Thermodynamic basis for the design of efficient conformational change-based biosensors
A. Vallee-Belisle, F. Ricci, K.W. Plaxco
University of California, Santa Barbara, US
Keywords: biosensors, ligand-induced conformational change, thermodynamics, rational optimization, molecular beacons
Abstract:Recent years have seen the development of a number of biosensor platforms based on binding-induced conformational changes in oligonuclotides, polypeptides and proteins (Fig. 1). Examples include both optical and electrochemically-interrogated molecular beacons for the detection of oligonucleotides , aptamer-beacons for the detection of proteins, small molecules and inorganic ions , and a number of sensors based on binding-induced conformational changes in proteins . A key and hitherto poorly explored aspect of these sensors is that their performance is largely dictated by a compromise in their switching thermodynamics. Namely, while the conformational equilibrium underlying the sensor should favor the non-binding, non-signaling state in order to optimize the population shift observed upon target binding, over-stabilization of the non-binding state depopulates the binding-competent conformation and thus decreases the sensor’s affinity for its target (see Fig. 1). In my presentation, I will describe a universal three-state mathematical model that simulates the readout of conformational change-based biosensors and provides guidance for optimizing their switching thermodynamics. As a proof of principle, I will demonstrate that, consistent with our model, the gain of a representative molecular beacon can be varied by more than 4 orders of magnitude by altering the stability of its stem. These findings may be applicable to enhance the sensitivity and the detection limit of all conformational change-based biosensors currently in use.