Conformational and Dynamic Properties of Short DNA Minicircles in Aqueous Solution from Atomistic Molecular Dynamics Simulations
Terpsichori S. Alexiou, Panagiotis V. Alatas, Dimitrios G. Tsalikis, Vlasis G. Mavrantzas
Abstract
Detailed molecular dynamics (MD) simulations of aqueous solutions of short DNA minicircles ranging in size from 30 to 180 bp were performed for the investigation of the structure and dynamics at an atomistic level, by employing the recently developed parmbsc1 force field. The resulting MD trajectories were analyzed for the determination of local conformation in terms of backbone torsion angles and interbase pair helical parameters, and very good agreement was observed with respect to relevant experimental data. Minor groove hydration exhibits a bimodal structure for all nucleobases, with water molecules residing in the first subshell of hydration forming a highly ordered, chiral water layer that conforms to the topological state of DNA, even adopting a twisted, figure-eight shape in the case of 180 bp minicircles. The mean-squared radius of gyration of the simulated DNA minicircles was found to scale with the number of base pairs, Nbp, as ⟨Rg2⟩ ∼ Nbp2ν with ν ≈ 0.83, a scaling exponent in-between the values corresponding to a rigid rodlike behavior and the 3D self-avoiding walk limit for flexible chains. Ultrashort and very stiff 30 bp minicircles exhibit an unexpectedly pronounced degree of anisotropic diffusion, a phenomenon that is attenuated as the molecular length increases due to the emergence of out-of-plane bending motions.