Mechanism of Dual-Site\nRecognition in a Classic DNA\nAptamer

Nucleic acid aptamers\npossess unique advantages in specific recognition.\nHowever, the lack of in-depth investigation into their dynamic recognition\nmechanisms has restricted their rational design and potential applications\nin fields such as biosensing and targeted therapy. We herein utilized\nenhanced sampling molecular dynamics to address affinities of adenosine\nmonophosphate (AMP) to the dual binding sites in the DNA aptamer,\nfocusing on the dynamic recognition mechanism and pathways. The present\nresults indicate that in addition to the widely known intermolecular\ninteractions, inequivalence of chemical environments of the two binding\nsites leads to slightly higher stability of AMP binding to the site\nproximal to the aptamer terminus. In the presence of two AMPs captured\nby the two sites, each binding free energy is enhanced. In particular,\nan additional hydrogen bond of AMP to A10 is introduced in the dual-site\nbinding complex, which increases the binding energy from −4.25\n± 0.47 to −9.48 ± 0.33 kcal mol<sup>–1</sup> in the site close to the loop. For the dual-site recognition process,\nthe free energy landscape and minimum free energy pathway calculations\nelucidate the crucial role of electrostatic interactions between the\nAMP phosphate groups and Na<sup>+</sup> ions in positively cooperative\nbinding mechanisms.