ArticleNucleic acids research2016
Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 75 citations in OpenAlex.
- Assembly of Protein-DNA Framework Nanostructures: Structurally Defining Protein-DNA Interfaces With Aptamer.Angewandte Chemie (International ed. in English) · 2026Article
- Article
- Structural insights into the binding of CX-5461 and MTR-106 to G-quadruplex DNA.Nucleic acids research · 2026Article
- Topological rules and anomalies in intramolecular G-quadruplex folding: a comprehensive study.Nucleic acids research · 2026Article
- Turning on Protein Function Inhibited by DNA Aptamers Employing a Covalent DNA-Binding Protein.ACS nanoscience Au · 2026Article
- High-Affinity Six-Letter DNA XenoAptamer Generation by Genetic Alphabet Expansion.Journal of the American Chemical Society · 2026Article
- A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins.Bioinformatics (Oxford, England) · 2026Article
- 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
- Scaffolding Light-Up Aptamers on DNA Nanostructures for Fluorescence Enhancement.ACS biomaterials science & engineering · 2025Article
- Decoding aptamer-protein binding kinetics for continuous biosensing using single-molecule techniques.Science advances · 2025Article
- Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus.Nucleic acids research · 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
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- TBA for Sensing Toxic Cations: A Critical Analysis of Structural and Electrical Properties.International journal of molecular sciences · 2023Article
- Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.Nucleic acids research · 2023Article
- A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers.Molecular therapy. Nucleic acids · 2022Article
- High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.Nucleic acids research · 2022Article
- Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Enhancement of the Immunostimulatory Effect of Phosphodiester CpG Oligodeoxynucleotides by an Antiparallel Guanine-Quadruplex Structural Scaffold.Biomolecules · 2021Article
- Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.International journal of molecular sciences · 2021Review
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mixed duplex/quadruplex oligonucleotides have attracted great interest as therapeutic targets as well as effective biomedical aptamers. In the case of thrombin-binding aptamer (TBA), the addition of a duplex motif to the G-quadruplex module improves the aptamer resistance to biodegradation and the affinity for thrombin. In particular, the mixed oligonucleotide RE31 is significantly more effective than TBA in anticoagulation experiments and shows a slower disappearance rate in human plasma and blood. In the crystal structure of the complex with thrombin, RE31 adopts an elongated structure in which the duplex and quadruplex regions are perfectly stacked on top of each other, firmly connected by a well-structured junction. The lock-and-key shape complementarity between the TT loops of the G-quadruplex and the protein exosite I gives rise to the basic interaction that stabilizes the complex. However, our data suggest that the duplex motif may have an active role in determining the greater anti-thrombin activity in biological fluids with respect to TBA. This work gives new information on mixed oligonucleotides and highlights the importance of structural data on duplex/quadruplex junctions, which appear to be varied, unpredictable, and fundamental in determining the aptamer functional properties.
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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.