The molecular interaction of six single-stranded DNA aptamers to cardiac troponin I revealed by docking and molecular dynamics simulation.

Cardiac troponin I (cTnI) is a cardiac biomarker for diagnosing ischemic heart disease and acute myocardial infarction. Current biochemical assays use antibodies (Abs) due to their high specificity and sensitivity. However, there are some limitations, such as the high-cost production of Abs due to complex instruments, reagents, and steps; the variability of Abs quality from batch to batch; the low stability at high temperatures; and the difficulty of chemical modification. Aptamer overcomes the limitations of antibodies, such as relatively lower cost, high reproducibility, high stability, and ease of being chemically modified. Aptamers are three-dimensional architectures of single-stranded RNA or DNA that bind to targets such as proteins. Six aptamers (Tro1-Tro6) with higher binding affinity than an antibody have been identified, but the molecular interaction has not been studied. In this study, six DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the similar cTnI region. The interaction between aptamer and cTnI involved hydrophobic interaction, hydrogen bonds, π-cation interactions, π-stack interactions, and salt-bridge formation. The calculated binding energy of all complexes was negative, which means that the complex formation was thermodynamically favorable. The electrostatic energy term was the main driving force of the interaction between all aptamer and cTnI. This study could be used to predict the behavior of further modified aptamer to improve aptamer performance.

The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.

Aptamers are single-stranded DNA or RNA that bind to specific targets such as proteins, thus having similar characteristics to antibodies. It can be synthesized at a lower cost, with no batch-to-batch variations, and is easier to modify chemically than antibodies, thus potentially being used as therapeutic and biosensing agents. The current method for RNA aptamer identification in vitro uses the SELEX method, which is considered inefficient due to its complex process. Computational models of aptamers have been used to predict and study the molecular interaction of modified aptamers to improve affinity. In this study, we generated three-dimensional models of five RNA aptamers from their sequence using mFold, RNAComposer web server, and molecular dynamics simulation. The model structures were then evaluated and compared with the experimentally determined structures. This study showed that the combination of mFold, RNAComposer, and molecular dynamics simulation could generate 14-16, 28, or 29 nucleotides length of 3D RNA aptamer with similar geometry and topology to the experimentally determined structures. The non-canonical basepair structure of the aptamer loop was formed through the MD simulation, which also improved the three-dimensional RNA aptamers model. Clustering analysis was recommended to choose the more representative model.