The free-energy landscape of a mechanically bistable DNA origami
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bis...
| Váldodahkkit: | , |
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| Materiálatiipa: | Journal article |
| Giella: | English |
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MDPI
2022
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| _version_ | 1826312245164900352 |
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| author | Wong, CK Doye, JPK |
| author_facet | Wong, CK Doye, JPK |
| author_sort | Wong, CK |
| collection | OXFORD |
| description | Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally. |
| first_indexed | 2024-03-07T08:26:13Z |
| format | Journal article |
| id | oxford-uuid:71c249dc-c1dd-4222-bc66-5a3d7523f79f |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:26:13Z |
| publishDate | 2022 |
| publisher | MDPI |
| record_format | dspace |
| spelling | oxford-uuid:71c249dc-c1dd-4222-bc66-5a3d7523f79f2024-02-16T09:43:06ZThe free-energy landscape of a mechanically bistable DNA origamiJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:71c249dc-c1dd-4222-bc66-5a3d7523f79fEnglishSymplectic ElementsMDPI2022Wong, CKDoye, JPKMolecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally. |
| spellingShingle | Wong, CK Doye, JPK The free-energy landscape of a mechanically bistable DNA origami |
| title | The free-energy landscape of a mechanically bistable DNA origami |
| title_full | The free-energy landscape of a mechanically bistable DNA origami |
| title_fullStr | The free-energy landscape of a mechanically bistable DNA origami |
| title_full_unstemmed | The free-energy landscape of a mechanically bistable DNA origami |
| title_short | The free-energy landscape of a mechanically bistable DNA origami |
| title_sort | free energy landscape of a mechanically bistable dna origami |
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