Lithography has given us the ability to take an exact spatial arrangement of circuits, etc., and produce a result that exactly fits that specification. Likewise, scaffolded DNA-origami has allowed the production of beautiful nanoscale shapes to order: smiling faces, Trojan horses, maps of the Western hemisphere and even giant "buckeyballs". But what do you do if what you know what the thing you want to make should do -- maybe act as a wire between two devices -- but not exactly the size and shape it needs to be to do that? In biology, the specification for complex objects is often imprecise. Structures can either be somewhat random, or more interestingly, details of the environment where the organism grows determine exact feature shapes. Trees, for example, grow branches towards light.
We are working to understand how we can program environmentally adaptive self-assembly processes with DNA nanotubes. For example, we have devised a method by which DNA nanotubes might form interconnections. Many of our processes rely on controlled nucleation and growth of DNA nanotubes, an animation of which is shown above.
Chemical patterns can act as blueprints in biology, directing the growth of organisms. For instance, striped patterns of mRNA in the fruit fly embryo determine which cells develop into the head, the abdomen, the thorax, etc.
We have developed designs for synthetic DNA-computing circuits that generate chemical patterns in vitro. These circuits can be programmed to generate a wide variety of patterns, including a stick figure, a flag, cellular automata, and a "hello world" video display. An example simulation of the stick figure generation is shown to the right.
The image to the right (from this paper) shows a set of tile assemblies nucleated from DNA origami structures. Each assembly is made from the same tile components, but the structure of the nucleus determines what pattern assembles. These structures can grow to be several microns long.
The conventional wisdom is that to effectively self-assemble a structure, the interactions between components need to be as close to equilibrium as possible. This allows the components to interact reversible many times, and eventually allows the system to converge to a configuration that looks like the equilibrium configuration.
This picture doesn't hold up well under simulation however. In a simple model of self-assembly, we recently found that even very close equilibrium, the patterns of the assembled products tend to be very different than the equilibrium patterns. Even more surprisingly, for a given set of conditions, the same pattern could either be produced at equilibrium with one set of component concentrations and affinities, or arbitrarily far from equilibrium by varying the component concentrations and affinities for one another.
What is a minimal life form like? In the 1990's a panel gathered by NASA concluded that the essential attribute of life was the ability to undergo self-sustained replication and evolution. Erik Winfree and I have postulated that DNA tile crystals could be used to make a very simple experimental system satisfying this criterion.
The basic ideas come from the work of A. Graham Cairns-Smith, who thought that crystals could carry information in their arrangements of monomer types and/or defects in such a way that the information was propagated during crystal growth. If physical forces in the environment (such as those in non-uniform flows) broke a crystal into pieces, each piece could then grow and propagate the same information, thereby replicating it.
We recently experimentally demonstrated the replication of DNA tile crystals bearing particular sequences. We used the system of templated crystal growth to produce elongational fluid flows to stimulate their breakage into pieces.