Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles

We propose a method for analyzing the magnitude and direction of curvaturewithin nucleic acids, based on the curvilinear helical axis calculated by Curves+. The method is applied to analyzing curvaturewithin minicirclesconstructed with varying degrees of overor under-twisting. Using the molecular dynamics trajectories of three different minicircles, we are able to quantify how curvaturevaries locally both in space and in time. We also analyze how curvatureinfluences the local environment of the minicircles, notably via increased heterogeneity in the ionic distributions surrounding the double helix. The approach we propose has been integrated into Curves+ and the utilities Canal (time trajectory analysis) and Canion ( environmental analysis) and can be used to study a wide variety of static and dynamic structural data on nucleic acids.