Detection for folding of the thrombin binding aptamer using label-free electrochemical methods

Area of Science:

• Biosensors
• Electrochemistry
• Biophysical Chemistry

Background:

• DNA aptamers are crucial for molecular recognition.
• Understanding aptamer folding is key to optimizing biosensor performance.
• Label-free detection methods offer sensitive and direct analysis.

Purpose of the Study:

• To detect DNA aptamer folding using label-free electrochemical techniques.
• To investigate the influence of monovalent cations on aptamer conformation.
• To analyze the interaction between aptamer and thrombin based on aptamer folding.

Main Methods:

• Electrochemical impedance spectroscopy (EIS) for detecting aptamer folding.
• X-ray photoelectron spectroscopy (XPS) for conformational analysis.
• Electrochemical quartz crystal microbalance (EQCM) for quantitative analysis.

Main Results:

• Monovalent cation-induced aptamer folding follows the order K(+) > NH(4)(+) > Na(+) > Cs(+).
• Potassium (K+) and ammonium (NH(4)+) ions induce stable aptamer-cation complexes.
• Thrombin shows stronger interaction with folded aptamer structures, with evidence of thrombin stabilizing aptamer folding.

Conclusions:

• Label-free electrochemical methods can effectively detect aptamer folding.
• Monovalent cations play a significant role in modulating aptamer conformation.
• Aptamer folding enhances its binding affinity and interaction with target molecules like thrombin.