Predicting the Cardiac Troponin I (cTnl) Aptamer/Methylene Blue Configuration Using Computational Modeling Studies: A Screening Search Method for Constructing Aptasensors

Acute Myocardial Infarction (AMI) is the most common cause of mortality, and cardiac troponin I (cTnI) is the gold standard for AMI diagnosis. Some aptamers have been reported to detect cTnI, but there is rarely any structural information on their binding with cTnI. There are many studies involving electrochemical aptasensors with methylene blue (MB) as a redox indicator that does not provide any significant new information. Our study, however, involves the computational modeling of the complexes of a documented 40-mer ssDNA-cTnI aptamer with its target and MB. Here, MB was used as a model system to investigate the rather complex interaction modes between small redox molecules and a cTnI-aptamer. Understanding these modes is an important facet in designing electrochemical aptasensors to ascertain the effectiveness of a redox indicator. In our study, docking and molecular dynamics (MD) were used to provide information on the stability, fluctuations, and interaction analysis of the complexes. Based on computational evaluations, we understand how the structure of the cTnI-aptamer steers the MB releasing after inducing cTnI. In order to evaluate the sensing performance of the cTnI-aptamer in the presence of MB experimentally, after covalent immobilization of the 5-amino terminated cTnI-aptamer at a pre-functionalized carboxylated multi-walled carbon nanotube (COOH-MWCNT) glassy carbon electrode, some techniques including spectroscopy and voltammetry were employed.