[youtube=http://www.youtube.com/watch?v=zrejvnVfZJE]
[Jeri Ellsworth] stopped by Pearl Biotech’s booth at Maker Faire and took a look at their open source DNA sequencing work. It is by no means a grab-and-go solution for anyone, but from what we’ve seen in the video they’re breaking down those laboratory walls and letting us in to dabble at this work (assuming you’ve got a few hundred bucks to burn). There is a community for info and help that you can check out at BioCurious, and Pearl Biotech has gel box kits available (or the details if you care to source parts yourself), traditionally an extremely expensive part of the process. You’ll still need a centrifuge and a heating/cooling device to separate the strands but as you can see in the video, these can be hacked together rather easily.
We’re glad that [Jeri] shot and posted this clip. She does a great job of explaining projects, whether it’s someone else’s like this or her own, like the transistor fabrication method.
[Thanks Shazzner]
Thanks for digging up the links, I couldn’t find any to the Gel Box kit.
Around 6 minutes in, I wish she would have smacked him and said “more tech, less selling”.
BioCurious? really? with that mullet?
for the centrifuge you can use those salad spinners.
@shazzner
here are some cheap gel boxes (theres no need to buy a brand new one.. they last forever): http://shop.ebay.com/?_from=R40&_trksid=p3902.m38.l1313&_nkw=Gel+electrophoresis&_sacat=See-All-Categories
Make sure you get a decent power supply.. it makes a big difference.
also that box, a pcr, does not separate dna… it heats and cools dna polymerase to amplify dna. strands. a commercial one is MAD expensive. Biotech’s project is pretty innovative as the components look pretty cheap.
And it’s Arduino based! *duck*
@alex
actually it does seperate the double strands by melting them … necause the dna polymerase only works on single stranded dna
it’s pel-tee-ay, dammit!
OK, that’s not quite the French pronunciation, but pel-tee-er is way annoying.
It’s great to see this sort of equipment being made for prices that mortals could afford. Scientific supplies are always grossly overpriced.
Some corrections: This is NOT DNA sequencing, it is PCR, followed by agarose gel electrophoresis. PCR amplifies a small, specific stretch of DNA a zillion times or so, so that there is enough DNA to see it in a band on the gel. You then know what length that particular stretch of DNA is (and this can vary in different species or individuals for example).
Sequencing is ‘reading’ the actual A C G T sequence of a stretch of DNA.
Lastly, when DNA is heated and cooled (to about 72degC) it does not “heal itself” as the guy said. The single strands are replicated to double strands by an enzyme called “DNA polymerase”. I’m all for simplifying the science but that was just misleading. I do this stuff for a living.
Still, very cool.
I wonder if PCR could be used for the purpose of identification? Home made CSI on the cheap?
yeah it can be used for identification. If you have the right primers for the PCR-reaction to amplify the right spots of the DNA (VNTRs and STRs aka “variable number of tandem repeats” or “short tandem repeats), and if you do it with enough spots to rule out a statistical possibility a match is just found by accident. Go have fun!
= DIY paternity tests! :-0
Gotta be very careful with that sort of stuff though, it’s easy to make mistakes or get DNA contamination into the reactions.
I was impressed by the light attenuation of the LEDs when the filter was placed over it.
“Pocket PCR for pennies”
http://www.lava-amp.com/
How do you choose what part of the dna to look at?
Yeah I’m confused!
I’m baaaaoocurious.
Brilliant! Absolutely brilliant! It’s so cool to see that there are *still* very smart people around!
This is dangerous as fuck.
Ethidium bromide used in agarose gel electrophoresis is extremely carcinogenic.
What was the URL he said for the company making the boxes he had?
Well, the biggest problem they didn’t solve: cheap supplies. While the technological stuff might be easily made, where do you get the chemicals to do the real stuff? I mean PCR- come on, it’s only interesting, if you have the right primers for your problem. And to get them is difficult and expensive. Same counts for all the isolation of DNA/protein and all the stuff that is sold as kits by Invitrogen etc. If one buys their stuff the result will simply be, that one has a bunch of crap at home and maybe one or two reactions. Simple demonstrations but nothing more. For anything relevant you need a real lab with UV decontamination, reactants, sterile bench etc. No fucking way to do this at home without serious investments. And if one puts in money, the SDS PAGE will not be the limiting factor, even with off the shelf devices.
The centrifuge is covered: I designed a Makerbot/Reprap printable centrifuge that uses a Dremel for power. I work in a genetics lab, and I can vouch for the power of my design if not its relative safety. :P Google “Dremelfuge” for details.
As to the safety of the Pearl Biotech Gelbox and their approach, it’s not as dangerous as some here are suggesting. They designed the box to use the “Sybr-safe” dye rather than a more dangerous one such as Ethydium Bromide. Also, if you’re too poor to buy Sybr-Safe, you can use Methylene blue from an aquarium supply store if you have enough DNA.
Finally, some forms of PCR can be used to determine the sequence of DNA at a particular one-to-three base-pair site. If a particular mutation has taken place, for example, a well-tuned PCR reaction will pass/fail depending on the sequence.
Great to see so much interest in DIYbio on this comments list! I’m planning to make affordable, DIYable science my career in the near future, and I know the Pearl Biotech guys are doing a great job pushing for this already!
Other than the “BrusselSprourt” analysis, is it possible to sequence the DNA exhibiting unique sequences of people?