ArticleMolecular therapy. Nucleic acids2021
Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12.
Article in Molecular therapy. Nucleic acids, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Aptamer-based DNA nanoswitches for multiplexed protein detection.Chemical communications (Cambridge, England) · 2026Article
- Article
- Aptamer-based DNA nanoswitches for multiplexed protein detection.bioRxiv : the preprint server for biology · 2026Article
- Chemically modified DNA aptamers and DNAzymes for expanded functional capabilities.Chemical science · 2026Review
- Designing nucleic acid-based therapeutics for cancer treatment: Updates on the state of the art.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Review
- Thymidine-Inosine Dimer Building Block for Reversible Modification of Synthetic Oligonucleotides.Molecules (Basel, Switzerland) · 2025Article
- Controlled Sensing of User-Defined Aptamer-Based Targets Using Scanning Ionic Conductance Spectroscopy.ACS nano · 2025Article
- Recent advances in aptamer discovery, modification and improving performance.Biochemistry and biophysics reports · 2024Review
- 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
- Unique quinoline orientations shape the modified aptamer to sclerostin for enhanced binding affinity and bone anabolic potential.Molecular therapy. Nucleic acids · 2024Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.Nucleic acids research · 2023Article
- The Regioselective Conjugation of the 15-nt Thrombin Aptamer with an Optimized Tripeptide Sequence Greatly Increases the Anticoagulant Activity of the Aptamer.Pharmaceutics · 2023Article
- Chemically modified aptamers for improving binding affinity to the target proteinsFrontiers in cell and developmental biology · 2023Review
- A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers.Molecular therapy. Nucleic acids · 2022Article
- Solution structure of a thrombin binding aptamer complex with a non-planar platinum(ii) compound.Chemical science · 2022Article
- Anticoagulant Oligonucleotide-Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics.International journal of molecular sciences · 2022Article
- Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.International journal of molecular sciences · 2021Review
- Structural Biology for the Molecular Insight between Aptamers and Target Proteins.International journal of molecular sciences · 2021Review
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5 authors.
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Abstract
Post-SELEX modification of DNA aptamers is an established strategy to improve their affinity or inhibitory characteristics. In this study, we examined the possibility of increasing the recognition interface between the thrombin-binding aptamer HD1 (TBA) and thrombin by adding a chemically modified side chain to selected nucleotide residues. A panel of 22 TBA variants with N3-modified residues T3 and T12 was prepared by a two-step modification procedure. Aptamers were characterized by a combination of biophysical and biochemical methods. We identified mutants with enhanced affinity and improved anticoagulant activity. The crystal structures of thrombin complexes with three selected modified variants revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. The modifications induced an increase in the contact areas between thrombin and the modified TBAs. Comparative analysis of the structural, biochemical, and biophysical data suggests that the non-equivalent binding modes of the mutants with thrombin in the T3- and T12-modified series account for the observed systematic differences in their affinity characteristics. In this study, we show that extending the recognition surface between the protein and modified aptamers is a promising approach that may improve characteristics of aptamer ligands.
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