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Biology's McGyver: DIY DNA P.C.R.

Posted by michael on from the cheaper-is-better dept.

joesao writes "In this short, charming interview, Dr. Eva Harris talks about popularizing biology by doing what she calls "knowledge-based" technology transfer: "...people purify DNA for P.C.R. processing with a fancy substance made of silica particles, which costs about $100 for a few milliliters. [...] So what we've done is buy a 20-pound bag of ceramic dust for $5 at the hobby store. And you wash the stuff in nitric acid and sterilize it, and then you have thousands of tubes of that substance. We're not violating anything because the commercial manufacturers have their way of doing this, and we have ours." Open-source biology, anyone?"

34 of 55 comments (clear)

  1. What I want... by TitaniumFox · · Score: 4, Funny

    Is a DYI thermocycler. Programmable. With a heated top.

    Additionally, you can snag the silica gel needed for PCR purification from Vacutainers used to collect and subsequently separate blood.

    --
    -- I'd say your post was about 3 monkeys, 18 minutes.
    1. Re:What I want... by mcdrewski42 · · Score: 3, Funny

      How do I moderate this as (+1 Huh?)

      --
      /* affect != effect */ void affect(int *thing,int effect) { *thing += effect; }
    2. Re:What I want... by dexter+riley · · Score: 1

      I read about this method recently: it performs PCR of a drop of liquid in a mineral oil-filled capillary by moving the droplet through different static heating elements. Kinda like the old way of moving the tube from heat bath to heat bath, but without the tube. The drop is small, so you don't get a lot of product, but the heat transfer is really great, so it works very quickly. Alternatly, you could probably make a hot-air cycler, like the one that Idaho Technologies (?) sells, much easier and cheaper than making a peltier/heated lid cycler. Enjoy!

      J. Chiou et al., "A closed-cycle capillary polymerase chain reaction machine," Analytical Chemistry, 73:2018-21, May 1, 2001.

      "A capillary PCR machine has been built and demonstrated to perform 30-cycle PCR runs of a 500-bp target from genomic lambda-DNA with 78% efficiency in 23 minutes, which compares to coventional PCR machines that take 1 to 2 hours. The system moves a 1-microliter droplet between three heat zones in a 1-mm-i.d., oil-filled capillary and uses multielement scattered light detection with active feedback to detect the position of the fluid slug. This paper goes into detailed analysis of the potential optimal cycling times based upon device geometry and fundamental constraints of the biology."

  2. talk about a markup! by bscott · · Score: 2, Insightful

    Looks like I.T. markups are tame by comparison...

    --
    Perfectly Normal Industries
    1. Re:talk about a markup! by nhaze · · Score: 1

      That doesn't really tell you how much you are getting...you generally buy custom oligos at a certain synthesis scale... ~200 ul of what concentration? /end nitpicking

      Yeah, then if you change a few TaqMan base pairs enough to change its configuration into a stem-loop structure...even though it is essentially the same sequence with a few base pair modifications you will be paying over 3x the TaqMan price, because you have stepped into the molecular beacon patent. Friggin' ridiculous

  3. Focused liberalism by Dancin_Santa · · Score: 2, Interesting

    It really warms my heart to see liberals focus their concern for the poor in a specific and effective way. I feel the same when a conservative does so as well. No one is so callous as to completely not give a rat's ass about their neighbor, but it is more than difficult to find ways to help them than to feign contempt.

    When effective people like Dr. Eva here go out and turn their ideas into reality it benefits everyone. If she were to go into politics the world would have been less one innovative scientist. Worse, the world would have been up one know-it-all politician.

    There are several politicians out there today who could no doubt have been effective in changing society for the better had they pursued a specific profession other than politics.

    1. Re:Focused liberalism by Jahf · · Score: 1

      I see where you're coming from, but that IMO is the biggest problem with liberals today. We are too disorganized politically. How many innovative scientists do you think we've -lost- due to the current Bush shenanigans (hint: read up on what the PATRIOT act and its ilk have done to the ability of scientists to be honest with their reports versus having to fudge or simply not research in certain areas to keep their jobs).

      The more the liberal community cedes the political realm, the harder it will be to be liberal in other aspects of life. Like it or not, politics is a very large part of how the world runs. Everytime one liberal quits voting or quits running for office it weakens their cause and simultaneously strengthens all oppoising sides.

