DMREF: Computational Design of Next-generation Nanoscale DNA-based Materials

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Biological organisms utilize DNA to encode the synthesis of a remarkably diverse variety of materials ranging from photosynthetic plants to pearly substances from mollusks to silk from spiders and worms. In recent years, it has become possible to utilize DNA itself as a construction material and to turn it into a wide range of materials not readily produced from naturally evolved organisms. To this end, this research project focuses on identifying computational design rules that will accelerate the discovery of DNA-based, structured materials possessing unusual chemical, mechanical, and optical properties. The synthetic DNA materials are being designed with open pore configurations suitable for further modification with proteins, enzymes, chromophores, metallic particles, and other organic and inorganic materials. These combinations offer a next-generation platform for the creation of complex multi-scale DNA-based materials for diverse chemical, biological, mechanical, optical, and sensing applications. The predictive software tools developed in the course of the project are being made broadly accessible and open-sourced to facilitate engagement worldwide of researchers and practitioners in the custom design and synthesis of complex DNA-based materials. This research project aims to develop a generalized computational framework for the rational design of structured DNA-based materials of nearly arbitrary nanoscale geometric composition. Computational models of DNA-based self-assembly and structure are being validated experimentally in a highly iterative and integrative manner. Similar to unstructured and non-porous colloidal particles that have previously been organized rationally using DNA, structured DNA nanoparticles and single-stranded DNA tiles are being used to realize complex structured and porous 3-dimenional materials in infinite, extended lattices or finite, discrete nanoscale clusters. Utilization of purely synthetic, single-stranded tile oligos facilitates the realization of up to gigadalton-scale DNA-based materials with unique nanoscale addressability using sequence specification amenable to downstream functionalization with metallic nanoparticles, enzymes, or other functional moieties. Web-based dissemination of computational models is being done to make the results of this research project available worldwide. Software developed during the course of the project also is being made freely available, under an open source license, for further development and integration into other software packages by researchers worldwide. This broad dissemination of computational results facilitates the broader materials and nanotechnology communities to study this novel class of hierarchical DNA-based materials. For example, computational models could be used to perform in silico screens for target structural and functional properties, reducing significantly the time needed to deploy functional DNA-based materials for industrial applications.