Engineering cooperativity for the control of biomolecular self-assembly

Abstract

How does the complexity of biology reliably emerge from the interactions of individual molecules? This dissertation takes a deeper look at one of the mechanisms involved in ensuring the robustness of biomolecular self-assembly processes: the use of cooperativity to generate entropic barriers against the formation of undesired assemblies. We develop a scalable method of engineering such cooperativity called crisscross polymerization to build micron-scale structures with nano-scale precision purely out of DNA. We then apply these same principles to create an enzyme-free isothermal exponential amplification strategy based on the self-replication of crisscross ribbon fragments. We also develop a rule-based modelling framework to simulate complex molecular behaviors like crisscross assembly, and examine the validity of such a modelling approach through the study of DNA-droplet nucleation. This work ultimately expands our molecular toolkit for enabling applications such as ultrasensitive diagnostics and nanofabrication.