      FWIW I'm more Libertarian as I get older, but that means I'm a social/privacy liberal. I vote Libertarian where feasible (and when the candidate isn't a dipstick, being a small party is like a magnet for folks who've been rejected everywhere else). However to keep with strength in numbers I vote Democrat in the larger elections and I will keep doing so until there is enough of a Libertarian political base to be effective because the divisions (like voting for Nader in 2000) are just WAY too good for the other side. The "other" side for me is not necessarily Republican (I voted for a couple last time just because they had better platforms) but is all sides that are social/privacy conservatives.

      If everyone would pay attention to issues and vote their morals, I wouldn't have to go through this to such a degree and I would agree 100% with your original post. But the world is grey.

      --
      It is more productive to voice thoughtful opinions (reply) than to judge (moderate) others.
    2. Re:Focused liberalism by Otter · · Score: 1
      How many innovative scientists do you think we've -lost- due to the current Bush shenanigans (hint: read up on what the PATRIOT act and its ilk have done to the ability of scientists to be honest with their reports versus having to fudge or simply not research in certain areas to keep their jobs).

      Three? Zero? I would be astonished if the number is more than ten. (And that's before you get to "innovative".) Maybe in a handful of sensitive areas there'll be some useful work that doesn't get done. But the idea that there is a massive exodus of scientists is absurd.

      --
      What I'm listening to now on Pandora...
    3. Re:Focused liberalism by Jahf · · Score: 1

      Wow ... 3 ... then in that case every single scientist who is either being stifled or worried about being stifled must have already been interviewed. And these were only in relation to PATRIOT specifically, not the administration's policies having similar effects in general.

      http://www.suntimes.com/output/zinescene/cst-fin -e col30.html

      http://www.mafhoum.com/press4/129P1.htm

      http://www.thorsett.org/archives/000013.html

      http://www.research.ucla.edu/ocga/memo_OFAC.htm

      Still believe 10 is a high number?

      --
      It is more productive to voice thoughtful opinions (reply) than to judge (moderate) others.
    4. Re:Focused liberalism by Otter · · Score: 1
      Number of scientists "lost" as described in those articles: zero

      I stand by what I said -- there will be some useful work that doesn't get done but I would be astonished if the number of people who leave research will reach double digits.

      --
      What I'm listening to now on Pandora...
  4. NYTimes Article by Momomoto · · Score: 1, Offtopic

    Remember, folks, if you don't want to register with the New York Times you can always use:

    User: slashdoteffect
    Password: slashdot

    --
    "Max, come over here. French-Canadian bean soup. I want to pay. Let them leave me alone." - Dutch Schultz
  5. Re:Hmmm...I wonder.. by nhaze · · Score: 2, Informative

    But since (amazingly) the process is patented you can't make a buck off it unless you pay some licensing fees. But yes, those that have paid those licensing fees have made RIDICULOUS profits from 16 well cyclers.

  6. pffft! by ziggles · · Score: 2, Informative

    It's MacGyver, not McGyver.. how ignorant can you be! :P

    1. Re:pffft! by bill_mcgonigle · · Score: 1

      It's MacGyver, not McGyver.. how ignorant can you be! :P

      Yeah, really, like some Irish guy is going to be able to figure out how to get out of a maximum security prison using a nail clipper and a watch battery. A Scot, sure, but - OK, well, maybe if the Irish guy was trying to get to a pint of Guinness. ;)

      --
      My God, it's Full of Source!
      OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
  7. Two mistakes by hummassa · · Score: 1

    1. it's not resequence DNA, just test it (think paternity tests)
    2. it's not /. running gag, it's an obligatory Simpsons quote

    --
    It's better to be the foot on the boot than the face on the pavement. ~~ tkx Kadin2048
  8. Rather hyperbolic by Otter · · Score: 4, Insightful
    I'm sure this work is very valuable, but either she or the reporter (or both) make her come across as far, far more revolutionary than she is.

    For instance, people purify DNA for P.C.R. processing with a fancy substance made of silica particles, which costs about $100 for a few milliliters.

    I incubate a piece of tissue with a couple of cents worth of buffer and proteinase, and then dilute the resulting glop in water. Obviously different protocols call for different methods, but routine clinical preps shouldn't call for anything nearly as elaborate as what she describes. Anyone know what this silica thing she's talking about is? Qiagen spin preps?

    This is called manual cycling. Suddenly, you don't need that $10,000 machine. Now, I didn't discover manual cycling or P.C.R., but I've helped popularize it.

