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| Autori principali: | , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| Accesso online: | https://arxiv.org/abs/2409.05510 |
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| _version_ | 1866916386305998848 |
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| author | Skoruppa, Enrico Schiessel, Helmut |
| author_facet | Skoruppa, Enrico Schiessel, Helmut |
| contents | Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent approaches, such as the twistable worm-like chain. However, research over the past decade has illuminated the substantial impact of DNA sequence even at the kilo-base pair scale. Several robust sequence-dependent models have emerged, capturing intricacies at the base pair-step level. Here we introduce an analytical framework for coarse-graining such models to the 2 to 40-base pair scale while preserving essential structural and dynamical features. These faithful coarse-grained parametrizations enable efficient sampling of large molecules. Rather than providing a fully parametrized model, we present the methodology and software necessary for mapping any base pair-step model to the desired level of coarse-graining. Finally, we provide application examples of our method, including estimates of the persistence length and effective torsional stiffness of DNA in a setup mimicking a freely orbiting tweezer, as well as simulations of intrinsically helical DNA. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_05510 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Systematic Coarse-Graining of Sequence-Dependent Structure and Elasticity of Double-Stranded DNA Skoruppa, Enrico Schiessel, Helmut Soft Condensed Matter Statistical Mechanics Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent approaches, such as the twistable worm-like chain. However, research over the past decade has illuminated the substantial impact of DNA sequence even at the kilo-base pair scale. Several robust sequence-dependent models have emerged, capturing intricacies at the base pair-step level. Here we introduce an analytical framework for coarse-graining such models to the 2 to 40-base pair scale while preserving essential structural and dynamical features. These faithful coarse-grained parametrizations enable efficient sampling of large molecules. Rather than providing a fully parametrized model, we present the methodology and software necessary for mapping any base pair-step model to the desired level of coarse-graining. Finally, we provide application examples of our method, including estimates of the persistence length and effective torsional stiffness of DNA in a setup mimicking a freely orbiting tweezer, as well as simulations of intrinsically helical DNA. |
| title | Systematic Coarse-Graining of Sequence-Dependent Structure and Elasticity of Double-Stranded DNA |
| topic | Soft Condensed Matter Statistical Mechanics |
| url | https://arxiv.org/abs/2409.05510 |