Forward engineering of synthetic bio-logical AND gates

Kavita Iyer Ramalingam; Jonathan R. Tomshine; Jennifer A. Maynard; Yiannis N. Kaznessis

doi:10.1016/j.bej.2009.06.014

Forward engineering of synthetic bio-logical AND gates

Kavita Iyer Ramalingam, Jonathan R. Tomshine, Jennifer A. Maynard, Yiannis N. Kaznessis

Chemical Engineering and Materials Science

Research output: Contribution to journal › Article › peer-review

51 Scopus citations

Abstract

The field of synthetic biology has produced genetic circuits capable of emulating functional paradigms seen in digital electronic circuits. Examples are bistable switches, oscillators, and logic gates. The present work combines detailed mechanistic-kinetic models and stochastic simulation techniques as well as the techniques of in vivo molecular biology to study the potential of a synthetic, single promoter AND gate. This device is composed of elements of the tet, lac, and λ-phage promoters and is responsive to the commonly used inducers IPTG and aTc, producing GFP as an output signal. The quantitative behavior of the AND gate phenotype is studied both in numero and in vivo as a function of promoter topology. The model is constructed from kinetic data obtained from the literature and yields clearly defined ON/OFF logical behavior at realistic inducer concentrations. These behaviors are matched with observed in vivo data obtained through fluorescence-activated cell sorting. The effect of incomplete repression by weaker LacI repressor is also investigated and quantified. The simulation results, coupled with in vivo data, not only identify important design degrees of freedom, but also provide parameters that can be used to guide future synthetic designs using these common regulatory elements.

Original language	English (US)
Pages (from-to)	38-47
Number of pages	10
Journal	Biochemical Engineering Journal
Volume	47
Issue number	1-3
DOIs	https://doi.org/10.1016/j.bej.2009.06.014
State	Published - Dec 1 2009

Bibliographical note

Funding Information:
This work was supported by a grant from the National Science Foundation (BES-0425882, CBET-0425882 and CBET-0644792) and the University of Minnesota Biotechnology Institute. Computational support from the Minnesota Supercomputing Institute (MSI) is gratefully acknowledged. This work was also supported by the National Computational Science Alliance under TG-MCA04N033. In addition, we would like to thank Jin Cui Tomshine for her preparation of the schematic diagrams in Fig. 1 .

Keywords

Biocomputing
Computer-aided design
Gene regulatory networks
Logical AND gate
Multiscale models
Stochastic simulations
Synthetic biology

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10.1016/j.bej.2009.06.014

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title = "Forward engineering of synthetic bio-logical AND gates",

abstract = "The field of synthetic biology has produced genetic circuits capable of emulating functional paradigms seen in digital electronic circuits. Examples are bistable switches, oscillators, and logic gates. The present work combines detailed mechanistic-kinetic models and stochastic simulation techniques as well as the techniques of in vivo molecular biology to study the potential of a synthetic, single promoter AND gate. This device is composed of elements of the tet, lac, and λ-phage promoters and is responsive to the commonly used inducers IPTG and aTc, producing GFP as an output signal. The quantitative behavior of the AND gate phenotype is studied both in numero and in vivo as a function of promoter topology. The model is constructed from kinetic data obtained from the literature and yields clearly defined ON/OFF logical behavior at realistic inducer concentrations. These behaviors are matched with observed in vivo data obtained through fluorescence-activated cell sorting. The effect of incomplete repression by weaker LacI repressor is also investigated and quantified. The simulation results, coupled with in vivo data, not only identify important design degrees of freedom, but also provide parameters that can be used to guide future synthetic designs using these common regulatory elements.",

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note = "Funding Information: This work was supported by a grant from the National Science Foundation (BES-0425882, CBET-0425882 and CBET-0644792) and the University of Minnesota Biotechnology Institute. Computational support from the Minnesota Supercomputing Institute (MSI) is gratefully acknowledged. This work was also supported by the National Computational Science Alliance under TG-MCA04N033. In addition, we would like to thank Jin Cui Tomshine for her preparation of the schematic diagrams in Fig. 1 . ",

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Forward engineering of synthetic bio-logical AND gates

Abstract

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