ArticleBiophysics and physicobiology2019
Prediction of the secondary structure of short DNA aptamers.
Article in Biophysics and physicobiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Test Strips Based on Gated Nanoporous Anodic Alumina for the Rapid and Accurate Detection ofAnalytical chemistry · 2026Article
- Cell SELEX-based DNA aptamer selection targetingVeterinary research forum : an international quarterly journal · 2026Article
- Rapid detection of herpes simplex virus types 1 and 2 using a G-quadruplex aptamer-based biosensor.Virology journal · 2025Article
- Designing the Future of Biosensing: Advances in Aptamer Discovery, Computational Modeling, and Diagnostic Applications.Biosensors · 2025Review
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- Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management.JACC. Basic to translational science · 2024Review
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- Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools.BMC bioinformatics · 2023Article
- One Single Tube Reaction of Aptasensor-Based Magnetic Sensing System for Selective Fluorescent Detection of VEGF in Plasma.Biosensors · 2023Article
- A massively parallel screening platform for converting aptamers into molecular switches.Nature communications · 2023Article
- G4Boost: a machine learning-based tool for quadruplex identification and stability prediction.BMC bioinformatics · 2022Article
- In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein.International journal of molecular sciences · 2022Article
- Optimization of Short RNA Aptamers for TNBC Cell Targeting.International journal of molecular sciences · 2022Article
- A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers.PLoS computational biology · 2021Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Aptamers have a spectrum of applications in biotechnology and drug design, because of the relative simplicity of experimental protocols and advantages of stability and specificity associated with their structural properties. However, to understand the structure-function relationships of aptamers, robust structure modeling tools are necessary. Several such tools have been developed and extensively tested, although most of them target various forms of biological RNA. In this study, we tested the performance of three tools in application to DNA aptamers, since DNA aptamers are the focus of many studies, particularly in drug discovery. We demonstrated that in most cases, the secondary structure of DNA can be reconstructed with acceptable accuracy by at least one of the three tools tested (Mfold, RNAfold, and CentroidFold), although the G-quadruplex motif found in many of the DNA aptamer structures complicates the prediction, as well as the pseudoknot interaction. This problem should be addressed more carefully to improve prediction accuracy.
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