ArticleFrontiers in bioengineering and biotechnology2015
Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device.
Article in Frontiers in bioengineering and biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 66 citations in OpenAlex.
- tRNA modifications in cancer: from molecular mechanisms to clinical translation.Biomarker research · 2026Review
- Review
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Nanopore sequencing of intact aminoacylated tRNAs.Nature communications · 2025Article
- Article
- A robust method for measuring aminoacylation through tRNA-Seq.bioRxiv : the preprint server for biology · 2024Article
- T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition.Bioinformatics (Oxford, England) · 2024Article
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- Transfer RNAs as dynamic and critical regulators of cancer progression.Nature reviews. Cancer · 2023Review
- Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations.Micromachines · 2023Review
- Active learning for efficient analysis of high-throughput nanopore data.Bioinformatics (Oxford, England) · 2023Article
- tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes.Molecular cell · 2022Review
- [Unsupervised deep learning for identifying the OSheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2022Article
- Modification mapping by nanopore sequencing.Frontiers in genetics · 2022Review
- Article
- Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A.Nature communications · 2021Article
- Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing.Nucleic acids research · 2021Article
- Applying genomic and transcriptomic advances to mitochondrial medicine.Nature reviews. Neurology · 2021Review
- Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs.NAR genomics and bioinformatics · 2021Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transfer RNAs (tRNA) are the most common RNA molecules in cells and have critical roles as both translators of the genetic code and regulators of protein synthesis. As such, numerous methods have focused on studying tRNA abundance and regulation, with the most widely used methods being RNA-seq and microarrays. Though revolutionary to transcriptomics, these assays are limited by an inability to encode tRNA modifications in the requisite cDNA. These modifications are abundant in tRNA and critical to their function. Here, we describe proof-of-concept experiments where individual tRNA molecules are examined as linear strands using a biological nanopore. This method utilizes an enzymatically ligated synthetic DNA adapter to concentrate tRNA at the lipid bilayer of the nanopore device and efficiently denature individual tRNA molecules, as they are pulled through the α-hemolysin (α-HL) nanopore. Additionally, the DNA adapter provides a loading site for ϕ29 DNA polymerase (ϕ29 DNAP), which acts as a brake on the translocating tRNA. This increases the dwell time of adapted tRNA in the nanopore, allowing us to identify the region of the nanopore signal that is produced by the translocating tRNA itself. Using adapter-modified Escherichia coli tRNA(fMet) and tRNA(Lys), we show that the nanopore signal during controlled translocation is dependent on the identity of the tRNA. This confirms that adapter-modified tRNA can translocate end-to-end through nanopores and provide the foundation for future work in direct sequencing of individual transfer RNA with a nanopore-based device.
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