On Wed, Feb 18, 2015 at 11:57 AM, GO <gobiowork@gmail.com> wrote:
I am lurking here for a while since I have a very tangential experience with bio. My phd is in nano but biohacking looks very interesting and promising. Anyway I was hoping that the community can help me with some questions.For example, I am confused why is gel electrophoresis so popular compared to liquid choromatography.
If you consider [silica] spin-columns as being a form of liquid chromatography (they are), then I'd wager that LC in this sense is as popular these days and possibly utilized /more/ often in day-to-day lab operations.
One constantly needs to buy agarose and visually label dna (have a UV imager) while the same column would work for a long time.
With common gel electrophoresis, you essentially get a new column each time, so you don't have to think so much about rinsing and carryover from previous experiments. You certainly /could/ continue to use a gel-electrophoresis gel and I bet you'd get a long life out of a given gel. I think you'd still need to refresh the buffer as often.
So one reason could be that schools/industry have enough $$$ to use a new gel each time, and DIYers don't run gels often enough to benefit (because maybe in the down-time the buffer/gel starts to grow something).
We can also co-pass a already known strands with some fluoro or other label that can be detected at wavelength other than 260 nm (this would serve as a ladder in electrophoresis). Also its more difficult to collect DNA later in gel compared to HPLC.
Well yeah, but the whole instrument itself is much more complex than cutting your section of gel and grabbing a spin-column or a piece of dialysis tubing... so you could think that gels are super-low entry cost, higher per-run... but for the cost you get simplicity, and it works. When a gel breaks, you just whip up a new one... if you break a column or an HPLC/LC controller, most lab-tech types won't be able to do anything. Even with imaging a gel, the common user has a few options they can try out (use a blacklight or UV spot light, use a visible gel dye, use 405nm LEDs, etc). With any kind of 'instrument' that user is stuck, especially if it's an expensive one (and they aren't in an institution with a service contract, or some 70-year old polymath who never graduated high-school but 'started with radios in the army').
Liquid chromatography can be used to detect other things as well (not just charged DNA) so it's even more useful for DIY people.What bothers me is the constant need of supply chain for doing DIYbio compared to computer revolution.
In what sense though? Computers need minerals, floppy disks and thumbdrives go bad over time, need fed electricity constantly. Things are just different.
I would love to simplify detection (at least) to have minimum of consumables possible. Any ideas?
Microfluidics is a big idea (haha, didn't intend the pun). You still need some pumps though, even for a capillary gel electrophoresis, I tried the easiest idea of cutting a microchannel and scraping liquid agarose gel over it, then slapping a microscope slide on top and it didn't work, at that scale the channel surface ('electrics') was repulsive enough such that pretty much no gel ended up in the channel.
The detector is another thing, but essentially, there are lots of things that are complex, and the integration of them is complex too. Then you have to work on cost of materials and labor to build the thing, you have to consider user-experience and making it better than whatever convoluted/expensive procedure the user is already using. And then make sure the cost is also acceptable.
Building an HPLC isn't something hard to do for a group like DIYbio, but doing it well and such that it is useful/reproducible outside the group is harder. Getting all the key players to work for months with no pay is also a factor. Plenty if not all the people on this list are willing to type messages to the world for no pay, which means they're likely to devote some time for free elsewhere... but getting everyone's schedule to line up is tough. Science and engineering is tough, tougher than code because you have to leave your keyboard, you have to think about the logic that makes up the real world, not just the logic of whatever the programming language supports. It's much wider and deeper, move nuanced.
If you have some ideas, let's hear them!
I'm up to work on microfluidic gel electrophoresis capillaries, if other folks were willing to help with choosing things like what port/connector to use on the microfluidic portion of the system and other parts of the system too.
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