ArticleComputational and structural biotechnology journal2023
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution.Computational and structural biotechnology journal · 2026Article
- Designing the Future of Biosensing: Advances in Aptamer Discovery, Computational Modeling, and Diagnostic Applications.Biosensors · 2025Review
- Using aptamers for targeted delivery of RNA therapies.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Active targeting of type 1 diabetes therapies to pancreatic beta cells using nanocarriers.Diabetologia · 2025Review
- StructRMDB: A database of RNA modification sites that affect RNA secondary structure.Computational and structural biotechnology journal · 2025Article
- Using Computer Modeling and Experimental Methods to Screen for Aptamers That Bind to the VV-GMCSF-LACT Virus.Molecules (Basel, Switzerland) · 2024Article
- Systematic design and evaluation of aptamers for VEGF and PlGF biomarkers of Preeclampsia.BMC biotechnology · 2024Article
- New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers.International journal of molecular sciences · 2024Review
- RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics.ACS synthetic biology · 2024Review
- AptaDB: a comprehensive database integrating aptamer-target interactions.RNA (New York, N.Y.) · 2024Article
- Anti-nucleolin aptamer AS1411: an advancing therapeutic.Frontiers in molecular biosciences · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With advances in force fields and algorithms, robust tools have been developed for molecular simulation of three-dimensional structures of nucleic acids and investigation of aptamer-target interactions. The traditional aptamer discovery technique, Systematic Evolution of Ligands by EXponential enrichment (SELEX), continues to suffer from high investment and low return, while in vitro screening by simulated SELEX remains a challenging task, where more accurate structural modeling and enhanced sampling limit the large-scale application of the method. Here, we proposed a modified aptamer enhanced library design strategy to facilitate the screening of target-binding aptamers. In this strategy, a comprehensive analysis of the original complexes and the target secondary structure were used to construct an enhanced initial library for screening. Our enhanced sequence library design strategy based on the target secondary structure explored a certain sequence space while ensuring the accuracy of the structural conformation and the calculation method. In an enhanced library of only a few dozen sequences, four sequences showed a similar or better binding free energy than the original aptamer, with consistently high binding stability over three rounds of multi-timescale simulations, ranging from - 30.27 to - 32.25 kcal/mol. Consequently, the enhanced library strategy based on the target secondary structure is shown to have very significant potential as a new aptamer design and optimization strategy.
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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.