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Design, modeling and synthesis of an in vitro transcription rate regulatory circuit

Franco, Elisa and Forsberg, Per-Ola and Murray, Richard M. (2008) Design, modeling and synthesis of an in vitro transcription rate regulatory circuit. In: American Control Conference, 2008. IEEE , Piscataway, NJ, pp. 2786-2791. ISBN 978-1-4244-2078-0. https://resolver.caltech.edu/CaltechAUTHORS:20100512-105503658

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Abstract

This paper describes the design, modeling and realization of a synthetic in vitro circuit that aims at regulating the rate of mRNA transcription. Two DNA templates are designed to interact through their transcripts, creating negative feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis-Menten kinetics involving all the present chemical species. The DNA strands were accordingly designed, following thermodynamics principles and minimizing unwanted interactions. Preliminary experimental results show that the circuit is performing the expected task, by matching at steady state the transcription rates of the two DNA templates.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1109/ACC.2008.4586915DOIArticle
ORCID:
AuthorORCID
Franco, Elisa0000-0003-1103-2668
Murray, Richard M.0000-0002-5785-7481
Additional Information:© 2008 IEEE. Issue Date: 11-13 June 2008; Date of Current Version: 05 August 2008. Research supported in part by the Institute for Collaborative Biotechnologies through grant DAAD19-03-D-0004 from the U.S. Army Research Office. All the experiments presented in this paper were done in Erik Winfree’s laboratory. The authors would like to thank Erik Winfree, Jongmin Kim and all the members of the DNA group at Caltech for their helpful advise during the development of this project.
Funders:
Funding AgencyGrant Number
Army Research Office (ARO)DAAD19-03-D-0004
Subject Keywords:DNA; biochemistry; biomolecular electronics; biothermics; circuit feedback; differential equations; molecular biophysics; network synthesis; reaction kinetics theory; thermodynamics
DOI:10.1109/ACC.2008.4586915
Record Number:CaltechAUTHORS:20100512-105503658
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20100512-105503658
Official Citation:Franco, E.; Forsberg, P.-O.; Murray, R.M.; , "Design, modeling and synthesis of an in vitro transcription rate regulatory circuit," American Control Conference, 2008 , vol., no., pp.2786-2791, 11-13 June 2008 doi: 10.1109/ACC.2008.4586915 URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4586915&isnumber=4586444
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:18251
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:24 Jun 2010 18:51
Last Modified:08 Nov 2021 23:42

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