Structure-Based Design, Synthesis, and Characterization of Custom DNA Nanoparticles

A top-down computational design framework is presented to program synthetic DNA to self-assemble into a diverse array of 3D particles of prescribed symmetry and size on the 10 to 100 nanometer scale. Single-stranded DNA serves as a scaffold to span each arm of the particle, which consists of two parallel duplexes joined by at least one anti-parallel crossover to ensure structural rigidity. This design approach allows for high structural fidelity and quantitative synthetic yield. Minimal top-down, geometry-based sequence design, which uses input target nanoparticle size and shape to generate automatically optimal oligonucleotide sequences for structural synthesis, is explored together with folding characterization and thermodynamic modeling to optimize particle yield and stability. Experimental characterization of self-assembled structures using gel electrophoresis, atomic force microscopy, and cryo-electron microscopy indicate high folding yields and high structural fidelity of target particles folded in diverse media that include magnesium-free and cellular buffers.