STUDY OF THE INTERACTION OF SIX SINGLE-STRANDED DNA APTAMERS TO CARDIAC TROPONIN I BY DOCKING AND MOLECULAR DYNAMICS SIMULATION

• Main Author: Ropii, Bejo
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/63677
• Institution: Institut Teknologi Bandung

ABSTRACT STUDY OF THE INTERACTION OF SIX SINGLE-STRANDED DNA APTAMERS TO CARDIAC TROPONIN I BY DOCKING AND MOLECULAR DYNAMICS SIMULATION By Bejo Ropii Student ID: 23219348 (Master’s Program in Electrical Engineering) Cardiac troponin I (cTnI) has been used as a cardiac biomarker for diagnosis of ischemic heart disease. Current assays are using antibodies (Abs) as the bioreceptor due to 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 temperature; and the difficulty for chemical modification. Aptamers are single-stranded RNA or DNA that fold into three-dimensional architectures and bind to targets such as proteins. Aptamer offers many advantages to overcome the limitation of antibodies such as relatively lower cost, high reproducibility, high stability, and ease to be chemically modified. Six aptamers (Tro1-Tro6) with higher binding affinity than antibodies have been identified, but the molecular interaction has not been studied. In this study, six single-stranded DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the same cTnI region which is the early and last residues of cTnI chain. The interaction between aptamer and cTnI involved hydrophobic interaction and hydrogen bond with or without additional ?-cation interactions and salt-bridge formation. Tro4 binding energy was the lowest among all aptamers which agrees with the previously reported experimental data. Electrostatic energy was the main driving force of the interaction between aptamer and cTnI. This study could predict the behavior of modified Tro4 aptamer to improve aptamer performance. Keywords: aptamer, cardiac troponin I, molecular docking, molecular dynamics.