Design of a Biological Sensor for Potassium Ions using a DNA Aptamer and Calorimetry

DNA quadruplexes are an unusually stable potassium‐binding structural motif that has the potential for wide‐reaching biological implications. While significant work has been performed towards the general development of these motifs as potassium sensors, little work has been done to rationally design these motifs with predictable, and wide‐ranging potassium binding constants. This project aims to correlate the [K + ] required for quadruplex formation with the stability associated with an alternative hairpin structure. In an effort to facilitate such a rational design of ligandbinding oligonucleotides, we used nearest‐neighbor parameters to derive a set of DNA quadruplexes whose binding constants were determined by potassium titration experiments and circular dichroism. In addition, HT‐ITC (High‐Throughput Isothermal Titration Calorimetry) and HT‐DSC (High‐Throughput Differential Scanning Calorimetry) were used to provide a more complete picture of the ways in which alternative secondary structure formation can be used to tune the affinity of RNA and DNA sensors of small molecules. Our findings demonstrate that free energy values for both of these processes (hairpin to quadruplex formation and stability of hairpin structure) are linearly correlated, such that a DNA quadruplex‐forming sequence can be rationally designed to selectively bind K + at any desired K D .