Powered DNA Strand Displacement Circuits for Continuous Environmental Monitoring and Memory | AIChE

Powered DNA Strand Displacement Circuits for Continuous Environmental Monitoring and Memory

Authors 

Scalise, D., Johns Hopkins University

In vitro biomolecular circuits seek to emulate in vivo chemical
reaction networks that can control the concentrations of chemical
outputs in response to the concentration levels of chemical inputs.
While such circuits can be built using small molecules, proteins, RNA and DNA
components, enzyme-free circuits based on strand displacement
reactions offer important benefits in terms of scaling,
robustness to physical conditions and reliable in silico design.
Currently, DNA strand displacement circuits can perform complex
computations, but they lack the capacity to respond dynamically to
environmental changes because portions of the circuit can become
nonfunctional after a single input/output cycle. This limitation
makes it impossible to build systems that can monitor changes in the
physical environment or store state information.

We are building a system of DNA-based strand displacement circuits
that overcome these limitations. The circuits are based on two types
of components that operate on separate time scales: fast reactions
between computational components compute an answer based on the
current input concentrations, while a second class of components
slowly restores the components to a steady state value. In many ways
this system mirrors the process of in vivo computation, in which
transcription and degradation processes restore concentrations to a
steady state, while fast reaction produce an output state dependent on
the concentration of circuit inputs.

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