Nanopore microscope identifies RNA isoforms with structural colours
Open accessAbstract
Identifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colours. Structural colours consist of DNA structures, protein labels, native RNA structures or a combination of all three. The sequence of structural colours of RNA identifiers enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. Our Amplification-free RNA TargEt Multiplex Isoform Sensing (ARTEMIS) method reveals structural arrangements in native transcripts in agreement with published variants. ARTEMIS discriminates circular and linear transcript isoforms in a one-step, enzyme-free reaction in a complex human transcriptome using single-molecule read-out.
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Increased storage density beyond binary barcodes can be achieved by creating blocks of repeating structural units that appear as a single protrusion within the nanopore, creating "structural colors" to generate up to 10 data levels.
“Increased storage density beyond binary barcodes can also be achieved by creating blocks of repeating structural units that appear as a single protrusion within the nanopore, which creates “structural colors” to generate up to 10 data levels.130”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [130]
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References 43 · Cited by 57
- Authors
- Bošković, F., & Keyser, U. F.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Keyser, Ulrich Felix
- Venue
- Nature Chemistry
- Published
- 2022-09-19
- Volume
- 14
- Issue
- 11
- Pages
- 1258-1264
- ISSN
- 1755-4330 (ISSN-L)
- 1755-4349
- OpenAlex
- W4296381520
- Cited by
- 57
- References
- 43
- Citations by year
- 2026: 11 · 2025: 14 · 2024: 18 · 2023: 11 · 2022: 3
- FWCI
- 3.34
- Type
- journal article
- Language
- en
- Open access
- Locations
- Nature Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- structural color, single-molecule RNA sequencing, Artemis, transcript quantification, enzyme-free detection, human transcriptome
- MeSH terms
- Color, Humans, Microscopy, RNA, Protein Isoforms, Nanopores, RNA Isoforms
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