Today, the need for biosensors with improved detection limits has been enhanced to detect specific targets with a high selectivity. Aptamers, as a group of nucleic acid sequences, are introduced to meet this demand. The T30695 aptamer, with the ability to form the G-quadruplex structure, is selectively bonded to Pb2+. Therefore, it is significantly utilized to design the Pb2+ biosensors. The investigation of the aptamer interactions with different ions can be an effective strategy to determine the aptamer selectivity toward a specific ion. Molecular dynamic (MD) simulations provide information about the type and strength of interactions between the aptamer and its target. Hence, MD simulations were applied in this article to study the selectivity of the T30695 aptamer towards Pb2+ in comparison with the other ions. The Free Energy Landscape (FEL) analysis illustrates that Pb2+ ion remains within the aptamer during the MD simulation while the others leave it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding Gibbs energies demonstrate the greatest conformational stability of the aptamer in the presence of Pb2+. The ion-aptamer complex with the most compaction is induced in the presence of Pb2+, which confirms the highest aptamer interaction with the ion. These results verify the selectivity of the aptamer toward Pb2+. The contact maps clarify the appearance of the new contacts in the presence of Pb2+, which is another confirmation for the aptamer selectivity toward Pb2+.

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