Rational design of self-assembled, three-dimensional DNA crystals

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NONTECHNICAL SUMMARYNature uses self-assembly in order to organize multiple nonliving components into living systems. Information-coding polymers such as DNA, RNA, and proteins have been used as ideal building blocks in the assembly of designer nano-architectures, with the goal of engineering biomimetic and bioinspired materials and devices. DNA based nanotechnology exploits the programmability of DNA molecules to accurately position functional molecules for applications including directed material assembly, structural biology, biocatalysis, artificial photosynthesis, molecular computing, nanorobotics, disease diagnosis, and drug delivery. An important goal of DNA nanotechnology is to rationally design, construct, and characterize self-assembling 3D DNA lattices as hosts to organize other guest molecules with atomic precision. This project aims to reveal the scientific principles and rules for designing novel DNA crystals with prescribed geometries, and with defined cavity and channel sizes. It will also elucidate the pathway for 3D crystal assembly and create a computational model that can be used broadly to design novel, user-specified crystals. These crystals are especially well suited for hosting other species (like proteins, small molecules, or nanoparticles) in a repeating lattice, for applications that include structural determination, purification, delivery, or materials with novel optical or catalytic properties. In this way, this project will enable both fundamental discoveries on self-assembly, and help address practical applications that rely on arranging other materials in 3D with high precision. The project will have significant societal and educational impact by developing an online curriculum for K-12 education and virtual lab research. This program will engage undergraduate, graduate, and underrepresented minority students to gain knowledge and pursue research in the science, technology, engineering, and math (STEM) fields, and help develop a new paradigm for online and distance education in nanotechnology.TECHNICAL SUMMARYThe goal of this project is to determine the design rules for self-assembled, 3D DNA crystals in order to engineer porous, addressable scaffolds with well-defined cavities at the nanometer scale. The molecular control and tunable symmetries attainable with these materials will enable the arrangement of guest species, such as proteins, small molecules, or nanoparticles with atomic resolution. This project will systematically probe and test the parameters that affect rationally designed DNA crystals, including DNA Holliday junction sequence, duplex and sticky end length and sequence, and experimental assembly pathway. The structures of the resulting crystals will be solved by X-ray crystallography to determine their symmetry, and the size of their channels and cavity size. The pathway of self-assembly (e.g. nucleation-growth vs. hierarchical nanostructure assembly) will also be probed experimentally and used to inform a computational model of crystal self-assembly for predictive simulation of novel crystal designs. The effect of sequence in DNA duplexes and junctions will be modeled, as well as the multi-scale assembly of the crystals. Fully atomistic simulations will be used to parameterize coarse-grained models to probe the kinetic assembly pathway and symmetry of the crystals, and the model predictions will help optimize sequences for the lattice assembly. Finally, the above results will be used to design crystals with very large cavities (~40 nm) in order to accommodate guest species such as nanoparticles or mid-sized proteins. DNA-binding proteins (and fusions thereof) will be immobilized in these void spaces to create functional materials with a regular presentation of the guests in 3D space. Taken together, the work will provide: (1) a better scientific understanding of DNA crystal design; (2) a toolkit for understanding DNA structural parameters for the nanotechnology community at large; and (3) a library of 3D lattices with tunable symmetries and cavity sizes for the 3D arrangement of guest species.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.