ArticleProceedings of the National Academy of Sciences of the United States of America2024
Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. 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.
- CompELS vs SELEX: Comparative Aptamer Discovery Integrating Rational Libraries and Enzymatic Elution.ACS nano medicine · 2026Article
- Nucleic acid aptamers: new methods for selection, target validation, molecular diagnostics and therapeutics.Signal transduction and targeted therapy · 2026Review
- Chemical Modification Strategies for Therapeutic Oligonucleotides: Mechanism Compatibility, Design Trade-Offs, and Translational Barriers.Molecules (Basel, Switzerland) · 2026Review
- Dual-mode aptamer-driven biosensing platform for ultrasensitive and mutation-resilient detection of the SARS-CoV-2 nucleocapsid protein.Genes & diseases · 2026Article
- A DNA Origami-Based Cobweb Facilitates Precise and Receptor-Interference Free Modification of Extracellular Vesicle Mimetic for Enhanced Delivery Efficacy.Journal of the American Chemical Society · 2026Article
- De novo design of functional nucleic acids of aptamers.Nature computational science · 2026Article
- DNA-drug conjugates enable logic-gated drug delivery amplified by hybridization chain reactions.Nature biotechnology · 2026Article
- In silico conversion of ssRNA aptamers to ssDNA: molecular dynamics assessment of structural stability and conformational preservation.Journal of computer-aided molecular design · 2026Article
- Chemically modified DNA aptamers and DNAzymes for expanded functional capabilities.Chemical science · 2026Review
- Aptamer-Based Delivery of Genes and Drugs Across the Blood-Brain Barrier.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Aptamers and aptamer-drug conjugates as synthetic immune modulators for cancer immunotherapy.Frontiers in immunology · 2026Review
- Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution.Computational and structural biotechnology journal · 2026Article
- Aptamer-Engineered Ellipsometry for Clinical Detection of BALF-Derived Exosomes: Multi-Level Engineering for Prognostic Evaluation of Immunotherapy Responses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Hierarchical core-shell DNA condensates enable programmable information storage and encryption.Nature communications · 2025Article
- Structural basis and affinity improvement for an ATP-binding DNA aptamer.Proceedings of the National Academy of Sciences of the United States of America · 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
- Aptamer Sequence Optimization and Its Application in Food Safety Analysis.Foods (Basel, Switzerland) · 2025Review
- Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Molecular Programming Design of Glyconucleic Acid Aptamer with High Stability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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7 authors.
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Abstract
DNA aptamers have emerged as novel molecular tools in disease theranostics owing to their high binding affinity and specificity for protein targets, which rely on their ability to fold into distinctive three-dimensional (3D) structures. However, delicate atomic interactions that shape the 3D structures are often ignored when designing and modeling aptamers, leading to inefficient functional optimization. Challenges persist in determining high-resolution aptamer-protein complex structures. Moreover, the experimentally determined 3D structures of DNA molecules with exquisite functions remain scarce. These factors impede our comprehension and optimization of some important DNA aptamers. Here, we performed a streamlined solution NMR-based structural investigation on the 41-nt sgc8c, a prominent DNA aptamer used to target membrane protein tyrosine kinase 7, for cancer theranostics. We show that sgc8c prefolds into an intricate three-way junction (3WJ) structure stabilized by long-range tertiary interactions and extensive base-base stackings. Delineated by NMR chemical shift perturbations, site-directed mutagenesis, and 3D structural information, we identified essential nucleotides constituting the key functional elements of sgc8c that are centralized at the core of 3WJ. Leveraging the well-established structure-function relationship, we efficiently engineered two sgc8c variants by modifying the apical loop and introducing
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