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

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...

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Main Authors: Haley, NEC, Ouldridge, TE, Mullor Ruiz, I, Geraldini, A, Louis, AA, Bath, J, Turberfield, AJ
Formato: Journal article
Idioma:English
Publicado em: Springer Nature 2020
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author Haley, NEC
Ouldridge, TE
Mullor Ruiz, I
Geraldini, A
Louis, AA
Bath, J
Turberfield, AJ
author_facet Haley, NEC
Ouldridge, TE
Mullor Ruiz, I
Geraldini, A
Louis, AA
Bath, J
Turberfield, AJ
author_sort Haley, NEC
collection OXFORD
description 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.
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spelling oxford-uuid:c2e56147-451c-44e6-8787-b8e11ea35c7c2022-03-27T06:12:27ZDesign of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacementJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:c2e56147-451c-44e6-8787-b8e11ea35c7cEnglishSymplectic ElementsSpringer Nature2020Haley, NECOuldridge, TEMullor Ruiz, IGeraldini, ALouis, AABath, JTurberfield, AJRecent 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.
spellingShingle Haley, NEC
Ouldridge, TE
Mullor Ruiz, I
Geraldini, A
Louis, AA
Bath, J
Turberfield, AJ
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
title Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
title_full Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
title_fullStr Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
title_full_unstemmed Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
title_short Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
title_sort design of hidden thermodynamic driving for non equilibrium systems via mismatch elimination during dna strand displacement
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