ArticleACS chemical biology2017
Multiplex Aptamer Discovery through Apta-Seq and Its Application to ATP Aptamers Derived from Human-Genomic SELEX.
Article in ACS chemical biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Discovery of a G-rich ultra stable human ncRNA G-quadruplex that binds ATP.Non-coding RNA research · 2026Article
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- Screening biotoxin aptamer and their application of optical aptasensor in food stuff: a review.Frontiers in chemistry · 2024Review
- Emergence of ATP- and GTP-Binding Aptamers from Single RNA Sequences by Error-Prone Replication and Selection.ChemSystemsChem · 2023Article
- Discovering riboswitches: the past and the future.Trends in biochemical sciences · 2023Review
- Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing.Nucleic acids research · 2021Article
- Hovlinc is a recently evolved class of ribozyme found in human lncRNA.Nature chemical biology · 2021Article
- Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology.International journal of molecular sciences · 2020Review
- Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine.Computational and structural biotechnology journal · 2019Review
- Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
- Single-round isolation of diverse RNA aptamers from a random sequence pool.Biology methods & protocols · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Laboratory-evolved RNAs bind a wide variety of targets and serve highly diverse functions, including as diagnostic and therapeutic aptamers. The majority of aptamers have been identified using in vitro selection (SELEX), a molecular evolution technique based on selecting target-binding RNAs from highly diverse pools through serial rounds of enrichment and amplification. In vitro selection typically yields multiple distinct motifs of highly variable abundance and target-binding affinities. The discovery of new aptamers is often limited by the difficulty of characterizing the selected motifs, because testing of individual sequences tends to be a tedious process. To facilitate the discovery of new aptamers within in vitro selected pools, we developed Apta-Seq, a multiplex analysis based on quantitative, ligand-dependent 2' acylation of solvent-accessible regions of the selected RNA pools, followed by reverse transcription (SHAPE) and deep sequencing. The method reveals, in a single sequencing experiment, the identity, structural features, and target dissociation constants for aptamers present in the selected pool. Application of Apta-Seq to a human genomic pool enriched for ATP-binding RNAs yielded three new aptamers, which together with previously identified human aptamers suggest that ligand-binding RNAs may be common in mammals.
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Registered trials
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