DNA structure and properties sensitively depend on its environment, in particular on the ion atmosphere. One of the most fundamental properties of DNA is its helicity and here we investigate how it changes with concentration and identity of the surrounding ions. To resolve how metal cations influence the helical twist, we have combined magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases with increasing ion concentration. Secondly, for a given salt concentration, DNA twist strongly depends on cation identity. Metal cations with high charge density (such as Li+ or Ca2+) are most efficient at inducing DNA twist and lead to overwinding. By contrast, metals with intermediate charge density (such as Na+ or Ba2+) reduce the twist and underwind the helix compared to higher density ions. Our molecular dynamics simulations reveal that preferential binding of the metals to the DNA backbone and the nucleobases has opposing effects on DNA twist and provide a microscopic explanation of the observed ion specificity. The comprehensive view gained from our combined approach provides a foundation to understand and predict metal-induced structural changes in nature or in DNA nanotechnology.
Thermodynamic stability of magnetic states of monovacancy in graphene revealed by ab initio molecular dynamics simulations
