ArticleNucleic acids research2012
High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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Who cites it
103 citing papers in PubMed, 253 citations in OpenAlex.
- Protein-protein interaction disruption as a next-generation antithrombotic strategy.Journal of thrombosis and thrombolysis · 2026Review
- Article
- Structural insights into the binding of CX-5461 and MTR-106 to G-quadruplex DNA.Nucleic acids research · 2026Article
- Unlocking chemical diversity in aptamers with DNA orthogonal barcodes.Nature chemistry · 2026Article
- Dissecting the Chemical and Thermal Stabilities of Tetrads in G-Quadruplexes to Derive a Structure-Activity Relation for a Thrombin-Binding DNA G-Quadruplex Aptamer.Chembiochem : a European journal of chemical biology · 2026Article
- Covalent aptamers: agents with promising therapeutic and diagnostic potential.RSC chemical biology · 2026Review
- When the Position of Pendant Groups Makes the Difference in G-Quadruplex Behavior: The Case of Bis-Conjugated Thrombin-Binding Aptamers.Journal of chemical information and modeling · 2026Article
- An Aptamer-Based EXACT Anticoagulant as a Sustainable, Animal-Free Alternative to Unfractionated Heparin.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation.PLoS computational biology · 2025Article
- 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
- Vertical DNA Nanostructure Arrays: Facilitating Functionalization on Macro-Scale Surfaces.ACS nano · 2025Article
- Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter.Nucleic acids research · 2024Article
- Investigating Protein-Nucleic Acid Binding Interactions with Diethylpyrocarbonate Covalent Labeling-Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Plug-and-play protein biosensors using aptamer-regulated in vitro transcription.Nature communications · 2024Article
- Aptamer-Based DNA Allosteric Switch for Regulation of Protein Activity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Aptamer AS411 interacts with the KRAS promoter/hnRNP A1 complex and shows increased potency against drug-resistant lung cancer.RSC medicinal chemistry · 2024Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- Improving the Biological Properties of Thrombin-Binding Aptamer by Incorporation of 8-Bromo-2'-Deoxyguanosine and 2'-Substituted RNA Analogues.International journal of molecular sciences · 2023Article
43 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The G-quadruplex architecture is a peculiar structure adopted by guanine-rich oligonucleotidic sequences, and, in particular, by several aptamers, including the thrombin-binding aptamer (TBA) that has the highest inhibitory activity against human α-thrombin. A crucial role in determining structure, stability and biological properties of G-quadruplexes is played by ions. In the case of TBA, K(+) ions cause an enhancement of the aptamer clotting inhibitory activity. A detailed picture of the interactions of TBA with the protein and with the ions is still lacking, despite the importance of this aptamer in biomedical field for detection and inhibition of α-thrombin. Here, we fill this gap by presenting a high-resolution crystallographic structural characterization of the thrombin-TBA complex formed in the presence of Na(+) or K(+) and a circular dichroism study of the structural stability of the aptamer both free and complexed with α-thrombin, in the presence of the two ionic species. The results indicate that the different effects exerted by Na(+) and K(+) on the inhibitory activity of TBA are related to a subtle perturbation of a few key interactions at the protein-aptamer interface. The present data, in combination with those previously obtained on the complex between α-thrombin and a modified aptamer, may allow the design of new TBA variants with a pharmacological performance enhancement.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.