Probing DNA-Induced Colloidal Interactions and Dynamics with Scanning-Line Optical Tweezers

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Doctor of Philosophy (PhD)
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Chemical and Biomolecular Engineering
colloidal interactions
functional particles
multivalent binding
nucleic acids
optical tweezers
Chemical Engineering
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A promising route to forming novel nanoparticle-based materials is directed self-assembly, where the interactions among multiple species of suspended particles are intentionally designed to favor the self-assembly of a specific cluster arrangement or nanostructure. DNA provides a natural tool for directed particle assembly because DNA double helix formation is chemically specific — particles with short single-stranded DNA grafted on their surfaces will be bridged together only if those strands have complementary base sequences. Moreover, the temperature-dependent stability of such DNA bridges allows the resulting attraction to be modulated from negligibly weak to effectively irreversible over a convenient range of temperatures. Surprisingly, existing models for DNA-induced particle interactions are typically in error by more than an order of magnitude, which has hindered efforts to design complex temperature, sequence and time-dependent interactions needed for the most interesting applications. Here we report the first spatially resolved measurements of DNA-induced interactions between pairs of polystyrene microspheres at binding strengths comparable to those used in self-assembly experiments. The pair-interaction energies measured with our optical tweezers instrument can be modeled quantitatively with a conceptually straightforward and numerically tractable model, boding well for their application to direct self-assembly. In addition to understanding the equilibrium interactions between DNA-labeled particles, it is also important to consider the dynamics with which they bind to and unbind from one another. Here we demonstrate for the first time that carefully designed systems of DNA-functionalized particles exhibit effectively diffusion-limited binding, suggesting that these interactions are suitable to direct efficient self-assembly. We systematically explore the transition from diffusion-limited to reaction-limited binding by decreasing the DNA labeling density, and develop a simple dynamic model that is able to reproduce some of the anomalous kinetics observed in multivalent binding processes. Specifically, we find that when compounded, static disorder in the melting rate of single DNA duplexes gives rise to highly non-exponential lifetime distributions in multivalent binding. Together, our findings motivate a nanomaterial design approach where novel functional structures can be found computationally and then reliably realized in experiment.

John C. Crocker
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