DIYBio PCR Challenge

PCR ChallengeThe PCR Challenge on the 19th of April brought together a lot of eager amateurs interested in the tools and techniques behind CSI-style DNA analysis; looking to see how is it done and whether we could do it too. There are two parts to this process – PCR, a lab technique whereby you select a particular piece of DNA you’re interested in and produce lots of it (amplification), followed by another technique Gel Electrophoresis, the end result of which is a supercool CSI-style gel graph.

If this sounds super-technical you’d be right – fortunately we had two things going for us. Firstly, these two techniques have been around for decades and are incredibly well documented. However, more importantly, we had assistance from Dr. Trish Linton at MMU who prepared everything for us and provided a super-simple set of instructions to follow which ultimately ensured that, despite no-one at the meetup having done this before, meant that we at least got some kind of result out of the process (more on this later!)

And so, to the challenge. For PCR you need… a PCR machine! We had not one but three – a commercial-grade machine (kindly supplied by Trish), an OpenPCR which we built at the last DIYbio meetup, and… the BBQPCR! We’re super-proud of this version – built by Alex from HACman from an Arduino, some parts from B&Q and ample quantities of raw invention, we were keen to see how it would hold up in the red-hot crucible of amateur biological experimentation.

We started the PCR part of the challenge the night before when Trish brought the ingredients around to the Madlab and we plugged everything into the machines to run the PCR reaction (excellently described by this Kubrick-style video here, and in rap form here). The whole cycle took just over 4 hours, after which our samples went into the fridge ready for…

Challenge day!

We had a great turnout, despite some gruesome Manchester springtime weather and, after a quick rundown of what we did the night before and the science behind PCR, we got stuck straight into the results analysis. Gel Electrophoresis as a technique has been around since the 1930s and at its simplest involves using a high voltage power source to push DNA through a very fine gel made from refined Agar (aka Agarose, which unlike Agar you can’t buy from Chinatown). Setting up the gels (one per machine in the challenge) and adding all the other ingredients was super simple (again, thanks Trish!) – the hardest part of the process was getting our samples into the gel using a micropipette.

PCR Challenge
It turns out there is a bit of an art to pipetting – a couple of attendees already knew their way around a micropipette but the majority of us didn’t. After a quick intro video on the dos and don’ts (do get your sample in the right place, don’t break the gel, no air bubbles etc.) we got stuck in. The more experienced pipettors claimed that it took them weeks to get the proper technique. Everyone tried it out and amazingly it seemed to work so we must have been a talented lot.
Gels prepared we hooked them up to the power supply and left them running for half an hour while people had a cup of tea and admired our soil-based microbial fuel cells from a previous meetup. Half an hour later we stained our gels (using non-toxic Fast Blast DNA stain, which it turns out also stains hands and tables equally well) to reveal the results, which were.. inconclusive!

Something obviously worked, because after a few minutes of staining some bands of DNA started to show up in the gels, but they never developed to an extent that we could determine a clear winner in the challenge (or tell if our John Doe was carrying TB or not). On the basis that we can just about see something I declare the PCR challenge a success!

After a night in stain

We decided to leave the gels in stain over night to see if something more will appear for the morning. Not the best idea it turns out…
Regardless of results, it’s been a learning process for all involved and we are very proud of our PCR machine and all the buzz around it. Seems like amateurs are gaining more and more knowledge in different spheres of science and we love to be part of that development. Stay tuned for a PCR rematch, as well as some more DIYbio experiments in the future!

*Post written by Asa Calow

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