In silico investigation of Field Effect Transistorbased aptasensor : molecular modelling of interfacial conformational switch of immobilized DNA structure upon target binding

Overview & Synopsis

Biosensors are analytical devices that combine the specificity of a biological component or bioreceptor, such as proteins, nucleic acids, tissues and even entire organelles or cells, to a physical transducing component capable of measuring and quantifying the interaction between the biological component and the analyte. One very powerful approach is to use bioreceptor-modified surfaces whose physiochemical properties depend on the neighboring environment. In this work, we perform computational studies on a DNA-based bioreceptor for an EGOFET-type biosensor using different computational methods. We have chosen ampicillin (AMP) as our molecule of interest for the biosensor. In order to detect the presence of AMP with our bioreceptor, we have added an anti-AMP aptamer sequence to our global DNA sequence, with the goal of better understanding the transduction process by analyzing the changes in ionic distribution in our system in both absence and presence of AMP. We have shown our results on the construction of our model biorecognition structure in both off- and on-states, representing the system in the absence and presence of ampicillin (AMP), respectively. We have effectively found stable conformations for both states, including the elucidation of the complex AMP-aptamer structure. We conclude that our proposed system is promising for any kind of electrical transduction based on a change in capacitance or field effect, and we have elucidated certain aspects of the biorecognition process that would not be so easily done experimentally, such as the ionic profiles and the possible de-hybridization mechanisms.