Open source PCR machine
July 7, 2011 8:11 AM   Subscribe

OpenPCR now has a kit available to build a thermal cycler for $512. The polymerase chain reaction (PCR) is one of molecular biology's most common and often indispensable techniques, used for wide ranging purposes including testing (e.g., uncovering sushi fish fraud) and genetic engineering. OpenPCR puts the technology within better reach of educators and amateurs: commercial thermal cyclers normally cost thousands of dollars. via.
posted by exogenous (40 comments total) 16 users marked this as a favorite

 
Huh. Apparently the PCR patents expired a couple of years ago.

[this is good]
posted by grouse at 8:21 AM on July 7, 2011


First we had the Radioactive Boy Scout (previously), so I wonder what this will bring ..
posted by k5.user at 8:22 AM on July 7, 2011


Yeah, PCR has been off patent for a little while now. The best part about this is that Taq has gotten really cheap (unless you buy it from Invitrogen).
posted by maryr at 8:24 AM on July 7, 2011 [1 favorite]


What's he building in there?
posted by The White Hat at 8:26 AM on July 7, 2011 [3 favorites]


Questions:

1) What are the associated costs with running one of these? The little demonstration flash bit has 5-6 other solutions you need to be mixing.

2) What do you have to do to the DNA sample to make it usable? Do you just drop a small bit of hair into the PCR vial, then add the primers et cetera, and run it?

3) This talks about "targeted DNA".. I assume that the primer and nucleotide additives need to be customized, and that's how the targeting takes place?

4) Presumably you'd need a large DNA database to check your target against and see what you've found. Is that information also available freely online, or more bucks to shell out?

5) How do you look at the DNA you've multiplied? What's the cost for that microscope?

This is a completely cool thing but it's obviously just one part of a lab, and I'm wondering what the real cost would be to, for example, go about investigating your local sushi restaurants.
posted by curious nu at 8:34 AM on July 7, 2011


Ok so now I have all this goo replicated from a sashimi piece I got at 'Joe's Sushi and Gas to Go', how do I tell if it's wild Alaskan salmon, or Atlantic caged frankenfish?
posted by stbalbach at 8:34 AM on July 7, 2011


what curius nu said..
posted by stbalbach at 8:35 AM on July 7, 2011


k5 - This is a long way from radioactivity on the loose.
posted by maryr at 8:36 AM on July 7, 2011


I was pretty excited about it until I realized it's basically just a heating pad with a timer attached. I thought it was going to do all the "drop the next bit in" part that the game on their site shows.

That said, DIY bio is going to be huge and I wish I knew enough to do stuff with it.
posted by DU at 8:38 AM on July 7, 2011


Partial answer to curious nu's questions (wikipedia to the rescue):

2) DNA extraction
4) Genbank
5) Gel electrophoresis
posted by cnanderson at 8:45 AM on July 7, 2011 [2 favorites]


Curios nu:

1) You hit on something important here. The reagent cost is really the big deal (although lab thermocyclers are usually a few thousand dollars). Prep chemicals, buffers, enzymes can cost hundreds of dollars, not to mention the equipment to get that all going safely.

2) You have to extract the DNA out of the source cells. The cost of prep kits for doing that can vary widely depending on how clean the source is and how clean you want the final product to be. Could be as simple as dish detergent or the more laborious assembly of BAC libraries and DNA purification.

3) Primer design is actually pretty straightforward. You design the primer DNA sequences you want and order them online. It's cheap and quick.

4) There are both public options and private options. But the UCSC Genome browser and the NCBI Entrez database are both great places to look.

5) How do you look at the DNA you've made copies of? Well there are many different approaches. You won't be using a microscope, but you can run the DNA out on a gel and look for characteristic patterns (usually by comparing it to known samples). You can have the DNA sequenced, which is fast these days, but you have to isolate the material you want, which can be trickier.

Bottom line is that PCR is powerful, and there are many things you can do with it, but usually in conjunction with a lot of other molecular biology techniques. It is getting to the point where you could pull it off in your own backyard though. Cheap PCR is just one of the links in that chain.
posted by Mercaptan at 8:47 AM on July 7, 2011 [8 favorites]


In the late 1990s (grad school) we bought Taq polymerase from Promega, who was much cheaper than any other source, apparently since they weren't paying any patent license fees. Some people I knew actually grew the polymerase protein in bacteria and purified it, but that wasn't anything we wanted to mess with.

