Hierarchical control of enzymatic actuators using DNA-based switchable memories

Nat Commun. 2017 Oct 24;8(1):1117. doi: 10.1038/s41467-017-01127-w.

Abstract

Inspired by signaling networks in living cells, DNA-based programming aims for the engineering of biochemical networks capable of advanced regulatory and computational functions under controlled cell-free conditions. While regulatory circuits in cells control downstream processes through hierarchical layers of signal processing, coupling of enzymatically driven DNA-based networks to downstream processes has rarely been reported. Here, we expand the scope of molecular programming by engineering hierarchical control of enzymatic actuators using feedback-controlled DNA-circuits capable of advanced regulatory dynamics. We developed a translator module that converts signaling molecules from the upstream network to unique DNA strands driving downstream actuators with minimal retroactivity and support these findings with a detailed computational analysis. We show our modular approach by coupling of a previously engineered switchable memories circuit to downstream actuators based on β-lactamase and luciferase. To the best of our knowledge, our work demonstrates one of the most advanced DNA-based circuits regarding complexity and versatility.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • DNA / genetics*
  • DNA, Single-Stranded / genetics
  • Enzymes / chemistry*
  • Feedback
  • Feedback, Physiological
  • Gene Regulatory Networks*
  • Kinetics
  • Metabolic Engineering*
  • Models, Genetic*
  • Signal Transduction
  • beta-Lactamases / chemistry

Substances

  • DNA, Single-Stranded
  • Enzymes
  • DNA
  • beta-Lactamases
  • beta-lactamase TEM-1