ABSTRACT
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 mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches 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 non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.
Subject(s)
DNA/chemistry , DNA/genetics , Base Pair Mismatch , Kinetics , Nucleic Acid Conformation , ThermodynamicsABSTRACT
We investigate the structural response of a dense peptide metal-organic framework using in situ powder and single-crystal X-ray diffraction under high-pressures. Crystals of Zn(GlyTyr)2 show a reversible compression by 13% in volume at 4 GPa that is facilitated by the ability of the peptidic linker to act as a flexible string for a cooperative response of the structure to strain. This structural transformation is controlled by changes to the conformation of the peptide, which enables a bond rearrangement in the coordination sphere of the metal and changes to the strength and directionality of the supramolecular interactions specific to the side chain groups in the dipeptide sequence. Compared to other structural transformations in Zn(ii) peptide MOFs, this behaviour is not affected by host/guest interactions and relies exclusively on the conformational flexibility of the peptide and its side chain chemistry.