Looks like the reagent costs are now about $0.40 per reaction (looking at master mix for 100 reactions). Custom primers are pretty cheap these days via mail order. Other costs would be PCR reaction tubes and pipettes, etc. - pipettes could be expensive as they would have to accurately and precisely deal with tiny volumes of fluid.
posted by exogenous at 8:48 AM on July 7, 2011


Curious nu -
1) Relatively low, given that taq is cheap these days. Assuming you just want to amplify a sequence of DNA from your cheek swab or something, the cost would be about: ~$8*2 for the nucleotide primers (ordered from a company), ~$10 per reaction for various solutions including the critical enzyme taq. $10 is a guess, but I doubt it's higher than that.
2) There are pretty simple DNA isolation techniques; usually you just add some detergent to lyse the cells, and make sure that the pH isn't going to do weird things to the DNA.
3) Yeah, you need to order the nucleotide primers - ie., the "flanking sequence" for whatever piece of DNA you want to amplify. My guess is $8 each, with one primer at each end, but those might be academic prices.
4) Oh, that's totally free. Look at ensembl.org if you want a reasonably nice way of looking at almost all known genome sequences.
5) The simplest kind of experiment you can do is to ask "is this piece of DNA 100bases long or 200 bases long?" A good example of that kind of question is the short tandem repeats associated with Huntington's disease, or with DNA fingerprinting in forensics cases: http://en.wikipedia.org/wiki/Short_tandem_repeat. For this, you would need to run the amplified DNA through a Gel Box to establish the size of the fragment you amplified. That costs ~$25 to build (http://hackteria.org/wiki/index.php/DIY_$25_Gel_Box) and probably $1 to actually run.

It's all pretty cheap! The expensive part is the enzymes, but those are getting cheaper and cheaper every day.
posted by metaculpa at 8:48 AM on July 7, 2011 [3 favorites]


Late to the party!
posted by metaculpa at 8:48 AM on July 7, 2011


2) You don't actually need to extract the DNA from the cells - at least, not all cells. I can PCR fragments from E. coli by simply resuspending a colony in 5 ul water and using that as a template. The heat from the reaction lyses the cells just fine. It's not the cleanest reaction you've ever seen, but with the right polymerase, it's a piece of cake.

Don't forget that there is an additional cost not mentioned above - sequencing the DNA. I'm assuming that even garage scientists aren't Sanger sequencing all their constructs. Ugh.

Also, I see that this kit does not include a heated lid. Blergh, mineral oil.
posted by maryr at 8:57 AM on July 7, 2011


For the more hardcore DIYers, you should also take a peek at my lab's attempt at a make-yer-own PCR machine (<$150). This was published in MAKE magazine a few years back. It also outlines a general primer on what PCR is all about. Game on!
posted by davidng at 8:59 AM on July 7, 2011 [4 favorites]


I should add that the electronic's schematics give you the basics. You could fancify so that more tubes are accepted, have tighter control of precision of temperature changes etc. Overall, the basics of most PCR machines are a heat block + peltier device + some sort of mother board for control.
posted by davidng at 9:05 AM on July 7, 2011


If NYC folks are interested in this sort of thing, they should check out Genspace, Brooklyn's premier bio-hackspace.
posted by zamboni at 9:07 AM on July 7, 2011 [1 favorite]


Maybe I've been in the lab too long, and am too accustomed to all of the tools available to me at a large university, but I just can't stop wondering... why? Okay, sure, it's kind of cool that you can run a PCR and a simple electrophoretic gel in your basement. But beyond that, why would you? What are you learning from it, scientifically? To me, PCR is generally one step in a long process to answer some kind of scientific question. What kind of questions are home scientists asking, that a) can be answered using only these tools, and b) haven't already been answered?

This is an honest inquiry, not snark, I swear. I just really don't get it.
posted by amelioration at 9:10 AM on July 7, 2011


This is about my favorite thread ever, now. I don't understand any of it, but it's giving me some great search terms for teh googles.

Bear in mind hobbyists spend tens of thousands of dollars on telescopes, or machine shop equipment - we're definitely in the home hobbyist price range for bioengineering, now.

I will be ordering a labcoat forthwith, in anticipation of low-cost monster-making in the garage. Do they still sell the ones like Dr. Horrible wears?
posted by Slap*Happy at 9:10 AM on July 7, 2011


I see this more as a tool for education than for garage science. There must be tons of teachers out there who would love to have one of these in their teaching labs.
posted by exogenous at 9:24 AM on July 7, 2011


If you're really interested in doing PCR cheaply you can do it the way it was originally done, which was with 3 pots of water at different temperatures. In fact people still use this method when they need to perform large scale amplifications which won't fit in a standard thermocycler.
posted by euphorb at 9:25 AM on July 7, 2011 [3 favorites]


Interesting, but I feel like the older used ones got down pretty close to $750 on LabX or eBay when I looked last.

