ArticleNucleic acids research2013
High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 63 citations in OpenAlex.
- Aptamers used for biosensors and targeted therapy.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2020Pooled it
- A Branched SELEX Approach Identifies RNA Aptamers That Bind Distinct HIV-1 Capsid Structural Components.ACS infectious diseases · 2024Article
- Post-transcriptional capping generates coenzyme A-linked RNA.RNA biology · 2024Article
- Minimizing amplification bias during reverse transcription for in vitro selections.RNA (New York, N.Y.) · 2023Article
- Target-switch SELEX: Screening with alternating targets to generate aptamers to conserved terminal dipeptides.STAR protocols · 2022Article
- FASTAptameR 2.0: A web tool for combinatorial sequence selections.Molecular therapy. Nucleic acids · 2022Article
- 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
- Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology.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
- AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX.Bioinformatics (Oxford, England) · 2020Article
- Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase.Nucleic acids research · 2020Article
- SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding.Journal of biological engineering · 2020Article
- High-throughput evolution of near-infrared serotonin nanosensors.Science advances · 2019Article
- Rapidly Neutralizable and Highly Anticoagulant Thrombin-Binding DNA Aptamer Discovered by MACE SELEX.Molecular therapy. Nucleic acids · 2019Article
- Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers.Molecular therapy. Nucleic acids · 2018Article
- Time-lapse imaging of molecular evolution by high-throughput sequencing.Nucleic acids research · 2018Article
- Aptamer Bioinformatics.International journal of molecular sciences · 2017Review
- Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15.BMC bioinformatics · 2017Article
- RNA-protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers.Nucleic acids research · 2017Article
- NMR monitoring of the SELEX process to confirm enrichment of structured RNA.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
Systematic evolution of ligands through exponential enrichment (SELEX) is a well-established method for generating nucleic acid populations that are enriched for specified functions. High-throughput sequencing (HTS) enhances the power of comparative sequence analysis to reveal details of how RNAs within these populations recognize their targets. We used HTS analysis to evaluate RNA populations selected to bind type I human immunodeficiency virus reverse transcriptase (RT). The populations are enriched in RNAs of independent lineages that converge on shared motifs and in clusters of RNAs with nearly identical sequences that share common ancestry. Both of these features informed inferences of the secondary structures of enriched RNAs, their minimal structural requirements and their stabilities in RT-aptamer complexes. Monitoring population dynamics in response to increasing selection pressure revealed RNA inhibitors of RT that are more potent than the previously identified pseudoknots. Improved potency was observed for inhibition of both purified RT in enzymatic assays and viral replication in cell-based assays. Structural and functional details of converged motifs that are obscured by simple consensus descriptions are also revealed by the HTS analysis. The approach presented here can readily be generalized for the efficient and systematic post-SELEX development of aptamers for down-stream applications.
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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.