Solution-Based Biophysical Methods for Guiding Design of Aptamers into Electrochemical Biosensors

Structure-switching aptamers are utilized in various applications and have increasingly been translated into electrochemical biosensors largely thanks to post-SELEX sequence engineering through computational and enzymatic approaches. We were curious to unravel if these successes originated from: 1) a diminished aptamer-target binding site distance to the electrode surface; or 2) an alteration in the aptamer structure-switching properties. We explore this here using a combination of solution- (i.e., isothermal titration calorimetry and nano differential scanning calorimetry) and surface-based (electrochemical impedance spectroscopy) methods to assess folding and binding thermodynamics of a series of quinine-binding aptamers on sensor performances. Our findings show that the magnitude of sensor response to be strongly correlated with the aptamer’s thermodynamics as measured in solution. Guided by these principles, we then successfully engineer a recently reported adenosine monophosphate (AMP) aptamer to support electrochemical sensing. We envision that by relying on solution-based biophysical methods and in addressing the above question, we will further accelerate the translation of aptamers into sensors.