Kim2011_Oscillator_SimpleI

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.

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