## DNA sculptures

tensegrity sculpture in the math department of TU München by Caspar Schwabe, arranged for by Juergen Richter-Gebert; photo: Tim Hoffmann

Last friday I attended a talk, which was organized by the munich center for nanoscience. The talk was given by Tim Liedl from the Shih Laboratory.

After a short motivation about the possible commercial applications, which are mainly of pharmaceutical nature he started out describing a joint work with the center for nanoscience, Bell labs and the munich Biomolecular Systems and Bioelectronics group. In the work a DNA-switchable polyacrylamide (PAAm) hydrogel is used for controlled trapping and release of fluorescent quantum dots.

At the beginning of the experiment the researchers copolymerized two “noncomplementary Acrydite-modified oligonucleotides” seperately with acrylamide, mixed the two solutions in order to obtain a highly viscous fluid and then complemented the fluid with fluorescent colloidal semiconductor quantum dots as tracer particles. You can imagine a liquid where the quantum dots are little beaming fluorescent dust particles (a bit like in here). In particular the quantum dots are easy to track with fluorescence microscopy and fluorescence correlation spectroscopy and in fact Tim Liedl could even present a video showing the experiment. After mixing the liquid the researchers added with a pipette socalled “gelation oligonucleotides complementary to the Acrydite strands” which transformed the fluid PAAm/nanoparticle mixture into a solid gel and thus trapped the beaming particles along the path of the pipette. So the quantum dots formed a more or less sculptural beaming structure (the particles cease to diffuse) within the liquid. I.e. the addition of the gelation oligonucleotides induced crosslinking of the DNA modified polyacrylamide strands or in simple words: the gel clogs together where the gelation oligonucleotides had been inserted. This process is reversible that is the DNA crosslinker strands are equipped with an additional “toehold” section that acts as a “recognition tag” for socalled DNA release strands. When release DNA is added to the gel, it gets attached to the toeholds and removes the crosslinker strands via branch migration und thus the gel is again liquid.

The possible commercial applications for this kind of research is formulated by the researchers as

Our work demonstrates that a DNA-cross-
linked PAAm gel could be used to release nanoparticles as
potential drug-delivery vehicles in response to the presence
of trigger DNA or RNA molecules.

I am not sure but I think Tim Liedl mentioned also a report by nanomarkets
in which a market for drug delivery in the range of 100 million $(?…I am not going to pay 250$ to check that number) was envisaged. So no wonder that there are already patent plagues on DNA hydrogels by…Motorola.

After the hydrogel experiment Tim Liedl gave a little overview about DNA origami, which already gained quite some attention last but not least since the funny DNA smiley by Paul Rothemund. However the field goes back to the eighties by work of pioneers such as Nadrian C. Seeman, see e.g. this article from 1994 with Yuwen Zhang where among others a DNA- truncated octahedron was presented. See also the links on the wikipedia site. The article “Conformational flexibility facilitates self-assembly of complex DNA nanostructures” by Chuan Zhang*, Min Su†, Yu He*, Xin Zhao†, Ping-an Fang†, Alexander E. Ribbe*, Wen Jiang†, and Chengde Mao*‡ holds nice images, so does the gallery of the computersoftware company nanorex. While talking about computer software one should also mention the molecular programming project who just got a little money boost. A nice review oriented towards the material aspects can be found in the article Review Constructing novel materials with DNA (via metamodern).

Some of the above mentioned researchers by the way wrote an essay “From DNA nanotechnology to synthetic biology” however biobricks (->wikipedia link) was not mentioned.

After that Tim Liedl reported about experiments of attaching metal atoms to DNA strands, which may be important for using DNA as a conductive material. However a collegues of Tim Liedl, whose talk was right before him, so that I catched the very last minutes seemed to have covered this type of research. He actually seemed to have also used the insertion of (cadmium?) atoms in between double strands in order to control the bending of the helix, so that I suggested to use this for constructing a triple-stranded DNA, which he found would be an interesting experiment.