    Uh, no kidding you didn't invent manual cycling. That's how everybody did PCR until the cyclers became available.

    Like I said, I can easily see where it's a very valuable activity to generate manuals and reagent sources for cheap techniques, but the interview makes her sound vastly more inventive than she is.

    --
    What I'm listening to now on Pandora...
    1. Re:Rather hyperbolic by Anonymous Coward · · Score: 3, Informative

      Almost every company that sells you some sort of PCR purification / gel purification / miniprep kit that has a spin column or a vac manifold column has some "proprietary formulation" in their columns, but it's silica based. Decrease the pH to about 3.5-4 and your DNA sticks via its phosphodiester backbone. Change it back to 7-8, and the DNA elutes into your TE/H2O/whatever. This is exactly what she is talking about. There were 2 papers published around '83-'84 that describe the use of silica gel for DNA purification. Finding some modification that makes your yield go up and slapping a sticker on it and selling it is big money.

      Kids. Back in the day, we'd make our own competant E. coli using the Hanahan method.

      In the walk-in -20C.
      Uphill.
      Both ways.

    2. Re:Rather hyperbolic by Muhammar · · Score: 1

      $10000 thermal cycling machine is nothing more than variable heating/cooling bath. It is about as complicated as a home-breadmaking machine and I am sure that if there was large market for it (if it was sold like home appliance) it would cost maybe $200. One can do just as well manualy, with a beaker of hot and cold water, as described in the article. This is completely common with all lab equipment and lab chemicals - being overpriced over comparable bulk or common products by order of magnitude.

      One business day of a qualified lab researcher or technician costs on average $1000 in th US (building cost and overhead, the administration etc, not mentioning lousy sysadmins). So you buy the $10 000 automated instrument and a nice PCS kit, no problem. Besides, nobody in US pharma or medical industry has incentive to do it cheaply.

      [Universities have limited grant money and can use student labor for purifying ceramic dust.]

      --
      I doubt that we will ever figure out - and I suspect that even if we did figure out we couldn't do much about it
    3. Re:Rather hyperbolic by Muhammar · · Score: 1

      PCR, sorry.

      --
      I doubt that we will ever figure out - and I suspect that even if we did figure out we couldn't do much about it
    4. Re:Rather hyperbolic by Anonymous Coward · · Score: 2, Insightful

      I'm sure this work is very valuable, but either she or the reporter (or both) make her come across as far, far more revolutionary than she is.

      For instance, people purify DNA for P.C.R. processing with a fancy substance made of silica particles, which costs about $100 for a few milliliters.

      Funny, I read it a different way. I took it as someone who was very politely saying that the 'Propietary' chemical supply stores are robbing medicals blind. If she was an IT worker, I would have expected to hear mention of the DMCA or of a lax Patent Office.

    5. Re:Rather hyperbolic by temojen · · Score: 1

      Many countries cannot afford $10,000 machines for their hospitals; they can afford lots of bags of ceramic dust and labour, though.

    6. Re:Rather hyperbolic by Sgt+York · · Score: 1
      Back in the day? Hell, we used to do PCR with Klenow and three water baths! And we purifed our own dNTPs! From ourselves!

      Actually, I was the source of our hemoglobin standard for a while....

      As for the technique, we've used a setup for gel purification from a Science technical QC for years. Freeze 'n Squeeze. Take a .5 mL tube and poke a hole in the bottom with a 18ga needle. Put some sterilized poly fiber in it (pillow stuffing from WalMart stuck in a strong uv source for ~10'. UV crosslinker works great) and pack it down. Cut out your gel slice and stick it in the -20 on a bit of foil for 30'. Put the slice on top of the fiber, put the whole thing in a 1.5 mL catch tube and spin. The elute is pretty pure, better than Qiagen, normally.

      --

      There is a reason for everything. Sometimes that reason just sucks.

    7. Re:Rather hyperbolic by forkboy · · Score: 1

      lab equipment and lab chemicals - being overpriced over comparable bulk or common products by order of magnitude.

      What you're paying for in lab-grade materials is purity. Bulk reagents have a lot of crap in them, depending on what you're working with. Bulk organics might have significant traces of solvents or purification substrate and bulk acids/minerals will have traces of heavy metals. When you're doing sensitive, small-scale biological research, these pollutants can really screw things up.

