ArticlePloS one2022
Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- A framework for the development and validation of an aptamer-based assay for pathogen detection using SARS-CoV-2 as a model.Scientific reports · 2026Article
- In Silico Study of Anti-CD40 DNA Aptamers as Vaccine Adjuvants for Chickens.International journal of molecular sciences · 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-linked immobilized sorbent assay for detection of VP1 of foot and mouth disease virus serotype O.Scientific reports · 2026Article
- Chemically modified DNA aptamers and DNAzymes for expanded functional capabilities.Chemical science · 2026Review
- Aptamers as target-specific recognition elements in drug delivery.Advanced drug delivery reviews · 2025Review
- Deciphering aptamer-protein interactions for bovine sperm sorting through in silico and in vitro studies.Molecular biology reports · 2025Article
- Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern.Frontiers in microbiology · 2025Article
- Deciphering the regulatory role of ELF5 in buffalo lactation.Frontiers in veterinary science · 2025Article
- On-site sensing for aflatoxicosis poisoning via ultraviolet excitable aptasensor based on fluorinated ethylene propylene strip: a promising forensic tool.Scientific reports · 2024Article
- Nucleic acid-based wearable and implantable electrochemical sensors.Chemical Society reviews · 2024Review
- Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals.Pathogens (Basel, Switzerland) · 2024Review
- MultiplexedNucleic acid therapeutics · 2024Article
- DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications.Frontiers in bioengineering and biotechnology · 2024Article
- Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods.Biosensors · 2023Review
- In Silico Approaches for the Identification of Aptamer Binding Interactions toTropical medicine and infectious disease · 2023Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aptamers are single-stranded oligonucleotides, formerly evolved by Systematic Evolution of Ligands by EXponential enrichment (SELEX), that fold into functional three-dimensional structures. Such conformation is crucial for aptamers' ability to bind to a target with high affinity and specificity. Unnatural nucleotides have been used to develop nucleic acid mimic (NAM) aptamers with increased performance, such as biological stability. Prior knowledge of aptamer-target interactions is critical for applying post-SELEX modifications with unnatural nucleotides since it can affect aptamers' structure and performance. Here, we describe an easy-to-apply in silico workflow using free available software / web servers to predict the tertiary conformation of NAM, DNA and RNA aptamers, as well as the docking with the target molecule. Representative 2'-O-methyl (2'OMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. All aptamers' tertiary structure and docking models were successfully predicted with good structural similarity to the experimental data. Thus, this workflow will boost the development of aptamers, particularly NAM aptamers, by assisting in the rational modification of specific nucleotides and avoiding trial-and-error approaches.
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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.