Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

Natalie E. C. Haley, Thomas E. Ouldridge (), Ismael Mullor Ruiz, Alessandro Geraldini, Ard A. Louis, Jonathan Bath and Andrew J. Turberfield ()
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Natalie E. C. Haley: University of Oxford
Thomas E. Ouldridge: Imperial College Centre for Synthetic Biology and Department of Bioengineering
Ismael Mullor Ruiz: Imperial College Centre for Synthetic Biology and Department of Bioengineering
Alessandro Geraldini: University of Oxford
Ard A. Louis: University of Oxford
Jonathan Bath: University of Oxford
Andrew J. Turberfield: University of Oxford

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.

Date: 2020
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DOI: 10.1038/s41467-020-16353-y

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