      The processes to remove these miniscule traces of pollutant are time-consuming and require expensive equipment. They have to use expensive analytic equipment to assay it initially, then purify, then assay again. (and purify again if necessary) Requirements for purity are usually on the scale of parts per billion or parts per trillion.

      That is what you're paying for when you buy a $100 bottle of lab-grade acetone instead of a $20 drum of the cheap stuff. (for example)

      --
      This message brought to you by the Council of People Who Are Sick of Seeing More People.
  9. Re:Oblicatory Google Affliate Link by awgriff279 · · Score: 1

    Thanks, for the link. I really don't care to use the nytimes if i have to register.

  10. Oops. Dyslexia. by TitaniumFox · · Score: 1

    I wanted a DIY thermocycler for PCR.

    Programmable.
    Heated top.

    I want more, though.

    It's got to:
    Run Linux
    Beowulf cluster
    Play OGGs
    Serve web pages (it's got to be slashdottable when I show it off)

    --
    -- I'd say your post was about 3 monkeys, 18 minutes.
  11. Re:Hmmm...I wonder.. by Rick+the+Red · · Score: 1

    Actually, if it's patented, they can. But they'd have to catch you first.

    --
    If all this should have a reason, we would be the last to know.
  12. Re:Hmmm...I wonder.. by Rick+the+Red · · Score: 1

    Careful -- I've got the patent on Pure, Crystallised Evil.

    --
    If all this should have a reason, we would be the last to know.
  13. Not a rebuttal, but additional thought. by Anonymous Coward · · Score: 1, Interesting

    Sometimes it's patented, but sometimes it's just "secret." (ie. not patented, but they're not telling you, either) For instance: Look at Zymo's Z-competent cell kit. They sure as heck won't tell you what is inside their special reagents, but if you walk them over to your local biochemistry lab with a GC/MS and run some of it through, you'll find it is simply a modification of the Hanahan protocol. What modification? It's not one that provides for higher efficiency, but a modification that provides for more success of producing competent cells. (If you've done the Hanahan protocol, you'll know it's high efficiency, but a fragile protocol.)

    I ran the numbers. The Hanahan/Zcomp cost ratio is something outrageous like 1/20 for an equivalent batch of cells, and the efficiencies are higher.

    In this case, I like old-school vs. new and wiz-bang.

  14. Business Model by Zarf · · Score: 2, Interesting

    Why not set up a business where the lab work gets done in a place where IP isn't enforced and use the cheaper methods and such that you can't in the US to do the lab work. Then you send the data back stateside over the 'net. Viola, you've got a cheaper lab! Does someone run a business like this? Why not? Can you use these primative techniques to get results as good as the fancier techniques?

    --
    [signature]
  15. Re:PCR by Sgt+York · · Score: 1

    I've always seen it used to purify PCR products from the leftover reagents and the template, or for purifying plasmids/plasmid fragments from bug preps and restriction digests. I don't think that silica beads are all that great in purifying larger (genomic) pieces of DNA, but I could be wrong. I just use the old phenol/chloroform/IAA method for big stuff, and freeze 'n squeeze on the small stuff from gels.

    --

    There is a reason for everything. Sometimes that reason just sucks.

  16. Re:Hmmm...I wonder.. by Sgt+York · · Score: 1

    They can, but they don't. At least not in academia. We used to make our on Taq from a plasmid we had in the lab, a HUGE no-no, as far as patent law goes. The vendors just looked the other way. They know that if they let us save money there, we will spend it somewhere else. By letting us get more work done cheaply, we get more grant money, and we buy more other stuff from them. Stuff that is difficult/prohibitive to make on our own.

    --

    There is a reason for everything. Sometimes that reason just sucks.

  17. Re:Did anyone else notice by dharmawan · · Score: 1

    was just about to say! daymn this girl's hot

  18. Re:Oblicatory Google Affliate Link by gacp · · Score: 1

    Me neither. I wonder when the NYT is going to dig this.

    --
    ``L'imagination au povoir.''
  19. Re:PCR by sd211 · · Score: 2, Informative

    Silica stuff works great when you do not want to think, or you do not have time for error. Just buy a kit from Qiagen. They use essentially the same columns for dna exctraction from blood, tissue, cells etc. For a relatively low sensitivity simple methods often work great. e.g. for PCR detection of Hepatitis B virus, one can incubate serum with 50 mM NaOH for 30 min at 37C, neutralize and go. But if you need to get a single-copy gene or low titer virus - silica columns or absorption on paper is your best bet.