Abstract:

Self-assembly is ubiquitous in biological systems, but remains challenging for synthetic structures. These typically form under diffusion-limited, near-equilibrium conditions.  DNA-mediated self-assembly is a powerful method with which to build multi-functional, molecularly-addressable nanostructures of arbitrary shape.  While there have been many recent developments in DNA nanostructure fabrication that have expanded the design space, fabrication based on DNA alone can suffer from low yields and is hampered by the need to strike a balance between size and mechanical rigidity. ,   Despite recent efforts,  typical assembly protocols, employing large numbers of discrete components, offer little control over the assembly pathway, limiting structure size, complexity, and yield.

We have been working to both understand the factors that limit the yield of self-assembled structures, and to devise approaches to overcome them.  In this talk, I will discuss our attempts to build a simple, but predictive model, that describes the process of forming a single fold in a DNA origami structure.  Using this model, we show that yield decreases exponentially as a function of the number of discrete components used to assemble a structure.  To circumvent this limit, we have developed a two-stage, hierarchical self-assembly process, to create large structures with high yield.   Our process employs a limited number of discrete, sequence-specific element to shape the structure at the nanoscale and control the large-scale geometry.  A generic building block – a DNA binding protein, RecA – rigidifies the structure without requiring any unnecessary information to be added to the system.

Expanding the self-assembly toolbox by blending sequence-specific and structure-specific elements, enables us to make micrometer-scale, rigid, molecularly-addressable structures.  More generally, our results indicate that the scale of finite-size self-assembling systems can be increased by minimizing the number of unique components and instead relying on generic components to construct a framework that supports the functional units.