This Designing Materials to Revolutionize and Engineer our Future (DMREF) grant provides funding for the development of a computational tool to determine optimal design parameters for the synthesis of DNA-based materials. The developed tool will determine the optimal DNA sequences and environmental assembly conditions, including solvent and temperature, to realize pre-specified design criteria for two-dimensional and three-dimensional DNA-based nanoscale structures and materials. Physics-based computational models will be used to incorporate mechanical, electrostatic, and hybridization free energies into an overall structural-thermodynamic model of the target DNA-based assembly. This model will be used together with numerical optimization and highly parallel computation to optimize the design and synthesis process. Detailed experimentation will be used to test and validate the computational tool, including two-dimensional and three-dimensional characterization of target structural properties and assembly kinetics.
The results of this research will lead to a broadly accessible, automated design tool for the production of custom DNA-based nanostructures and materials. Optimal sequence design and assembly conditions for target DNA-based material properties will be generated using this tool, enabling its broad use in diverse nanotechnology applications. Target properties may include complex two- and three-dimensional nanoscale structural features, mechanical response, and operating temperature and solvent conditions. Determining computationally the sequence design parameters to achieve these target properties will reduce the financial cost and time required to manufacture DNA-based materials, as well as optimize the quality and uniformity of the final product. This computational tool will also enable the simulation and design of diverse functional aspects of custom DNA-based nanomaterials using complementary computational modeling approaches.
