Modeling Bending and Kinking of DNA Minicircles in Elongational Flow

DNA minicircles are a model system for DNA bending mechanics, and their response to nonuniform forcing, such as flow, provides insight into the deformation of broader DNA nanostructures in application environments. In this work we use molecular dynamics simulations to investigate DNA minicircles undergoing deformation and structural transitions in strong elongational flow. We derive an analytical model based on the worm-like chain and the extensional flow potential that predicts the extent of deformation without additional fitting parameters, and show that the data collapse across chain lengths when expressed in terms of the elasto-viscous number. Under uniaxial extensional flow, minicircles adopt a "racetrack" shape, concentrating bending energy toward the extrema of the minicircle along the extensional axis. At large flow strengths, the localized bending disrupts the double helix, resulting in a kink that is predicted by a dimensionless kinking number. DNA minicircles are relevant in biological processes such as gene expression, plasmids, and histone wrapping and, more generally, as building blocks for DNA nanostructures at similar length scales. These results provide a framework for understanding DNA deformation under nonuniform forcing in environments such as nanopores and microfluidic devices.