(3k) Characterization and Control of Functional Nucleic Acid System

The programmable chemistry of nucleic acid base pairing has led to the development of entire new fields of scientific inquiry collectively known as DNA nanotechnology. From little more than knowledge of the canonical Watson-Crick base pairs and an appreciation for the topology of the double-helix, researchers have been able to create nearly arbitrary nanometer scale two- and three-dimensional shapes, biological circuits capable of logical computation, and autonomous machines composed of several hundred molecules and operating at the nanometer length scale. More recently, these technologies have been playing an expanded role as both sensing and regulatory elements capable of  directly interacting with biological substrates.

As a specific example, in our lab we developed the hybridization chain reaction (HCR). Employed as programmable in situ amplifiers, HCR enables simultaneous mapping of multiple target mRNAs within intact vertebrate embryos. Employed as programmable mechanical transducers, HCR enables selective killing of cultured human cancer cells containing targeted cancer mutations. At the core of these efforts has been the use of a combined theoretical and experimental approach to elucidate and improve the properties of HCR systems. By successive iteration between theoretical postulation, experimental observation, and model refinement we have been able to develop a theoretical framework sophisticated enough to re-engineer equilibrium and kinetic properties of the assembly mechanisms.

Future progress will require that we continue to develop accurate models, but the staggering complexity of phenomena in biology necessarily makes a full theoretical description impossible. Our efforts to develop accurate models, abstractions, and simulation methods will not succeed if we look only for experimental validation. Experimental observation must accompany the theoretical efforts at every step, allowing us to inform and refine these models. It is this iteration between approaches that will offer us the most opportunity for success and which is at the core of my proposed research program.