless, this machine has and will continue to revolutionize the realm of science education.

Let’s end this post by amending some Shakespeare: And though it be but little, it is fierce.

Check out Szaniszlo’s article in the Boston Herald on Zeke and Sebastian: Device opens DNA testing to masses

Check out Alia‘s original blog post here.

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