Theory of bimolecular reactions in a solution with linear traps: Application to the problem of target search on DNA

One-dimensional sliding along DNA as a means to accelerate protein target search is a well-known phenomenon occurring in various biological systems. Using a biomimetic approach, we have recently demonstrated the practical use of DNA-sliding peptides to speed up bimolecular reactions more than an order of magnitude by allowing the reactants to associate not only in the solution by three-dimensional (3D) diffusion, but also on DNA via one-dimensional (1D) diffusion [A. Turkin et al., Chem. Sci. (2015)]. Here we present a mean-field kinetic model of a bimolecular reaction in a solution with linear extended sinks (e.g., DNA) that can intermittently trap molecules present in a solution. The model consists of chemical rate equations for mean concentrations of reacting species. Our model demonstrates that addition of linear traps to the solution can significantly accelerate reactant association. We show that at optimum concentrations of linear traps the 1D reaction pathway dominates in the kinetics of the bimolecular reaction; i.e., these 1D traps function as an assembly line of the reaction product. Moreover, we show that the association reaction on linear sinks between trapped reactants exhibits a nonclassical third-order behavior. Predictions of the model agree well with our experimental observations. Our model provides a general description of bimolecular reactions that are controlled by a combined 3D+1D mechanism and can be used to quantitatively describe both naturally occurring as well as biomimetic biochemical systems that reduce the dimensionality of search.