The Kinetics of Charge Recombination in DNA Hairpins Controlled by Counterions

The slow charge recombination in DNA hairpins of various lengths is investigated. The distance dependence for the charge recombination rate between stilbene donor (Sd(+)) and stilbene acceptor (Sa(-)) linkers separated by AT bridges of various lengths has the double exponential form. We suggest that this puzzling dependence is associated with two tunneling channels distinguished by the presence or absence of a Cl(-) counterion bound to an Sd(+) linker. When Cl(-) is associated with Sd(+) the energy of positive charge is lower compared to Sd(+) without a counterion. Therefore the potential barrier for charge recombination is higher in the presence of Cl(-) bound to Sd(+), and the recombination is characterized by the larger tunneling exponent than the tunneling exponent in the absence of counterions. Experiment-based estimates of binding parameters agree within reasonable expectations. The control experiment replacing the Cl(-) ion with other ions is suggested. This replacement enables the control of the charge recombination rate modifying it in either direction by orders of magnitude.