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Towards Conditional RNAi : Shape and Sequence Transduction with Small Conditional RNAs


Hochrein, Lisa Marie (2013) Towards Conditional RNAi : Shape and Sequence Transduction with Small Conditional RNAs. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/NTZT-8Q67.


RNA interference (RNAi) is a powerful biological pathway allowing for sequence-specific knockdown of any gene of interest. While RNAi is a proven tool for probing gene function in biological circuits, it is limited by being constitutively ON and executes the logical operation: silence gene Y. To provide greater control over post-transcriptional gene silencing, we propose engineering a biological logic gate to implement “conditional RNAi.” Such a logic gate would silence gene Y only upon the expression of gene X, a completely unrelated gene, executing the logic: if gene X is transcribed, silence independent gene Y. Silencing of gene Y could be confined to a specific time and/or tissue by appropriately selecting gene X.

To implement the logic of conditional RNAi, we present the design and experimental validation of three nucleic acid self-assembly mechanisms which detect a sub-sequence of mRNA X and produce a Dicer substrate specific to gene Y. We introduce small conditional RNAs (scRNAs) to execute the signal transduction under isothermal conditions. scRNAs are small RNAs which change conformation, leading to both shape and sequence signal transduction, in response to hybridization to an input nucleic acid target. While all three conditional RNAi mechanisms execute the same logical operation, they explore various design alternatives for nucleic acid self-assembly pathways, including the use of duplex and monomer scRNAs, stable versus metastable reactants, multiple methods of nucleation, and 3-way and 4-way branch migration.

We demonstrate the isothermal execution of the conditional RNAi mechanisms in a test tube with recombinant Dicer. These mechanisms execute the logic: if mRNA X is detected, produce a Dicer substrate targeting independent mRNA Y. Only the final Dicer substrate, not the scRNA reactants or intermediates, is efficiently processed by Dicer. Additional work in human whole-cell extracts and a model tissue-culture system delves into both the promise and challenge of implementing conditional RNAi in vivo.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:conditional RNAi, small conditional RNA, nucleic acid engineering, hybridization cascades, nucleic acid logic gates
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemical Engineering
Minor Option:Biology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Pierce, Niles A.
Thesis Committee:
  • Tirrell, David A. (chair)
  • Pierce, Niles A.
  • Davis, Mark E.
  • Rossi, John J.
  • Burnett, John
Defense Date:31 May 2013
Record Number:CaltechTHESIS:06072013-160243112
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7873
Deposited By: Lisa Hochrein
Deposited On:19 Jan 2016 21:57
Last Modified:08 Nov 2023 00:43

Thesis Files

PDF (Final thesis for Lisa Marie Hochrein) - Final Version
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