Load capacity improvements in nucleic acid based systems using partially open feedback control

Vishwesh Kulkarni, Evgeny Kharisov, Naira Hovakimyan, Jongmin Kim

Research output: Contribution to journalArticle

Abstract

Synthetic biology is facilitating novel methods and components to build in vivo and in vitro circuits to better understand and re-engineer biological networks. Recently, Kim and Winfree have synthesized a remarkably elegant network of transcriptional oscillators in vitro using a modular architecture of synthetic gene analogues and a few enzymes that, in turn, could be used to drive a variety of downstream circuits and nanodevices. However, these oscillators are sensitive to initial conditions and downstream load processes. Furthermore, the oscillations are not sustained since the inherently closed design suffers from enzyme deactivation, NTP fuel exhaustion, and waste product build up. In this paper, we show that a partially open architecture in which an L1 adaptive controller, implemented inside an in silico computer that resides outside the wet-lab apparatus, can ensure sustained tunable oscillations in two specific designs of the Kim-Winfree oscillator networks. We consider two broad cases of operation: (1) the oscillator network operating in isolation and (2) the oscillator network driving a DNA tweezer subject to a variable load. In both scenarios, our simulation results show a significant improvement in the tunability and robustness of these oscillator networks. Our approach can be easily adopted to improve the loading capacity of a wide range of synthetic biological devices.

Original languageEnglish (US)
Pages (from-to)617-626
Number of pages10
JournalACS synthetic biology
Volume3
Issue number8
DOIs
StatePublished - Aug 15 2014

Fingerprint

Nucleic acids
Nucleic Acids
Feedback control
Enzymes
Synthetic Biology
Waste Products
Synthetic Genes
Networks (circuits)
Gene Regulatory Networks
Computer Simulation
DNA
Genes
Engineers
Equipment and Supplies
Controllers
In Vitro Techniques

Keywords

  • DNA strand displacement
  • adaptive control
  • feedback
  • genelet
  • load capacity improvement
  • molecular programming
  • nucleic acid circuits

ASJC Scopus subject areas

  • Biomedical Engineering
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Cite this

Load capacity improvements in nucleic acid based systems using partially open feedback control. / Kulkarni, Vishwesh; Kharisov, Evgeny; Hovakimyan, Naira; Kim, Jongmin.

In: ACS synthetic biology, Vol. 3, No. 8, 15.08.2014, p. 617-626.

Research output: Contribution to journalArticle

Kulkarni, Vishwesh ; Kharisov, Evgeny ; Hovakimyan, Naira ; Kim, Jongmin. / Load capacity improvements in nucleic acid based systems using partially open feedback control. In: ACS synthetic biology. 2014 ; Vol. 3, No. 8. pp. 617-626.
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