This a model from the article: Synthetic in vitro transcriptional oscillators. Kim J, Winfree E Mol. Syst. Biol. 2011 Feb 1;7:465. 21283141 , Abstract: The construction of synthetic biochemical circuits from simple components illuminates how complex beha viors can arise in chemistry and builds a foundation for future biological technologies. A simplified analog of genetic regulatory networks, in vitro transcriptional circuits, provides a modular platform for the systematic construction of arbitrary circuits and requires only two essential enzymes, bacteri ophage T7 RNA polymerase and Escherichia coli ribonuclease H, to produce and degrade RNA signals. In t his study, we design and experimentally demonstrate three transcriptional oscillators in vitro. First, a negative feedback oscillator comprising two switches, regulated by excitatory and inhibitory RNA si gnals, showed up to five complete cycles. To demonstrate modularity and to explore the design space fu rther, a positive-feedback loop was added that modulates and extends the oscillatory regime. Finally, a three-switch ring oscillator was constructed and analyzed. Mathematical modeling guided the design p rocess, identified experimental conditions likely to yield oscillations, and explained the system's ro bust response to interference by short degradation products. Synthetic transcriptional oscillators cou ld prove valuable for systematic exploration of biochemical circuit design principles and for controll ing nanoscale devices and orchestrating processes within artificial cells. Note: The paper describes 7 models (MODEL1012090000-6) and all these are submitted by the authors. This model (MODEL1012090000) corresponds to the Simple model for both mode I and II (Design I and II). The model reproduces timecourse figure plotted in the supplementary material (page 10 of Supplementary material) of the reference publication. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.