Is there a west coast equivalent to Genspace?
posted by deludingmyself at 9:44 AM on July 7, 2011


Exogenous, I certainly agree about this being fantastic for teaching, both in classroom and community outreach settings. The Genspace projects that zamboni linked are intriguing too, but again you're getting into an institutional/outreach level and category of work (larger groups, this type of equipment being but one component in use, a focus on individualizing genetics to make it interesting to non-scientists). However, the marketing seems so focused on individuals using the technology at home that I can't help but wonder what kind of projects these home scientists are considering doing.
posted by amelioration at 9:44 AM on July 7, 2011


"What kind of questions are home scientists asking, that a) can be answered using only these tools, and b) haven't already been answered?"

Yes, trying to do the cloning for stuff like structural genomics or hell even optimizing your own reaction, much less just about anything a typical research lab might do with a thermocycler would be beyond pointless, but there are more things that PCR is useful for.

-A doctor, or enterprising graduate student could take one of these machines out to the middle of nowhere with primers for whatever ailes where they are going and to do their own high quality diagnosis of viral, bacterial, or genetic diseases.

-Hobbyists at home could test food for contamination, their children for paternity, their sweet harts for genetic disorders, their livestock for viral bacterial or genetic disease, or their themselves and friends for whatever.

-Hobbyist at home could also make creative things, the FDA couldn't do anything to stop a hobbyist from making GFP lactic acid bacteria for glowing green yoghurt much less anything else, or GFP M. smegmatis to make your cave or basement glow, and this is just off the top of my head.

As the genetic system for lactococcus gets better I can see all hell breaking loose in a lot of cool, and undoubtably quite a few bad, ways with machines like the one in the FPP. Doing any of this is a very non-trivial amount of work, but neither is building San Francisco out of toothpicks. This coming trend should be excite and scare us.
posted by Blasdelb at 10:00 AM on July 7, 2011 [1 favorite]


Maybe I've been in the lab too long, and am too accustomed to all of the tools available to me at a large university, but I just can't stop wondering... why?

I know a handful of people involved in the DIYBio movement in Europe (interested Londoners should MeMail me, I can introduce you to a group at the London Hackspace. Some people are either associated with professional labs or working on getting GMO licenses for themselves to let them do proper cloning.* For example, there's a guy in Germany (Leipzig, IIRC) who is developing a lovely little system for a switchable plasmid making HIS-tagged Taq or DNA ligase to let DIYBio hobbyists make their own enzyme in a fermenter and purify them using simple spin-columns. He's a bio undergrad, doing this stuff in a garage using obsolete or previously broken equipment begged and borrowed from labs around his region.

In London, we have plans to use our thermal cycler (an old commercial one from eBay for £120) and home-made gel box for a bunch of different gene detection experiments. Popular suggestions involve: testing fish and meat from various sources to see if they're really what they claim (lots of white fish gets mis-sold as cod, and who knows what really goes into the curries on Brick Lane?); detecting specific strains of bacteria in samples of food/water/body swabs; determining whether a foodstuff contains genetically modified crops (almost all GM food uses one of about three synthetic/viral promoters). There's a bunch of medically relevent stuff that's possible too (there's a woman in the states with a tiny lab set up in her kitchen who developed, validated and used her own test for Huntington's), but most of us think that it's not territory that we want to get into.

We also want to use it to prepare samples for sequencing. Pick a bit of genome, PCR it up and send it to one of the sequencing services to get a ~500bp read for about £6. Could be interesting to look at various SNPs (tiny variations in people's DNA), some people just want some of their own DNA sequenced because it's cool, or to turn into art. We can broaden this to, again, looking at foodstuffs, e.g. looking at rRNA or tRNA sequences and determining whether all of a given crop (plants and animals) are inbred, or even clones. There's talk of doing enough samples to get e.g. a phylogenetic tree of chickens sold in supermarkets to see how our food sources relate to each other.

I work in a professional lab, and it is hard to think about what we can get up to with just PCR, but explain it to enough hackers and creative geeks and you'll soon have more suggestions than you know what to do with!

Unfortunately, our biggest problem is suppliers of enzymes and primers. They're only really available at sane prices from the big guys (Invitrogen, Sigma, NEB, etc), and these companies simply aren't set up to sell to private individuals. And a lot of the refusals seem to be tinged with a degree of confusion and suspicion; I wouldn't be surprised if my shopping efforts have landed me on some sort of terrorism watch list. Which will make my upcoming emigration plans interesting.

