Abstract
Self-assembly of nanoscale building blocks with programmable geometries and interactions offers a powerful route to engineer materials that mimic the complexity of biological structures. DNA origami provides an exceptional platform for this purpose, enabling precise control over subunit shape, binding angles, and interaction specificity. In this dissertation, a modular DNA origami design strategy is developed to address the challenge of assembling geometrically complex nanostructures, including architectures with nonuniform curvature. The approach employs a common core structure that fully preserves scaffold routing across designs and reuses more than 70% of staple strands, substantially reducing redesign effort, cost, and fabrication time. Independent programming of subunit interactions and binding angles is achieved through tunable overhang lengths and sequences. Using cryogenic electron microscopy, agarose gel electrophoresis, and coarse-grained simulations, robust design rules are established and applied to the assembly of diverse self-limiting structures, including anisotropic shells, a T=13 icosahedral shell, and a toroid with globally varying curvature.
To quantitatively characterize these reversible assemblies, an actively regulated-temperature agarose gel electrophoresis platform (ARTGEL) is also developed. By independently controlling thermal and electrical conditions during long-duration experiments, ARTGEL enables electrophoresis without suppressing reaction and permits direct extraction of in-gel kinetic and thermodynamic parameters. Together, these results establish a framework that combines modular nanoscale design with quantitative measurement, advancing predictive fabrication of complex self-assembled materials.