ArticleScientific reports2017
Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
80 citing papers in PubMed.
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- Article
- Histopathological Assessment of IFI6- and RSAD2-DNA Aptamers in Oral Squamous Cell Carcinoma: A Preliminary Study Based onBiomedicines · 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
- Aptamer-Based Delivery of Genes and Drugs Across the Blood-Brain Barrier.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Aptamer Engineering: Strategies for Discovering Functional Nucleic Acids for Next-Generation Diagnostics and Biosensing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Structural Modeling of Protein-DNA Interactions Underlying Genome Copy Number Variation in Nanoviruses.Computational and structural biotechnology journal · 2026Article
- Breaking barriers through driving innovation: sensitivity enhancement strategies for lateral flow assays.Mikrochimica acta · 2025Review
- Designing the Future of Biosensing: Advances in Aptamer Discovery, Computational Modeling, and Diagnostic Applications.Biosensors · 2025Review
- A Novel Aptamer Selection Strategy forMolecules (Basel, Switzerland) · 2025Article
- DNA aptamer AptScientific reports · 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
- Article
- Refinement and Truncation of DNA Aptamers Based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation.Journal of chemical information and modeling · 2025Article
- Engineering aptamer-directed phosphatase recruiting chimeras: a strategy for modulating receptor function and overcoming drug resistance.Nature communications · 2025Article
- Plant-nanoparticles enhance anti-PD-L1 efficacy by shaping human commensal microbiota metabolites.Nature communications · 2025Article
- Exploring precision therapeutics: computational design of antisense oligonucleotides targeting AXL gene transcripts in multiple sclerosis treatment management.Frontiers in chemistry · 2025Article
- Aptamer based immunotherapy: a potential solid tumor therapeutic.Frontiers in immunology · 2025Review
- Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.
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