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Engineering Ligand Control of RNA Interference


Beisel, Chase Lawrence (2009) Engineering Ligand Control of RNA Interference. Dissertation (Ph.D.), California Institute of Technology.


RNA is a rich and versatile substrate for the construction of information processing devices. These devices detect the levels of specified intracellular biomolecules and control cellular behavior accordingly. With few superficial constraints on the identity of the recognized biomolecule or the targeted gene, RNA-based information processing devices can be rapidly implemented toward various applications in medicine and biotechnology. To advance the design and implementation of RNA-based information processing devices, we delineated general design principles and applied these principles to the construction of devices that operate through RNA interference (RNAi).

RNAi represents an endogenous enzymatic pathway present in humans and other eukaryotes that mediates targeted gene silencing. The pathway has garnered recent interest as a revolutionary biological research tool and as a targeted therapeutic strategy. While RNAi has left an indelible mark on the scientific community, exerting greater control would advance the applicability and safety of this already impressive gene silencing mechanism. Toward this goal, we engineered ligand control of three types of RNAi effectors in mammalian cells: small interfering (si)RNAs, small hairpin (sh)RNAs, and microRNAs (miRNAs). Engineering frameworks enabled facile replacement of the biomolecule sensory and gene targeting domains, thus lending to rapid implementation as biosensors or autonomous control devices. Experimental and computational characterization studies provided a comprehensive understanding of device behavior, thereby facilitating forward design.

Naturally-occurring analogs of RNA-based information processing devices are riboswitches. Riboswitches predominantly mediate dynamic feedback in metabolism and share many traits with current examples of engineered information processing devices. Various experimental characterization studies of riboswitches showed that kinetics underlying events such as conformational switching and ligand binding have a substantial impact on device performance, although these factors remain to be comprehensively evaluated or considered when formulating design principles for synthetic riboswitch construction. We explored the contribution of kinetic factors to riboswitch performance in silico, where model predictions matched experimental observations, including results from our ligand-responsive RNAi effectors. From our modeling results, we developed a general set of design principles that guide riboswitch assembly and performance tuning.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:sequence-to-function relationship; RNA interference; RNA; riboswitch; aptamer; folding dynamics; gene regulation; nucleic acid engineering; rational design
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemical Engineering
Minor Option:Biology
Awards:Constantin G. Economou Memorial Prize, 2006
Thesis Availability:Mixed availability, specified at file level
Research Advisor(s):
  • Smolke, Christina D.
Thesis Committee:
  • Smolke, Christina D. (chair)
  • Asthagiri, Anand R.
  • Davis, Mark E.
  • Pierce, Niles A.
Defense Date:14 May 2009
Non-Caltech Author Email:cbeisel (AT)
Record Number:CaltechETD:etd-05212009-144705
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5264
Deposited By: Chase Lawrence Beisel
Deposited On:01 Nov 2010 20:55
Last Modified:15 Mar 2017 22:01

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