ArticleNucleic acids research2023
Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 23 citations in OpenAlex.
- Design and Evaluation of Sticky End-Type Bivalent DNA Aptamers Containing M08s-1 as Anticoagulant Agents.ChemMedChem · 2025Article
- CRISPR-driven diagnostics: Molecular mechanisms, clinical efficacy and translational challenges.Clinical and translational medicine · 2025Review
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Aptamer Sequence Optimization and Its Application in Food Safety Analysis.Foods (Basel, Switzerland) · 2025Review
- Macromolecular crystallography at Elettra: current and future perspectives.Journal of synchrotron radiation · 2025Article
- Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.Biophysical reviews · 2024Review
- Recent Advances in Aptamer-Based Biosensors for Bacterial Detection.Biosensors · 2024Review
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- A neutralizable dimeric anti-thrombin aptamer with potent anticoagulant activity in mice.Molecular therapy. Nucleic acids · 2023Article
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.
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