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Therapeutic Opportunities and Approaches to Sequence Control for Nucleic Acids


Gethers, Matthew Leroy, III (2018) Therapeutic Opportunities and Approaches to Sequence Control for Nucleic Acids. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/WE1E-EZ49.


RNA interference (RNAi) is a powerful mechanism to regulate gene expression. A key feature of RNAi is its sequence specificity: a short interfering RNA (siRNA) assembles into the RNA induced silencing complex (RISC) and then targets cellular transcripts complementary to the siRNA for degradation. RNAi has been adapted for therapeutic applications, but is challenged by the need to identify unique target transcripts for each disease that are both effective and result in few off-target effects. This challenge could be eased if siRNAs could be activated only and specifically in diseased cells. If this were the case, rather than targeting a new transcript for each new disease, the same cellular housekeeping genes could be reused. Targeting housekeeping genes would result in greater potency, both effectively treating the disease and requiring less drug for treatment, alleviating problems associated with toxicity and delivery. A new class of nucleic acid therapeutics called conditional siRNAs (Cond-siRNA) is designed to act in this environment-specific manner. The first part of this thesis uses molecular dynamics simulations to understand the structure of Cond-siRNA and to suggest improvements in future designs.

Bioengineering like the work done in the development of Cond-siRNAs depends on the existence of tools that make work simple, fast, cheap, and reproducible. In the case of nucleic acids, de novo synthesis of custom constructs is a fundamental tool. While approaches to synthesis have improved immensely since their inception, increasing ambition demands increasingly powerful tools. As target constructs get longer, the synthesis can become intractably complicated, slowing the process, increasing costs, and making it less likely to be replicated by others. The source of complexity in nucleic acid synthesis is the inability to directly synthesize long fragments without errors. Finding a new means of sequence-controlled synthesis that results in fewer errors and perhaps allows for correction could address this challenge. The second part of this thesis looks at using graphene as a mask for patterning the deposition of molecules on a surface with an eye towards arranging and coupling reactants in a sequence-specific way.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:RNA; DNA; RNAi; Sequence Control
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Goddard, William A., III (co-advisor)
  • Weiss, Paul S. (co-advisor)
Thesis Committee:
  • Tirrell, David A. (chair)
  • Rothemund, Paul W. K.
  • Goddard, William A., III
  • Weiss, Paul S.
Defense Date:2 April 2018
Non-Caltech Author Email:mattgethers (AT)
Record Number:CaltechTHESIS:06012018-190621868
Persistent URL:
Gethers, Matthew Leroy, III0000-0001-7455-4709
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:11009
Deposited By: Matthew Gethers
Deposited On:04 Jun 2018 19:31
Last Modified:04 Jun 2024 23:21

Thesis Files

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