Nano Origami for DNA, Complete With Software

wisebabo writes "Some researchers at Technische Universitaet Muenchen and Harvard have developed a way to make DNA 'Origami' fold up into all sorts of desired nanoscale shapes. While this has been done before, there now seems to be a much greater assortment of shapes they can create. What's particularly interesting is that they've developed some software that can be used (presumably with a DNA assembler) that will create what you want; think of CAD/CAM on a molecular scale! 'The toolbox they have developed includes a graphical software program that helps to translate specific design concepts into the DNA programming required to realize them. Three-dimensional shapes are produced by "tuning" the number, arrangement, and lengths of helices.'"

Comments

Well...?

[Ketto]

I wonder if this is similar in scope to the microscopic engine they built a few years back... Really neat in concept and design, but of small practical significance...

Call me dense...

[Anachragnome]

I'm missing the application.

Is the idea to create new structures WITHIN the human body(or whatever species, plant, animal, fungus...), or externally, such as another means to create nano-scale devices, but with bio-materials as opposed to non-biological components such as carbon molecules? Both?

It does make sense, either way, as DNA can be coded to self-replicate making any manufacturing processes far easier.

And yes, I am aware that biological entities are, for the most part, made of carbon molecules, at least here on Earth.

Re:Call me dense...

[Anonymous Coward]

I'm not sure about other techniques, but these DNA nanostructures can create potentially any 3-D (and to me, deposition sounds like a 2-D process, with a very tediuous 3-D aspect). I'm fairly certain that the combination of ease of use, manufacturing, and customizability is unmatched by any other technology, but feel free to correct me.

The talk I attended by William Shih had excellent AFM pictures of various 3-d shapes, including a trojan horse(think wooden sculpture). However, he did mention that the more complicated the structure, the longer it took to "cure", or go from mixture of oligos and structural strands to the completed form.

One particular application I could see this making significant headway into would be gene therapy. Cationic liposomes are currently the most effective vectors, but they are very toxic, among other negative qualities. DNA capsules may be more effective, especially if capsules can be easily modified for different payloads.

Prone to UV light?

[modrzej]

I wonder what is a half-life of such a macromolecule. Not an expert in the field, but during my first biochemistry course I was taught that DNA is only kinetically stable (in contrast with thermodynamic stability), so there is a chance that when making its shape extremely fancy, it becomes useless ephemeral compound. There are also mutations caused by interaction with high-energetic photons (UV light) which constantly appear and are repaired in human cells, but may cause obstacles when there's no natural maintenance system as in cells. This may not be the case because mutations may occur extremely rarely in the timescale of nanomachines activity, but thats what I'm curious about.

Re:Prone to UV light?

[Vesvvi]

Most highly-ordered large biomolecules are not "thermodynamically stable", since it takes so much entropy to maintain them (which is to say that the entropy is low). Some exceptions might be nasty molecules like prions or amyloids, which tend to form extended fibers and sheets, with very negative effects.

But kinetic stability can lead to effective thermodynamic stability due to some unique effects. For example, there can be a kinetic barrier to disassembly of a large biomolecule because it's tough to remove that first subunit. Once the first subunit is gone, the "chink in the armor" allows the whole thing to begin to fall apart. But because the whole assembly is stable until the first one leaves, it has the effect of being globally stable.

But getting back to the big picture, DNA can be very stable, as evidenced by recovery of DNA more than thousands of years old. Of course it won't be retaining complex quaternary structures like those developed by the researchers. On the other hand, it's very desirable to have nanostructures with a finite lifetime, especially one that can be controlled. If it's used for drug delivery packaging, you might want it to last only a few days. If it's a template for hard materials (iron-based magnetic structures, for example), you might want to be able to cause it to fall apart intentionally within a few hours. DNA isn't really a good candidate for permanent nanomaterials, since it can be degraded both passively and actively by quite a few different pathways.

Folding@Home?

[johnthorensen]

I'm just curious, did the researchers draw upon any of the Folding@Home work for this? Seems like simulating these sorts of interactions is sort of the point. I know F@H is primarily looking at proteins but just curious if any of the knowledge crosses over. Of course, 'Folding@Home' would make a great name for the desktop rapid prototyping machine based on this work. :)

Link to caDNAno software

[structural_biologist]

The research team that produced the paper in Science paper (link (subscription required to see more than the abstract)) described in the science daily writeup also published a paper in Nature (link) that more fully describes their method of creating three dimensional objects out of DNA (the newest paper expands these methods to construct more complicated objects with more precise curvature). Furthermore, they have published the open-source software that they used to design the DNA nanostructures (http://cadnano.org/). I was at a talk by the lead author of the Nature paper who said that, using their software, a high school student was able to design one of the structures they used in the paper as a summer project.