Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

TL;DR

This paper presents oxDNA2, an enhanced coarse-grained DNA model that incorporates detailed structural features and variable salt conditions, enabling more accurate simulations of large DNA structures and their salt-dependent behaviors.

Contribution

The authors extend the oxDNA model to include explicit grooves, improved interactions, and variable salt conditions, enhancing its accuracy for large DNA structures and biological environments.

Findings

Improved modeling of DNA origami structures.

Demonstrated salt-dependent properties of DNA.

Enhanced accuracy in single-stranded DNA flexibility.

Abstract

We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures such as DNA origami which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na$^+$]=0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.