ArticleNucleic acids research2020
Molecular dynamics study of the recognition of ATP by nucleic acid aptamers.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 49 citations in OpenAlex.
- Assessing Molecular Dynamics in Predicting Aptamer-Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers.Journal of chemical information and modeling · 2026Article
- Mechanism of Dual-Site Recognition in a Classic DNA Aptamer.Journal of chemical information and modeling · 2024Article
- Research progress on the detection of foodborne pathogens based on aptamer recognition.Mikrochimica acta · 2024Review
- Enhanced sensitivity in electrochemical detection of ochratoxin A within food samples using ferrocene- and aptamer-tethered gold nanoparticles on disposable electrodes.RSC advances · 2024Article
- Article
- Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia.Molecular therapy. Nucleic acids · 2023Article
- Detection of Biomarker Using Aptasensors to Determine the Type of Diabetes.Diagnostics (Basel, Switzerland) · 2023Review
- Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.Journal of chemical information and modeling · 2022Article
- Structure-based deep learning for binding site detection in nucleic acid macromolecules.NAR genomics and bioinformatics · 2021Article
- Functional Nucleic-Acid-Decorated Spherical Nanoparticles: Preparation Strategies and Current Applications in Cancer Therapy.Small science · 2021Article
- Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol.Mikrochimica acta · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite their great success in recognizing small molecules in vitro, nucleic acid aptamers are rarely used in clinical settings. This is partially due to the lack of structure-based mechanistic information. In this work, atomistic molecular dynamics simulations are used to study the static and dynamic supramolecular structures relevant to the process of the wild-type (wt) nucleic acid aptamer recognition and binding of ATP. The effects brought about by mutation of key residues in the recognition site are also explored. The simulations reveal that the aptamer displays a high degree of rigidity and is structurally very little affected by the binding of ATP. Interaction energy decomposition shows that dispersion forces from π-stacking between ATP and the G6 and A23 nucleobases in the aptamer binding site plays a more important role in stabilizing the supramolecular complex, compared to hydrogen-bond interaction between ATP and G22. Moreover, metadynamics simulations show that during the association process, water molecules act as essential bridges connecting ATP with G22, which favors the dynamic stability of the complex. The calculations carried out on three mutated aptamer structures confirm the crucial role of the hydrogen bonds and π-stacking interactions for the binding affinity of the ATP nucleic acid aptamer.
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Registered trials
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