DMREF: Self Assembly with DNA-Labeled Colloidal Particles and DNA Nanostructures

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NON-TECHNICAL SUMMARYCreating materials and devices that can assemble themselves has long been a holy grail in materials science, since it would introduce qualitatively new ways of making nano-scale structures and materials. The field of DNA nanotechnology has exploded with striking advances in creating robust and dynamic materials made entirely out of DNA, but the uses of DNA as a material on its own are much more limited than if it could be combined with other materials. A potentially vast synergy lies in the combination of colloidal assembly and DNA nanotechnology. Instead of mediating the interactions between particles by using DNA linkers (the current state of the art), one could control these interactions using more complex and potentially dynamic DNA nanostructures in solution. This project seeks to develop a fundamental understanding of how (dynamic) DNA nanostructures can control and program colloidal self-assembly. By putting this concept on a strong fundamental footing, it will be possible to exploit it to maximum effect through the design of DNA reaction networks that solve essential challenges to making colloidal self-assembly a practical materials fabrication platform. The set of possible interactions between building blocks is so large that this design space can only be systematically explored with a combined attack from theory, numerical simulation, and experiment. The project aims both to discover the fundamental principles underlying DNA particle-nanostructure interactions and to create new materials from plasmonic molecules to metafluids with immediate technological impact. The project will also involve Harvard undergraduates in a design curriculum for inner city middle schools, in a summer software development project through Harvard's Institute for Applied Computational Science, and in teams that participate in the International Genetically Engineered Machines competition.TECHNICAL SUMMARYThe investigators will work to understand and harness the different ways of making novel periodic and aperiodic colloidal structures out of particles and DNA nanostructures. Several types of DNA nanostructures can be used to control colloidal self-assembly. The simplest type of mediating DNA nanostructure involves single strands of DNA (ssDNA) in solution. Preliminary experiments show that free DNA strands give an unprecedented level of control over assembly and melting through strand displacement reactions. The investigators will also develop mediating DNA nanostructures that give an effective valence to inter-particle interactions, even when the particles are uniformly coated with ssDNA. Valence creates many new directions for robust self-assembly, from building large structures to designing structures that form spontaneously in a bath at finite concentration. Finally, they will investigate how DNA hairpins can lead to non-equilibrium interactions. This opens up new vistas for theory and experiments, including the design of self-replicating colloidal clusters and the development of kinetic proofreading schemes for significantly increasing the fidelity of the interactions over the equilibrium limit. For each type of DNA-mediated interaction, the team will use theory and simulation--which in some cases requires developing new methods--to enumerate the possibilities of what can be assembled. These will be used in conjunction with experiment to realize the assemblies described in the simulations, and these experiments will inform refinements of theory and simulations. Ultimately, they will arrive at a holistic view of what can be assembled with each mediating nanostructure.