Ctrl-X, Ctrl-V For DNA

Once upon a time, the aspiring nerdling’s gift of choice was the Gilbert chemistry set. Its tiny vials of reagents, rack of test tubes, and instruction book promised endless intellectual stimulation and the possibility of stink bombs on demand. Now a new genetic engineering lab-in-a-box Kickstarter, with all the tools and materials needed to create your own transgenic organisms, may help the young biohacker’s dreams come true.

The Kickstarter has been wildly successful. The initial goal was $1200AUD was met in a day, and currently stands at almost $6200AUD. Despite that success, color me skeptical on this one. Having done way more than my fair share of gene splicing, there seem to be a few critical gaps in this kit. For example, the list of materials for the full kit includes BL21 competent E. coli as the host strain. Those cells are designed to become porous to extracellular DNA when treated with calcium chloride and provided with a heat shock of 42°C. At a minimum I’d think they’d include a thermometer so you can control the heat shock process. Plenty of other steps also need fairly precise incubations, like the digestion and ligation steps needed to get your gene into the host. And exactly what technique you’d be using to harvest DNA from the animal, plant or fungal cells is unclear; the fact that most of the techniques for doing so require special techniques leads me to believe there’s a lot less here than meets the eye.

To be fair, I’ve been off the lab bench for the better part of two decades, and the state of the art has no doubt advanced in that time. There could very well be techniques I’m not familiar with that make the various steps needed to transform a bacterial culture with foreign DNA trivial. It could also be the case that the techniques I used in the lab were optimized for yield and for precise data, while the GlowGene kit provides the materials to get a “good enough” result. I hope so, because a kit like this could really expand the horizons of hackerdom and start getting the biohacking movement going.

[Thanks, Michael!]

23 thoughts on “Ctrl-X, Ctrl-V For DNA

    1. PS. You are correct, after 2 decades, a 45-60 second heat shock is still the mainstream method of transforming bacteria. Building an electroporation device would probably be more appeal more to the maker crowd though, and give you better transfection efficiency :)

      1. I think their aim is to clone random genes from an animal cell, using ‘quick-and-easy’ DNA extracts. The DNA transformation is probably the plate transformation method, it’s about one magnitude less than the usual heat-shock method but people still use it.

        I reckon they should add more genes that you can add directly instead of waiting on stretch goals, or just adding a whole palette of genes and getting rid of the “extract your own” DNA part.

    2. Restriction cloning for us old timers is something we can do before we even open our eyes and have our morning coffee this is why it is still used today widely. It is cheap and if done properly very effective. I see though why you prefer SLiCE. Maybe something like this: http://openpcr.org/ (An Open PCR cycler) could complement it?

      1. As someone who does a ton of cloning, I can say that slice cloning is a revolution. You can ligate up to 5 fragments in a single reaction, saving weeks of subcloning. The reagent is cheap enough to be considered free, and together with geneart strings (linear synthetic DNA up to kb’s in size), life in the lab is just nicer.

        As far as the PCR thing, that was a joke. Check out my projects page on Hackaday.io

    3. Did you get the special Slice bacteria or just use DH10B extracts? I tried the DH10B extracts and didn’t get anything, and it’s been approaching a year since I sent MTAs to the authors of the paper…..

      1. I got the strain from the authors. The prep is really easy, and makes tens of millilitres. You need about 1/2 a microliter per reaction. It’s impressive, considering kits of 10 equivalent reactions from invitrogen costs hundreds of dollars, and one batch of slice reagent from a 200 ml LB culture makes a lifetime supply.

  1. Holy crap, I had no idea people were doing this kind of stuff at home. Could someone give me an example of what one would want to accomplish with this kind of hacking? Or do people simply do this for the sake of the craft/experimentation? I’m usually very practical about hacking, so I find the possibilities of this very intriguing.

    1. Making ‘ethical’ cheese : http://www.eastbayexpress.com/oakland/inside-the-ethical-cheese-lab/Content?oid=3998300
      Making glowy stuff for fun and profit,
      Just having a gas. DIYBio is one movement, or just start googling around biohacking. People are realizing that you can sacrifice some quality and convenience and get good enough results for WAY cheaper than the lucky few with multi-million dollar research labs. There are even 3D printed micro-pipettes and stuff to make getting started simple(er). I can’t wait to see where this stuff goes in 10 years.

    2. I’ve been working on lab-on-a-chip for a few years, goal is to make a DNA compiler and debugging system, that basically looks and feels like a software programming IDE. The hardest and most challenging part is the DNA synthesis step… Lots of industry around this, but not as much active or novel research. It’s a good niche if you have the patience, as the potential payoffs are enormous (social or monetary).

      Checkout the Google group : DIYbio
      And the freebies chat: ##hplusroadmap
      The latter will direct people to a wiki with problem statement and list of ideas and equipment.

  2. The aspiring nerdling’s gift of choice was the golden book of chemical experiments. Bio hacking started latest 30 years ago when I isolated Penicillin from Penicillium at my basement lab. Note to myself: Need to do a write-up about that some times…

  3. It’s true, at least cloning in molecular biology is a lot different than 20, even 15, years ago – now it’s pretty routine to order “genes” for plasmid expression digitally, just like like oligonucleotides, but upwards of 10kbases – even for smaller labs. Just type up an email, paste in your sequence and add your restriction sites. (Not to mention the whole boom with CRISPR/Cas genome editing!)

  4. Lots of non-accurate statements here; Molecular Biology is full of lore however. First of all, steps like ligation are actually not very temperature dependent at all, The ‘ole 16C overnight is demonstrably wrong; read the insert someday. Secondly, cloning from anything other than bacteria or phage is non-trivial as you can’t directly clone from DNA in virtually all cases due to splicing. The DNA is not a direct copy of the intended gene product. I haven’t read the particulars, but I doubt this kit includes RT in order to make cDNA libraries for actual animal cloning. BL21 and BL21DE3 are fine choices for a lab, but not practical for most hacker cloning. The latter requires specialized promoters for expression and both of these are designed to be used with inducible promoters, Lac/Tac/T7/ara, of which IPTG and ara are not inexpensive. Autoinduction media could be used, but this requires somewhat detailed knowledge about catabolite repression

    As others have said things like SliCE are vastly superior. For those that use it, I would recommend using FAST cloning instead. Same basic idea as slice, but in vivo. Mix the vector/insert with 15bp flank and tform into E coli. Mismatch repair will fix the intermingled DNA and you are left with your desired product in 1 step. It is particularly nice because you can just PCR up vector with the frame and opening you want, no more polylinker, and design your insert primers to have 15bp of vector overlap. The efficiency is much higher than in vitro slice and the product of slice is typically transformed anyway to amplify it.

    1. Sure, but Autoinduction media is super easy to make. its just glucose, lactose and gycerol. If you can weigh stuff reasonable accurately, you can make it.

      My PCR machine (see my Hackaday.io project page) can do the necessary PCR stuff, and making a gel-box if relatively straight forward. If you have Dpn1 and pure faith that the reaction worked, you can even skip that step.

      As far as splicing goes, I have done PCR’s that copy out the exons, and join them with Slice. At least them you can get every gene, and not have to worry about expression levels.

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