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Bistability of an In Vitro Synthetic Autoregulatory Switch

Subsoontorn, Pakpoom and Kim, Jongmin and Winfree, Erik (2011) Bistability of an In Vitro Synthetic Autoregulatory Switch. California Institute of Technology , Pasadena, CA. (Submitted)

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The construction of synthetic biochemical circuits is an essential step for developing quantitative understanding of information processing in natural organisms. Here, we report construction and analysis of an in vitro circuit with positive autoregulation that consists of just four synthetic DNA strands and three enzymes, bacteriophage T7 RNA polymerase, Escherichia coli ribonuclease (RNase) H, and RNase R. The modularity of the DNA switch template allowed a rational design of a synthetic DNA switch regulated by its RNA output acting as a transcription activator. We verified that the thermodynamic and kinetic constraints dictated by the sequence design criteria were enough to experimentally achieve the intended dynamics: a transcription activator configured to regulate its own production. Although only RNase H is necessary to achieve bistability of switch states, RNase R is necessary to maintain stable RNA signal levels and to control incomplete degradation products. A simple mathematical model was used to fit ensemble parameters for the training set of experimental results and was then directly applied to predict time-courses of switch dynamics and sensitivity to parameter variations with reasonable agreement. The positive autoregulation switches can be used to provide constant input signals and store outputs of biochemical networks and are potentially useful for chemical control applications.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Kim, Jongmin0000-0002-2713-1006
Winfree, Erik0000-0002-5899-7523
Subject Keywords:Molecular Networks (q-bio.MN); Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)
Record Number:CaltechAUTHORS:20111020-092905148
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27325
Deposited By: Tony Diaz
Deposited On:09 Nov 2011 00:23
Last Modified:11 Nov 2020 21:08

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