Nanogel imprinting improving affinity and selectivity of domain-limited ssDNA aptamer to Pb: Interaction mechanisms revealed by molecular dynamics simulation.

Aptamer conformations are susceptible to environmental conditions, which makes it difficult to achieve stable targets detection in complex environments with aptasensors. Imprinting strategy was proposed to immobilize the specific conformation of aptamers, aiming to enhance their recognition anti-interference. However, it is mechanistically unclear how the imprinted polymers affect aptamers' recognition, which limits application of the strategy. Herein, MD simulation was applied to explore the structural reason why nanogel imprinting improves binding affinity and selectivity of T30695 aptamer to Pb observed experimentally. Results show the imprinted polymers stabilize the domain-limited T30695 by noncovalent interactions. The coating process undergoes three evolution stages, finally achieving a polymer-aptamer-polymer sandwich-shaped conformation. Notably, it was found the polymers provide additional non-specific binding of Pb at acylamine group of acrylamide monomers, which accounts for the improved binding affinity with association constant K 2.5 times larger. More importantly, imprinting enhances selectivity of aptamer to Pb by changing coordination mode of interfering ions (Ca, K, Mg, NH and Cu), which significantly destroys G-quadruplex conformation and thus its binding ability. This work revealed mechanistic effects of imprinting strategy on aptamers recognition at molecular level, which can guide rational design of high-performance aptamer-based biosensors applied in various detection areas.