article · 01/06/2015
Automated Design of Programmable Enzyme-Driven DNA Circuits
Résumé
Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.
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van Roekel, H.-W.-H., Meijer, L.-H.-H., Masroor, S., Garza, Z.-C.-F., Estevez-Torres, A., Rondelez, Y., Zagaris, A., Peletier, M.-A., Hilbers, P.-A.-J., & de Greef, T.-F.-A. (2015). Automated Design of Programmable Enzyme-Driven DNA Circuits. ACS Synth. Biol., 4(6). https://doi.org/10.1021/sb500300d@article{vanRoekel2015_86,
author = {van Roekel, Hendrik W. H. and Meijer, Lenny H. H. and Masroor, Saeed and Garza, Zandra C. Felix and Estevez-Torres, Andre and Rondelez, Yannick and Zagaris, Antonios and Peletier, Mark A. and Hilbers, Peter A. J. and de Greef, Tom F. A.},
year = {2015},
month = {6},
title = {Automated Design of Programmable Enzyme-Driven DNA Circuits},
journal = {ACS Synth. Biol.},
publisher = {AMER CHEMICAL SOC},
volume = {4},
number = {6},
address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
abstract = {Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.},
url = {http://www.dx.doi.org/10.1021/sb500300d},
doi = {10.1021/sb500300d},
issn = {2161-5063},
}TY - JOUR
AU - van Roekel, Hendrik W. H.
AU - Meijer, Lenny H. H.
AU - Masroor, Saeed
AU - Garza, Zandra C. Felix
AU - Estevez-Torres, Andre
AU - Rondelez, Yannick
AU - Zagaris, Antonios
AU - Peletier, Mark A.
AU - Hilbers, Peter A. J.
AU - de Greef, Tom F. A.
PY - 2015
DA - 2015/06/01
TI - Automated Design of Programmable Enzyme-Driven DNA Circuits
JO - ACS Synth. Biol.
VL - 4
IS - 6
PB - AMER CHEMICAL SOC
SN - 2161-5063
AB - Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.
DO - 10.1021/sb500300d
UR - http://www.dx.doi.org/10.1021/sb500300d
ER -