A dynamic Monte Carlo approach for studying competing nucleoprotein bindings on single-stranded DNA

The central step of homologous recombination (HR) involves the search for homology between two DNA molecules and the subsequent exchange of the DNA strands. To have a better understanding of the recombinase-mediated DNA strand exchange, we introduce a dynamical Monte Carlo model. In this computational model, we study the dynamics of the recombinase filament nucleation, extension, and disassembly and its competition with other binding nucleoproteins. These biochemical reactions are experimentally observed at the single-molecule level using Total Internal Reflection Fluorescence Microscopy. This model allows building a mechanistic model of the filament formation that matches the single-molecule data.