ArticleNucleic acids research2024
A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Chemical Modification Strategies for Therapeutic Oligonucleotides: Mechanism Compatibility, Design Trade-Offs, and Translational Barriers.Molecules (Basel, Switzerland) · 2026Review
- The Intrinsic Disordered N-Terminus of Nucleocapsid Protein of SARS-CoV-2 Is Critical in DNA Aptamer Binding.International journal of molecular sciences · 2026Article
- Translational opportunities in aptamer and nanobody lateral flow assays within the WHO REASSURED framework.Sensors & diagnostics · 2026Review
- Aptamer-Based Delivery Systems for VEGF and NGF Modulation in Ocular Therapies.Advanced healthcare materials · 2026Review
- Dual-mode aptamer-driven biosensing platform for ultrasensitive and mutation-resilient detection of the SARS-CoV-2 nucleocapsid protein.Genes & diseases · 2026Article
- Turning on Protein Function Inhibited by DNA Aptamers Employing a Covalent DNA-Binding Protein.ACS nanoscience Au · 2026Article
- Structural basis of DNA aptamer A58 targeting the N-terminal domain of sarbecoviruses nucleocapsid protein.The Journal of biological chemistry · 2026Article
- Mechanism of SARS-CoV-2 resistance to nucleotide analog-based antivirals.Nature communications · 2026Article
- Drugs against broad-spectrum of coronaviruses.Frontiers in immunology · 2026Review
- Structural and catalytic diversity of coronavirus proofreading exoribonuclease.Nature communications · 2025Article
- Green Fluorescent Protein SELEX: Immobilization Chemistry and His-Tag Epitope Bias.Angewandte Chemie (International ed. in English) · 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
- A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.Nature communications · 2024Article
- Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA.Biomolecules · 2024Article
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Authors and funding
9 authors.
Funding
Abstract
SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5'-TCGGAT-3') of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.
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