title: A self-regulating biomolecular comparator for processing oscillatory signals.
abstract: While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different in vitro and in vivo biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of in vitro transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream.
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Deepak K
authors.initials: DK
authors.lastname: Agrawal
authors.affiliation: Department of Mechanical Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA.
authors.forename: Elisa
authors.initials: E
authors.lastname: Franco
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA rschulm3@jhu.edu.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Schulman
mesh_terms: D000818:Animals; D002453:Cell Cycle; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D004581:Electronics; D020868:Gene Silencing; D006801:Humans; D008962:Models, Theoretical; D009119:Muscle Contraction; D009991:Oscillometry; D051736:Proto-Oncogene Proteins c-mdm2 / Q000378:metabolism; D012313:RNA / Q000737:chemistry; D012815:Signal Processing, Computer-Assisted; D013997:Time Factors; D014158:Transcription, Genetic; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D016159:Tumor Suppressor Protein p53; D012313:RNA; D004247:DNA; D051736:Proto-Oncogene Proteins c-mdm2
keywords: biomolecular comparator; dynamical systems; modular; oscillator; synthetic biology