Programmable energy landscapes for kinetic control of DNA strand displacement.
DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in au...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
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Nature Publishing Group
2014
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| _version_ | 1797097941539749888 |
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| author | Machinek, R Ouldridge, T Haley, N Bath, J Turberfield, A |
| author_facet | Machinek, R Ouldridge, T Haley, N Bath, J Turberfield, A |
| author_sort | Machinek, R |
| collection | OXFORD |
| description | DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics. |
| first_indexed | 2024-03-07T05:02:31Z |
| format | Journal article |
| id | oxford-uuid:d8c7612d-9aeb-4e32-9c08-a0b4e7b8522a |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T05:02:31Z |
| publishDate | 2014 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | oxford-uuid:d8c7612d-9aeb-4e32-9c08-a0b4e7b8522a2022-03-27T08:51:18ZProgrammable energy landscapes for kinetic control of DNA strand displacement.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:d8c7612d-9aeb-4e32-9c08-a0b4e7b8522aEnglishSymplectic Elements at OxfordNature Publishing Group2014Machinek, ROuldridge, THaley, NBath, JTurberfield, ADNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics. |
| spellingShingle | Machinek, R Ouldridge, T Haley, N Bath, J Turberfield, A Programmable energy landscapes for kinetic control of DNA strand displacement. |
| title | Programmable energy landscapes for kinetic control of DNA strand displacement. |
| title_full | Programmable energy landscapes for kinetic control of DNA strand displacement. |
| title_fullStr | Programmable energy landscapes for kinetic control of DNA strand displacement. |
| title_full_unstemmed | Programmable energy landscapes for kinetic control of DNA strand displacement. |
| title_short | Programmable energy landscapes for kinetic control of DNA strand displacement. |
| title_sort | programmable energy landscapes for kinetic control of dna strand displacement |
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