Later tonight I'll try to swing back into the thread and put up some more substantive links on the DIYBio scene in the UK (particularly London and Manchester) and dotted around Europe. Some of my contacts know a bunch of the American DIYBio people pretty well too, so if anyone's interested in getting involved please do get in touch.

*By "cloning", biologists almost always mean "taking a gene from one organism, chopping it about a bit, and putting it into another", where the recipient organism is generally another microorganism like a bacterium or yeast. Not dolly-the-sheep style cloning.
posted by metaBugs at 10:10 AM on July 7, 2011 [2 favorites]


As metaBugs alludes to, see also DIYbio
posted by lalochezia at 10:40 AM on July 7, 2011


I just can't stop wondering... why?

Some smaller university labs would probably buy one just because money is often tight. I've worked in small labs where every dollar was pretty precious -- we did a lot of shopping around on lab equipment, often buying used, etc. Heck, I've even...um, heard about making Taq rather than buying it (the E. coli strains carrying the genes for recombinant Taq and Pfu enzymes are passed around pretty freely, and the enzymes are easy to purify).

Only problem I see is that it appears to be only 16 wells. Seems like for lots of applications, 64 would be much more useful.
posted by statolith at 10:57 AM on July 7, 2011


You can also but a $20 heating plate and a thermometer then run your PCR reactions in a capillary tube. Heat exchange will create zones that are the exact temperature to induce melting, annealing, extension in addition to cycling the fluid slowly up and down the tube.

Unfortunately, the articles I've been finding to back me up on this are behind academic pay walls. Boo.
posted by Slackermagee at 11:08 AM on July 7, 2011


Also, also, my awesome old analytical chem prof was super into making his own equipment (and quite successful at it to boot). Its an older website but Dr. Fisher is, last I heard, still making things for the undergrads to use. If you're interested in making your own instrumentation, I highly suggest dropping him a line via the website to ask for advice/collaborations/etc.
posted by Slackermagee at 11:15 AM on July 7, 2011


I love the fact that the price is a power of 2.
posted by gene_machine at 1:36 PM on July 7, 2011 [1 favorite]


Also, thanks for the shout, bugs. Our Manchester group is at diybio.madlab.org.uk.
posted by gene_machine at 1:40 PM on July 7, 2011


Slap*Happy - real scientists don't wear lab coats most of the time. (Well, at least at BL1, which is all that should be happening at a DIY level.) Of course, we regularly bleach our favorite shirts, so maybe we should.

In fact people still use this [water bath] method when they need to perform large scale amplifications which won't fit in a standard thermocycler.

Oh gods, where? I'm pretty sure you can purchase cycler for 384 plates, if not 1536 plates. Why wouldn't you just go for a few round in a 96 well machine (which is fairly standard)? Gah. The only excuse I've ever heard for 3 water baths is that you eliminate the ramping time on the heat block. (My understanding is that a fast ramping time is also the reason most thermocyclers are expensive.)

For example, there's a guy in Germany (Leipzig, IIRC) who is developing a lovely little system for a switchable plasmid making HIS-tagged Taq or DNA ligase to let DIYBio hobbyists make their own enzyme in a fermenter and purify them using simple spin-columns. He's a bio undergrad, doing this stuff in a garage using obsolete or previously broken equipment begged and borrowed from labs around his region.

Maybe I'm oversimplifying, but... in a well equipped lab, that would be a summer project. For an undergrad. I assume His-purification columns are already commercially available (if expensive). Is he developing a cheaper alternative? Why do you need a "switchable plasmid"? Why not just use two strains? Hell, why not just produce both enzymes at once (under induction, natch) and use two tags (His tag one = Ni+ columns, MBP tag the other = maltose column) ?

(Also - why on earth would you look at tRNA? I ask this sincerely - I never think of tRNA as anything but an amino acid delivery system with the occaisional amber mutant.)

Actually, thinking about it, I would imagine the next expensive piece of equipment you'd need is a centrifuge. I fear for the DIY versions of those. I take it back, you can buy a $300 microfuge.
posted by maryr at 3:05 PM on July 7, 2011


Open Source PCR is a horrible idea. Without for-profit companies, how else will we get parody music videos for proprietary hardware and nucleobases? This must be fought, I tell you!
posted by honest knave at 3:56 PM on July 7, 2011


The same way everything else in molecular biology really gets done. Grad students.
posted by maryr at 4:39 PM on July 7, 2011


Is there a west coast equivalent to Genspace?
posted by deludingmyself at 10:44 AM on July 7 [+] [!]


