ArticlePloS one2023
The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- EWS-RNA Binding Protein 1: Structural Insights into Ewing Sarcoma by Conformational Dynamics Investigations.Current cancer drug targets · 2026Article
- Influence of contact map topology on RNA structure prediction.Nucleic acids research · 2025Article
- Designing the Future of Biosensing: Advances in Aptamer Discovery, Computational Modeling, and Diagnostic Applications.Biosensors · 2025Review
- Systematic design and evaluation of aptamers for VEGF and PlGF biomarkers of Preeclampsia.BMC biotechnology · 2024Article
- Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aptamers are single-stranded DNA or RNA that bind to specific targets such as proteins, thus having similar characteristics to antibodies. It can be synthesized at a lower cost, with no batch-to-batch variations, and is easier to modify chemically than antibodies, thus potentially being used as therapeutic and biosensing agents. The current method for RNA aptamer identification in vitro uses the SELEX method, which is considered inefficient due to its complex process. Computational models of aptamers have been used to predict and study the molecular interaction of modified aptamers to improve affinity. In this study, we generated three-dimensional models of five RNA aptamers from their sequence using mFold, RNAComposer web server, and molecular dynamics simulation. The model structures were then evaluated and compared with the experimentally determined structures. This study showed that the combination of mFold, RNAComposer, and molecular dynamics simulation could generate 14-16, 28, or 29 nucleotides length of 3D RNA aptamer with similar geometry and topology to the experimentally determined structures. The non-canonical basepair structure of the aptamer loop was formed through the MD simulation, which also improved the three-dimensional RNA aptamers model. Clustering analysis was recommended to choose the more representative model.
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