ArticleRNA (New York, N.Y.)2017
Efficient in situ detection of mRNAs using the Chlorella virus DNA ligase for padlock probe ligation.
Article in RNA (New York, N.Y.), 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, 27 citations in OpenAlex.
- Spatial tissue analysis of secondary sarcoma following CAR T cell therapy for B cell lymphoma.iScience · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.Nature biomedical engineering · 2023Article
- An instrument-free, programmable approach for nucleic acid detection.Nature biomedical engineering · 2023Article
- ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ.Nature methods · 2022Article
- Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.Nucleic acids research · 2021Article
- Visualization of Gene Reciprocity among Lactic Acid Bacteria in Yogurt by RNase H-Assisted Rolling Circle Amplification-FluorescenceMicroorganisms · 2021Article
- Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.Science (New York, N.Y.) · 2021Article
- SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution.PLoS biology · 2020Article
- Label-free detection of microRNA: two-stage signal enhancement with hairpin assisted cascade isothermal amplification and light-up DNA-silver nanoclusters.Mikrochimica acta · 2020Article
- Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues.RNA (New York, N.Y.) · 2019Article
- RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection.Scientific reports · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Padlock probes are single-stranded DNA molecules that are circularized upon hybridization to their target sequence by a DNA ligase. In the following, the circulated padlock probes are amplified and detected with fluorescently labeled probes complementary to the amplification product. The hallmark of padlock probe assays is a high detection specificity gained by the ligation reaction. Concomitantly, the ligation reaction is the largest drawback for a quantitative in situ detection of mRNAs due to the low affinities of common DNA or RNA ligases to RNA-DNA duplex strands. Therefore, current protocols require that mRNAs be reverse transcribed to DNA before detection with padlock probes. Recently, it was found that the DNA ligase from Paramecium bursaria Chlorella virus 1 (PBCV-1) is able to efficiently ligate RNA-splinted DNA. Hence, we designed a padlock probe assay for direct in situ detection of mRNAs using the PBCV-1 DNA ligase. Experimental single-cell data were used to optimize and characterize the efficiency of mRNA detection with padlock probes. Our results demonstrate that the PBCV-1 DNA ligase overcomes the efficiency limitation of current protocols for direct in situ mRNA detection, making the PBCV-1 DNA ligase an attractive tool to simplify in situ ligation sequencing applications.
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