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

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.

References in corpus (6)

• Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
• Sequence-dependent thermodynamics of a coarse-grained DNA model
• Determination of phase diagrams via computer simulation: Methodology and applications to water, electrolytes and proteins
• The role of collective motion in examples of coarsening and self-assembly
• The role of loop stacking in the dynamics of DNA hairpin formation
• Characterizing the bending and flexibility induced by bulges in DNA duplexes

Cited by in corpus (1)

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