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Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Citation

de los Santos, Emmanuel Lorenzo Cornejo (2015) Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9M61H64. http://resolver.caltech.edu/CaltechTHESIS:05182015-163708506

Abstract

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:synthetic biology; computational protein design; cell free prototyping
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Murray, Richard M. (advisor)
  • Mayo, Stephen L. (co-advisor)
Thesis Committee:
  • Tirrell, David A. (chair)
  • Elowitz, Michael B.
  • Murray, Richard M.
  • Mayo, Stephen L.
Defense Date:11 May 2015
Record Number:CaltechTHESIS:05182015-163708506
Persistent URL:http://resolver.caltech.edu/CaltechTHESIS:05182015-163708506
DOI:10.7907/Z9M61H64
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8865
Collection:CaltechTHESIS
Deposited By: Emmanuel Lorenzo De Los Santos
Deposited On:29 May 2015 20:51
Last Modified:12 Apr 2016 21:59

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