Rational design of hidden thermodynamic driving through DNA mismatch repair

Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a new mechanism for enhancing thermodynamic drive of DNA strand displacement reactions whilst barely perturbing forward reaction rates - introducing mismatches in an internal location within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of nonequilibrium systems that rely on catalytic control and must be robust to leak reactions.