A Systematic Method for Designing DNA Nanostructure Assembly Processes

Abstract

Inspired by the complexity and diversity of biological structures that self-assemble in vivo, a fundamental goal of bionanotechnology is to self-assemble biomolecular complexes with defined architecture from a set of starting components. To design such structures, many standard methods involve constructing components that strongly bind to their neighbors through orientation-specific interactions. While these design methods ensure the target structure is favored thermodynamically, in practice the yields of the resulting assembly processes vary widely and do not conform to equilibrium predictions.To investigate why yields might be limited, we have developed a simple model of biomolecular complex self-assembly using reported rate constants and thermodynamic parameters typical for biomolecular components. Such a coarse-grained model is particularly useful in cases where we consider the assembly of engineered components and purposely design the process to include simple interactions. With these kinetic simulations, we show that even though complexes are small and equilibrium is well defined, rarely is thermodynamic equilibrium achieved over timescales commensurate with experiments. We find that rates of complex nucleation and component rearrangement together determine assembly yields.Our goal is to use this model in conjunction with experimental information to build a computer-guided, scalable design process for DNA origami components. We have used fluorescence-quenching assays to measure origami-origami reaction rates and equilibrium constants that are driven by specific Watson-Crick complementary (i.e., “sticky end”) interactions. A feedback loop between experimental measurements of a self-assembly process and a coarse-grained, computationally tractable model can guide the design of the assembly process by making it possible to focus our assembly efforts on specific interactions that make a strong difference in yields, or to redesign the process to include qualitatively new types of component interactions.