Tim Liedl than began to talk about very new work, where an article is soon to be published using socalled 6-helix bundles. 6-helix bundles are tubes where 6 (double-stranded? scaffolded?) DNA helices interlink. Visualize a perpendicular cut helix viewed from above as a thick dot then the six helix dots of the six helices lie in the corners of a hexagon (see also the abstract image). I actually would like to learn a bit more about 6-helix bundles, there seems to be a good article on that Six-Helix Bundles Designed from DNA, but it costs \$30.00 for 48 hours of access. In particular involved combinatorics sounds interesting, it seems to play a part in the selfassembly:

We present a designed cyclic DNA motif that consists of six DNA double helices that are connected to each other at two crossover sites. DNA double helices with 10.5 nucleotide pairs per turn facilitate the programming of DNA double crossover molecules to form hexagonally symmetric arrangements when the crossover points are separated by seven or fourteen nucleotide pairs. We demonstrate by atomic force microscopy well-formed arrays of hexagonal six-helix bundle motifs both in 1D and in 2D.

 tensegrity prism, image source

Tim Liedl and his collegues used these 6-helix bundles as “rigid sticks” and attached to their ends flexible “DNA rods/strands”, just like rubberbands onto the ends of wood sticks. So the structure looked a bit like a Nunchaku. If you then connect sequences of these DNA Nunchakus and put the rubber DNA strands under tension (by “clamping” them with again “thick” DNA pieces) then you get something which was defined by Buckminster Fuller as a “tensegrity” structure and which was pioneered by the artists Kenneth Snelson and given the Wikipedia article about tensegrity as it seems also Karl Ioganson. I would like to mention at this place also the sculptures of Naum Gabo (examples: 1, 2, 3).

Architectural tensegrity structures can be seen as part of architectural thin shell strucures, in particular the works of Shukhov seem to be of a similar kind. You can find examples of thin shell structures also in an already mentioned book.

So the major aspect of the new work was that Tim Liedl and collegues could built not only a DNA version of a spanned cross, but also of -what I think was- the above prism. At least thats how the DNA images looked like. So may be they are not so far from building this scary looking Caspar Schwabe-sculpture of the math building:

update Aug. 11, 2009: More about DNA origami in an article in technology review.
update Nov. 01, 2016: An article about the role of 3D structures in the genome in Quanta magazine: Genetic Architects Untwist DNA’s Turns

### 2 Responses to “DNA sculptures”

1. Bibi Says:

I like the scientific style of that blog post. I had said this earlier – as a physicist you could do way more posts dealing with concrete physics, for example high energy physics is a hot topic. Why don’t you want to discuss things like Kaon decay – this might draw in more audience?

Bibi said:

I like the scientific style of that blog post. I had said this earlier – as a physicist you could do way more posts dealing with concrete physics, for example high energy physics is a hot topic. Why don’t you want to discuss things like Kaon decay – this might draw in more audience?

I had blogged about high energy physics. However there are rather few posts about some “allegedly awesome stunning” parts like for example kaon oscillation (for more on awe see what I interpreted as a kind of satire by Jason Silva which was achieved by overdoing the usual awestriking-off-the-wall-sunset-robot-AIapopeia), but there are rather more posts about the “ugly” byparts of high energy physics, like about aspects of what happens and what could happen with high energy physics (here nuclear fission in a commercial context). A summary of nuclear energy on randform can be found here. At this place and time I also would like to commemorate the atomic bombings of Hiroshima and Nagasaki.

Moreover I am not necessarily interested in drawing in more audience. This blog here has already some audience. The readership stayed somewhat constant (over quite some years) as a absolute number. And with respect to the blogpost frequency the number of visitors is still steadily growing. More audience would currently mean too much more work and costs. And it may be the case that a bigger audience can only be reached by changing the content and style of this blog too much in some undesired way. In some sense it is important that we may say on this blog some of what we think we want to say publicly while somewhat knowing that at least some people seem to be reading some of it. I guess this is more than one can ask for. Especially for the environmental posts this means at least that I can’t be really told: “why haven’t you told people?”.

Regarding the Kaon decay you can find something at wikipedia and there are probably a couple of physics blogs out there who may blog about it.
During my physics study we had to learn a big part of the particle zoo by heart and we learned about some experimental aspects of high energy physics but this was long time ago. So I would need to (re)learn quite some bit before feeling to blog about modern high energy physics. Moreover unfortunately it is not even the case that the theoretical framework of the particle zoo, namely the standard model was badly treated during my studies but – the standart model was completely left out.

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