Coarse-grained modelling of DNA-RNA hybrids

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension character...

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Hauptverfasser: Ratajczyk, EJ, Šulc, P, Turberfield, AJ, Doye, JPK, Louis, AA
Format: Internet publication
Sprache:English
Veröffentlicht: 2023
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author Ratajczyk, EJ
Šulc, P
Turberfield, AJ
Doye, JPK
Louis, AA
author_facet Ratajczyk, EJ
Šulc, P
Turberfield, AJ
Doye, JPK
Louis, AA
author_sort Ratajczyk, EJ
collection OXFORD
description We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.
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spelling oxford-uuid:3d72022d-543c-49d8-8f39-82ab17c3a4652024-04-04T14:27:18ZCoarse-grained modelling of DNA-RNA hybridsInternet publicationhttp://purl.org/coar/resource_type/c_7ad9uuid:3d72022d-543c-49d8-8f39-82ab17c3a465EnglishSymplectic Elements2023Ratajczyk, EJŠulc, PTurberfield, AJDoye, JPKLouis, AAWe introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.
spellingShingle Ratajczyk, EJ
Šulc, P
Turberfield, AJ
Doye, JPK
Louis, AA
Coarse-grained modelling of DNA-RNA hybrids
title Coarse-grained modelling of DNA-RNA hybrids
title_full Coarse-grained modelling of DNA-RNA hybrids
title_fullStr Coarse-grained modelling of DNA-RNA hybrids
title_full_unstemmed Coarse-grained modelling of DNA-RNA hybrids
title_short Coarse-grained modelling of DNA-RNA hybrids
title_sort coarse grained modelling of dna rna hybrids
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AT sulcp coarsegrainedmodellingofdnarnahybrids
AT turberfieldaj coarsegrainedmodellingofdnarnahybrids
AT doyejpk coarsegrainedmodellingofdnarnahybrids
AT louisaa coarsegrainedmodellingofdnarnahybrids