Engineering the Feedback Dynamics of in vitro Synthetic Biological Systems

Abstract

Building a biochemical system from scratch that rivals a living cell in ability to robustly perform many complex tasks in response to environmental signals is beyond the state-of-the- art. However, feedback is clearly a principle widely employed by cells — as it is by engineers — to enable robust dynamical behaviors, although a limited system-level understanding of feedback regulation and dynamical behavior in biochemical contexts hampers our ability to engineer such systems. Studying simple feedback systems in a rich, yet fully synthetic, biochemical context — like that provided by DNA nanotechnology — may therefore lead to a new state-of-the-art for synthetic biological systems. This thesis, in keeping with this philosophy, describes basic efforts in engineering bio- chemical feedback control systems in the form of simple, in vitro, nucleic-acid-based devices. I describe two such devices, which provide basic test-beds for engineering feedback dynamics in vitro. The first device is a DNA nanomotor, previously described in the literature, that is built from and operated by nucleic acid components, and that I modify by the introduction of a protein enzyme to improve the performance of the device in experimental tests. The second device I design and build from nucleic acid components and two protein enzymes to regulate the free quantity of an RNA molecule, which in turn can be used to dynamically drive the operation of other nucleic-acid-based systems — such as the first device — in a robust manner.