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Biology's McGyver: DIY DNA P.C.R.
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?"
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.
Looks like I.T. markups are tame by comparison...
Perfectly Normal Industries
Parts list:
1. Peltier/CPU fan+heatsink combos
2. Aluminum tube block
3. Java/BASIC Stamp chip
4. A thermocouple
5. Some time on your hands
6. ????
6. Profit!!
It's conceivable one could come up with a 16 well PCR machine that got within acceptable parameters, in comparison to the water-bath PCR Dr. Harris mentions.
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.
Wow just imagine, a book as popular as the TIME/LIFE series "do it yourself heart bypass surgery"
In this volue you can genetically change your cat into a hideous creature with fly wings and lobster claws. Lunch anyone?
Tsukasa: All I really want, is to be left alone...
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this is as bad as cutting-and-pasting the damn article here. do it anonymously you jackass!
It's MacGyver, not McGyver.. how ignorant can you be! :P
1. it's not resequence DNA, just test it (think paternity tests) /. running gag, it's an obligatory Simpsons quote
2. it's not
It's better to be the foot on the boot than the face on the pavement. ~~ tkx Kadin2048
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...
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.
While you're asking, could you get our Fisher Scientific rep to look more like Natalie Portman?
(mumble,mumble)
You youngins, these days, running around with your P - C - R, and your Taq polymerase. Ya think you're all ready to take over the world with your antibodies and your competant E. coli.
At least you had E. coli!
Do you know how long it takes to do a transformation with pebbles?!?
That Dr Harris appears to be hot, perhaps even a major babe?h arris.h tml
http://ist-socrates.berkeley.edu/~idgroup/
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.
Now I realize that there are many variations of PCR out there, and I've done many hundreds of DNA extractions and PCRs myself, but can someone tell me just what exactly the silica is used for? I've never done PCR nor DNA extraction that required silica and I am curious.
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?
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'nother trick for plasmid isolation - take one overnight colony of the bacteria with plasmid, resuspend in a few ul (6-8) of broth, or a few uL of liquid culture (can be spun down and resuspended to concentrate if you like) - add half of this to 8 uL of weak detergent solution (I use 0.2% Tween-20, but all the others I tried also worked once you get the concentration right, you could probably use very dilute dish soap if you wanted), heat to 100 C for half a minute or so, cool and add restriction enzyme and buffer - digest for a few minutes, add some load dye, run on a gel - you get enough DNA from half a colony for a single diagnostic digest to tell you if it's really what you want to prep DNA from.
The first time you do it it's easier from a liquid culture (stronger signal) but if you have a good-size colony it works well once you get used to it.