A computational model for structural dynamics and reconfiguration of DNA assemblies
Abstract Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework c...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-42873-4 |
| _version_ | 1797636850561581056 |
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| author | Jae Young Lee Heeyuen Koh Do-Nyun Kim |
| author_facet | Jae Young Lee Heeyuen Koh Do-Nyun Kim |
| author_sort | Jae Young Lee |
| collection | DOAJ |
| description | Abstract Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines. |
| first_indexed | 2024-03-11T12:40:05Z |
| format | Article |
| id | doaj.art-e061de6867a146b4ba77a9371107904a |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-11T12:40:05Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-e061de6867a146b4ba77a9371107904a2023-11-05T12:22:06ZengNature PortfolioNature Communications2041-17232023-11-0114111210.1038/s41467-023-42873-4A computational model for structural dynamics and reconfiguration of DNA assembliesJae Young Lee0Heeyuen Koh1Do-Nyun Kim2Institute of Advanced Machines and Design, Seoul National UniversitySoft Foundry Institute, Seoul National UniversityInstitute of Advanced Machines and Design, Seoul National UniversityAbstract Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines.https://doi.org/10.1038/s41467-023-42873-4 |
| spellingShingle | Jae Young Lee Heeyuen Koh Do-Nyun Kim A computational model for structural dynamics and reconfiguration of DNA assemblies Nature Communications |
| title | A computational model for structural dynamics and reconfiguration of DNA assemblies |
| title_full | A computational model for structural dynamics and reconfiguration of DNA assemblies |
| title_fullStr | A computational model for structural dynamics and reconfiguration of DNA assemblies |
| title_full_unstemmed | A computational model for structural dynamics and reconfiguration of DNA assemblies |
| title_short | A computational model for structural dynamics and reconfiguration of DNA assemblies |
| title_sort | computational model for structural dynamics and reconfiguration of dna assemblies |
| url | https://doi.org/10.1038/s41467-023-42873-4 |
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