Systematic Coarse-Graining of Sequence-Dependent Structure and Elasticity of Double-Stranded DNA

Enrico Skoruppa; Helmut Schiessel

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arXiv · 2409.05510

Systematic Coarse-Graining of Sequence-Dependent Structure and Elasticity of Double-Stranded DNA

Enrico Skoruppa·Helmut Schiessel

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Abstract

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.

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Enrico Skoruppa, Helmut Schiessel. 2024-09-09. Systematic Coarse-Graining of Sequence-Dependent Structure and Elasticity of Double-Stranded DNA. https://arxiv.org/abs/2409.05510

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