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...
| Hauptverfasser: | , , , , , , |
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| Format: | Journal article |
| Sprache: | English |
| Veröffentlicht: |
Springer Nature
2020
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| _version_ | 1826295108413161472 |
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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. |
| first_indexed | 2024-03-07T03:56:02Z |
| format | Journal article |
| id | oxford-uuid:c2e56147-451c-44e6-8787-b8e11ea35c7c |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:56:02Z |
| publishDate | 2020 |
| publisher | Springer Nature |
| record_format | dspace |
| 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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