ArticleNucleic acids research2020
Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.Current opinion in structural biology · 2025Review
- Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.Biophysical reviews · 2024Review
- Fluorescence, Circular Dichroism and Mass Spectrometry as Tools to Study Virus Structure.Sub-cellular biochemistry · 2024Review
- Design and Prediction of Aptamers Assisted by In Silico Methods.Biomedicines · 2023Review
- Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?Nano today · 2022Article
- Aptamers-Diagnostic and Therapeutic Solution in SARS-CoV-2.International journal of molecular sciences · 2022Review
- A Defective Viral Particle Approach to COVID-19.Cells · 2022Review
- Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.The journal of physical chemistry. B · 2021Article
- Aptamer based surface plasma resonance assay for direct detection of neuron specific enolase and progastrin-releasing peptide (31-98).RSC advances · 2021Article
- Aptamers for Anti-Viral Therapeutics and Diagnostics.International journal of molecular sciences · 2021Review
- Artificial Intelligence in Aptamer-Target Binding Prediction.International journal of molecular sciences · 2021Review
- Mass Spectrometry-Based Structural Virology.Analytical chemistry · 2021Review
- Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases.Frontiers in bioengineering and biotechnology · 2021Review
- Review
- Extended Interactions between HIV-1 Viral RNA and tRNAInternational journal of molecular sciences · 2020Article
- Methods and Applications of In Silico Aptamer Design and Modeling.International journal of molecular sciences · 2020Review
- 2'-fluoro-modified pyrimidines enhance affinity of RNA oligonucleotides to HIV-1 reverse transcriptase.RNA (New York, N.Y.) · 2020Article
- Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer.Current research in structural biology · 2020Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
Abstract
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit RT in enzymatic and viral replication assays. Some aptamers inhibit RT from only a few viral clades, while others show broad-spectrum inhibition. Biophysical determinants of recognition specificity are poorly understood. We investigated the interface between HIV-1 RT and a broad-spectrum UCAA-family aptamer. SAR and hydroxyl radical probing identified aptamer structural elements critical for inhibition and established the role of signature UCAA bulge motif in RT-aptamer interaction. HDX footprinting on RT ± aptamer shows strong contacts with both subunits, especially near the C-terminus of p51. Alanine scanning revealed decreased inhibition by the aptamer for mutants P420A, L422A and K424A. 2D proton nuclear magnetic resonance and SAXS data provided constraints on the solution structure of the aptamer and enable computational modeling of the docked complex with RT. Surprisingly, the aptamer enhanced proteolytic cleavage of precursor p66/p66 by HIV-1 protease, suggesting that it stabilizes the productive conformation to allow maturation. These results illuminate features at the RT-aptamer interface that govern recognition specificity by a broad-spectrum antiviral aptamer, and they open new possibilities for accelerating RT maturation and interfering with viral replication.
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Registered trials
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.