Comment by anateus | Hacker News Reader

Comment by anateus | Hacker News Reader

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I'll summarize how this would be used for those new to biotech:

- You buy some primers which are basically chunks of nucleic acid that match whatever gene you want to look at.

- You put DNA you've extracted together with these primers into the PCR machine. This makes lots of copies of the gene you're interested in.

- Then you put the resultant amplified DNA into an electrophoresis gel box (such as the one sold by http://www.pearlbiotech.com/ who also provide free plans. This is also run by Tito Jankowski of the OpenPCR project) which lets you look at the actual genotype (you compare the striations from your sample against other samples or a reference).

Primers are cheap and easy to get hold of and as other comments mentioned there are various software tools for letting you design them (you then place an order with a company like Invitrogen).

Edited to add:

The reason you need to amplify stuff is because biology is annoying like that. Let's use a simile:

If particle physics is figuring out how a watch works by smashing it against a wall and studying the debris

Then biotech is throwing gears and springs into a test tube and carefully stirring at certain temperatures until you can hear ticking.

I think it's also useful to note _just_ how versatile a PCR machine is in biotech. If every EE hacker needs an oscilloscope, every bioengineer hacker needs a PCR machine. PCR is good for much more than just amplification -- a huge number of variations on the basic technique have surfaced in the past few years, here are just a few:

- Need to synthesize a new gene or genetic circuit? Take a bunch of DNA fragments, design overlapping fragments which serve as the "glue", and use PCR to sew the whole thing together

- Want to know if your bacteria is the right strain? Microwave a colony and toss it into the PCR machine with some probes to check. Same thing if you want to test yourself for common disease risk factors such as the BRCA1 gene.

- Want to know the expression of protein A compared to protein B? Use Q-PCR to get quantitative data on the difference.

- Made a mistake in your latest gene synthesis order? Use PCR to change base-pairs or even edit out regions of DNA to fix the problem region. Conversely, if you want to _introduce_ mutations / randomize segments of DNA, PCR can do that too!

There are many more uses of the general technique including next-gen sequencing and DNA origami that are just too numerous to list. PCR is like the IDE of biology, containing an editor, a compiler, and a debugger all in one!

Really, my only complaint is that a PCR run takes an hour or more to run depending on the complexity.

That's a good summary.

To put it another way, this is really just a box that does programmed temperature cycling. This is a critical part of PCR, but there's nothing too terribly high-tech here. PCR is a relatively simple process.

PCR is frustrating for the undergrad? Sometimes. Historically dependent on overpriced equipment? Absolutely. Dependent on small temperature variations? You bet. Complex overall? No.

Yup. Highschool / Undergraduate labs that teach PCR with two water baths and a stopwatch really kill a lot of the "magic" bestowed on these absurdly expensive machines.

Is it possible to do projects like glowing bacteria and stuff like that with this kit ? (if that sounded like a noob question, that's because I'm one :) )

Not usually. The way that generally works is this:

- You get some competent cells ("competent" means "able to accept external DNA" there are different ways you can make different cells competent) - You place plasmids (circular DNA strands) containing the trait you're interested in imparting (e.g. glowing) unto the bacteria - Under favorable conditions the bacteria will take on the genetic information contained in the plasmids

You can order plasmid vectors much like primers, though iirc it's a bit more complicated--may be wrong about that.

Caveat: As Cixelyn mentions there are actually protocols for constructing DNA using PCR and and thus there are also protocols for constructing plasmids using PCR. So yes, you could technically use an OpenPCR machine to construct a plasmid vector which you then introduce to competent cells.

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