I just started a summer internship at the UAGC (at The University of Arizona, in Tucson). While I don't know much about Genspace, I do know that we do a lot of outreach into the community. The staff scientists run summer camps, go into classrooms and do dna extraction on strawberries using common household items and work on a lot of niche projects. They also take on student workers at both the undergraduate and high school level.
posted by lizjohn at 5:18 PM on July 7, 2011


Just how long is it before we see this I wonder:

1) Nab a DNA sample from someone.
2) Run PCR on it so you have lots.
3) Commit murder.
4) Sprinkle other person's DNA all over crime scene.
posted by HiroProtagonist at 8:32 PM on July 7, 2011


Tito here from OpenPCR. Just registered so I could add a few ideas. Hope I'm not too late to the party!

There was great discussion concerning "the cost of reagents" vs "the cost of the thermal cycler". If you're running a ton of reactions every day in a lab, the cost of reagents ($1/run) are going to add up quickly. But here's a simple example I like where I think price make the clearest difference. There's a bio kit for high schoolers to identify genetically modified foods using PCR. The DNA kit is $10/student. But the equipment (PCR machine + centrifuge) adds up to $4k when purchased new. So you pay $200 for the disposables, and $4,000 for the equipment. Instead maybe the teacher can spend about $1k for the same thing (which is still a lot for the average bio class).

Also the responses about "what would teachers/hobbyists do with PCR" are excellent. I'll add that DNA sequencing is about $5 or $10 a sample. Rather than "Home PhD Thesis" think "home sushi identification", "tree identification", "allergen detection (allergic to peantus?)", genetically modified food testing". Of course, we're excited to be getting OpenPCR out to university labs, industry labs, high schools and hobbyists.

Finally, biotech hackerspace on the West Coast:
BioCurious
www.biocurious.org, raised $35k on Kickstarter last September
Video on Kickstarter: http://www.kickstarter.com/projects/1040581998/biocurious-a-hackerspace-for-biotech-the-community
posted by tito_openpcr at 10:00 PM on July 7, 2011 [3 favorites]


maryr - Oh gods, where? I'm pretty sure you can purchase cycler for 384 plates, if not 1536 plates. Why wouldn't you just go for a few round in a 96 well machine (which is fairly standard)? Gah. The only excuse I've ever heard for 3 water baths is that you eliminate the ramping time on the heat block. (My understanding is that a fast ramping time is also the reason most thermocyclers are expensive.)

I think they meant "large scale" to mean "large volume". Maybe someone wants to do a big (>200ul) reaction to generate a huge amount of product, and the tube won't fit into the heat block? Not sure why you'd want to (or why you wouldn't just run a bunch of small reactions and pool them), but I can imagine someone deciding on that method. Specifically, someone with an undergrad/masters student that they can bully into standing over three water baths for a couple of hours...

Maybe I'm oversimplifying, but... in a well equipped lab, that would be a summer project. For an undergrad. I assume His-purification columns are already commercially available (if expensive). Is he developing a cheaper alternative? Why do you need a "switchable plasmid"? Why not just use two strains? Hell, why not just produce both enzymes at once (under induction, natch) and use two tags (His tag one = Ni+ columns, MBP tag the other = maltose column) ?

Sure, it's not a PhD-worthy project that's going to change the world. I think his reasons are somewhere between "because it's there" (it's a hobby, remember) and because he wants to create a resource that's useful to other hobbyists. As for making a single plasmid switch between producing the two enzymes, yeah, I thought that was a bit odd too. Setting up and validating an inducible system does seem like a lot more effort than just making two different plasmids. We had other stuff to talk about when I met him (contributing to discussions about a code of ethics that they guys at DIYBio.org are putting together), so I didn't get the fine details. But it's an interesting example of something that an amateur biologist is getting up to with these kinds of tools.

I take it back, you can buy a $300 microfuge.

The London group has a dremelfuge run off on our 3D printer. It's basically just a centrifuge rotor that clips onto the shaft of a Dremel hand drill. The prototypes were a bit terrifying (the one time I saw it used, a tube escaped and ricoched of both walls, via the ceiling, before stopping), but the latest version is rather good. It was designed by a lovely chap from Cork called Cathal Garvey, who's doing a pile of R&D geared toward setting himself up as a supplier and re-seller for DIYBio hobbyists.
posted by metaBugs at 11:54 AM on July 8, 2011


For those who are wondering, here's one example where large scale (up to 2.5 liter) PCR amplifications have been performed in water baths. The reason for the large volume is due to the large amount of starting template required.

In this application it is important to preserve the original molecular diversity and this can only be accomplished by diluting the starting template into a large volume.
posted by euphorb at 11:02 PM on July 11, 2011


« Older IRA Vs Al Qaeda   |   You're Gonna Miss Me Newer »


This thread has been archived and is closed to new comments