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A localized DNA finite-state machine with temporal resolution.

Lan Liu1,2, Fan Hong2, Hao Liu2

  • 1State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.

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|March 25, 2022
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Summary
This summary is machine-generated.

We created a DNA finite-state machine (FSM) to record the order of environmental signals. This DNA computing tool advances temporally resolved biosensing and smart therapeutics.

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Area of Science:

  • Synthetic Biology
  • Molecular Engineering
  • Biotechnology

Background:

  • Environmental stimuli critically influence biological signaling networks and phenotype development.
  • Understanding history-dependent signals is key to deciphering temporally regulated biological processes.
  • Temporal sensing in biological systems remains a significant challenge.

Purpose of the Study:

  • To develop a DNA finite-state machine (FSM) capable of sensing and recording the temporal order of multiple inputs.
  • To leverage DNA origami for precise spatial organization and control of DNA strand displacement reactions.
  • To create a modular and efficient FSM for temporally resolved biosensing applications.

Main Methods:

  • Designed a two-input, five-state DNA finite-state machine (FSM) utilizing DNA origami.
  • Employed spatial constraints on DNA origami to modulate the energy landscape of strand displacement reactions.
  • Engineered orthogonal components for modularity and minimized leaky reactions, ensuring fast kinetics.

Main Results:

  • The DNA FSM successfully sensed and recorded the temporal order of two specific microRNA inputs.
  • Spatial organization on DNA origami facilitated precise control over reaction pathways based on input sequence.
  • The FSM exhibited minimized leaky reactions and fast kinetic performance.

Conclusions:

  • The developed DNA FSM provides a novel platform for sensing and recording history-dependent signals.
  • This technology holds significant potential for advancing temporally resolved biosensing and developing smart therapeutics.
  • The modular design and efficient kinetics pave the way for more complex biological computation applications.