Numerical simulation of two-dimensional agarose gel electrophoresis of knotted and supercoiled DNA molecules

Abstract

"The present work introduces a mathematical model, based on conservation laws and Maxwell-Stefan equations of mass transport, to analyze the electrophoretic mobility of two topological DNA families: supercoiled and knotted DNA molecules with the same total molecular mass. Comparison of experimental results and numerical simulations showed that our model is able to accurately reproduce two-dimensional (2D) agarose gel electrophoresis of supercoiled dimers and nicked knotted dimers under different conditions of electrostatic potential. The implementation of this mathematical approach could be useful to optimize conditions for the separation of different types of DNA topoisomers during electrophoresis."