Fully addressable, designer superstructures assembled from a single modular DNA origami

Abstract

Intricate self-organization is essential in many biological processes, underpinning vital functions and interactions. In an effort to mimic such processes, synthetic biology aims to engineer dynamic structures with controllable functions using nanotechnological tools. A key requirement of engineered building blocks is the ability to assemble and disassemble hierarchically with precision. Using the DNA origami technique, we here present the moDON, a modular DNA origami nanostructure, which is capable of assembling into almost 20 000 diverse monomers, forming complex and controlled superstructures in three dimensions. While shape and addressability of DNA origami are nearly arbitrary, its overall size is limited by the scaffold size. Previous methods of extending the size of DNA origami (e.g. hierarchical assembly, modified scaffolds, etc.), either led to loss over control of shape and addressability beyond monomers or to proportionally increased cost and design effort. With the moDON we were able to overcome both issues. The modular design combines xy- and z-plane assembly methods, enabling the construction of finite and periodic structures beyond 1 GDa. We demonstrate xy-z orthogonality, by enabling controlled selective or parallel assembly and disassembly via distinct orthogonal triggers. The kinetic profile of assembly and disassembly aligns with biological time scales, paving the way for applications in dynamic nanomachinery and advanced biomaterials. Finally, we showcase the conjugation of gold nanoparticles to specific positions within superstructures, underscoring the efficacy of this approach for creating intricate and orthogonal nanoscale architectures with preserved site-specific addressability. The moDON thus offers an efficient, cost-effective solution for constructing large, precisely organized, and fully addressable structures with vast potential in synthetic cellular systems design.