Chapter 5. DIYbio Around the World, Part II

Noah Most

Until August 2014, I will be traveling the globe visiting people within the DIYbio community and playing around with biology. In October, I finished up what was a grand introduction to DIYbio in Victoria, Canada, at the Victoria Makerspace. Among many amazing experiences, I worked on a project to explore the feasibility of DNA origami for DIYbio.

DIY DNA Origami: Wrapping Up from Last Issue[1]

Paul Rothemund dropped a gauntlet in his 2008 TED talk, describing his new method in the field of DNA nanotechnology as "so easy you could do it at home in your kitchen and design the stuff on a laptop." That method is called DNA origami, and it enables you to treat DNA as a nanoscale construction material. For example, researchers have used this technique to create nanorobots for the delivery of drugs[2] as well as programmable nano-breadboards.[3] A long, single-stranded DNA "scaffold," typically the M13mp18 bacteriophage, is folded upon itself and pinched into the desired shape by oligonucleotide "staples" that are easily designed on the computer.[4] To our knowledge, no one has taken Rothemund up on the kitchen biology challenge and actually attempted DIY DNA origami. Last issue, I examined whether this could be a reasonable DIYbio project, and in this issue, I can happily report an answer: yes! We successfully synthesized a proof-of-concept design, a simple 2D light bulb, and imaged it with an atomic force microscope (AFM). In tandem, we produced a crash course in DNA origami that made it so conceptually accessible that even a 12-year-old understood it.

However, that "yes" should be qualified by a discussion of some of the difficulties we encountered while imaging our nanostructure. Although the design and synthesis of DNA origami structures is relatively straightforward, imaging takes some patience and adds further cost. Microscope time will typically cost you per hour. AFM probes cost around $30 each and typically come in packs of no fewer than 10, which is more than should be needed for a single design. (For a review of other major costs, see my article in the fall 2013 issue of BioCoder.[5]) The tip of a new probe can be destroyed in an instant if it is mishandled or dropped. More perplexingly, it took several sittings for us to produce decent AFM images without procedural changes clearly accounting for the difference in image quality. However, some of these problems may stem from using AFM probes with fewer floppy tips than is typical for the method. Finally, documentation of imaging protocol in the literature is often too brief to be useful to a newcomer. As a result, we somewhat blindly tried to figure out everything on our own, before finally, in a magical moment, we saw our tiny light bulb, less than 1,000th the width of a human hair.

These obstacles should not be prohibitive, and most can be avoided. To avoid them, we recommend that you contact us or convince a nearby professional DNA origami lab to let you observe its imaging protocol. While DNA origami remains more expensive than the typical DIY activity, the field oozes excitement because it is almost the Wild West—fresh, unexplored territory. Only a fraction of its potential applications have even been imagined, so give it a try!

[1] Most, Noah. "DIYbio Around the World," BioCoder, fall 2013.

[2] Douglas, Shawn M., Ido Bachelet, and George M. Church. “A Logic-gated Nanorobot for Targeted Transport of Molecular Payloads,” Science 335.6070, 2012, 831–834.

[3] Maune, Hareem T. et al. "Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates," Nature Nanotechnology, 5(1), 2009, 61–66.

[4] Rothemund, Paul W. K. “Folding DNA to create nanoscale shapes and patterns,” Nature, 440(7082), 2006, 297–302.

[5] Most, Noah. "DIYbio Around the World," BioCoder, fall 2013.