ArticleJournal of chemical information and modeling2024
Mechanism of Dual-Site Recognition in a Classic DNA Aptamer.
Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Aptamers targeting immune checkpoints for tumor immunotherapy: a comprehensive review.Frontiers in oncology · 2026Review
- Aptamers and aptamer-drug conjugates as synthetic immune modulators for cancer immunotherapy.Frontiers in immunology · 2026Review
- Exploring the antitumor potential of cucurbitacin B in hepatocellular carcinoma through network pharmacology, molecular docking, and molecular dynamics simulations.Naunyn-Schmiedeberg's archives of pharmacology · 2025Review
- Designing the Future of Biosensing: Advances in Aptamer Discovery, Computational Modeling, and Diagnostic Applications.Biosensors · 2025Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acid aptamers possess unique advantages in specific recognition. However, the lack of in-depth investigation into their dynamic recognition mechanisms has restricted their rational design and potential applications in fields such as biosensing and targeted therapy. We herein utilized enhanced sampling molecular dynamics to address affinities of adenosine monophosphate (AMP) to the dual binding sites in the DNA aptamer, focusing on the dynamic recognition mechanism and pathways. The present results indicate that in addition to the widely known intermolecular interactions, inequivalence of chemical environments of the two binding sites leads to slightly higher stability of AMP binding to the site proximal to the aptamer terminus. In the presence of two AMPs captured by the two sites, each binding free energy is enhanced. In particular, an additional hydrogen bond of AMP to A10 is introduced in the dual-site binding complex, which increases the binding energy from -4.25 ± 0.47 to -9.48 ± 0.33 kcal mol
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Registered trials
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