Kinetics of conformational fluctuations in DNA hairpin-loops in crowded fluids

Biochemical reactions in crowded fluids have been predicted to differ strongly from those in aqueous solutions. Both excludedvolume interactions with surrounding macromolecules and crowding-induced subdiffusion have been predicted to stabilize complex formation of reaction partners. Here we show that both facets of crowding strongly alter the stochastic opening and closing of a single-stranded DNA hairpin. Crowding not only slows down the kinetics but also increases the steady-state fraction of closed hairpins significantly. The latter is shown to be enhanced if crowding is associated with subdiffusion. Biochemical reactions in crowded fluids are therefore sensistive to both excluded-volume interactions and changes of the reactants’ diffusion characteristics.