Doctoral Dissertations

Date of Award

5-2022

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Chemical Engineering

Major Professor

Steven M. Abel

Committee Members

Steven M. Abel, Michael L. Simpson, Manolis Doxastakis, Maxim O. Lavrentovich, Eric Boder

Abstract

The intracellular environment is crowded with macromolecules that can occupy a significant fraction of the cellular volume. This can give rise to attractive depletion interactions that impact the conformations and interactions of biopolymers, as well as their interactions with confining surfaces. We used computer simulations to study the effects of crowding on biologically-inspired models of polymers. We showed that crowding can lead to attractive interactions between two flexible ring polymers, and we further characterized the adsorption of both flexible and semiflexible polymers onto confining surfaces. These results indicate that crowding-induced depletion interactions could play a role in the spatial organization of biopolymers in cells, and they also suggest that macromolecular crowding could be used to alter the spatial organization of cell-free synthetic systems. A major limitation of cell-free expression systems, which are widely used to study gene expression, is the lack of means to achieve spatial control of gene expression components. With a coarse-grained model of DNA plasmids and crowders, we showed that plasmids were uniformly distributed at low levels of crowding but, due to depletion interactions, became strongly adsorbed to confining surfaces at high levels of crowding. These results were experimentally validated by our collaborators using DNA and crowders in cell-sized vesicles. We used kinetic Monte Carlo simulations to study the effect of crowding and confinement on gene expression dynamics and noise, giving insight into experiments. Our work provides insights into the role of crowding and confinement on the spatial organization and dynamics of gene expression in cellular and cell-free systems.

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