ArticleNucleic acids research2017
Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 47 citations in OpenAlex.
- Non-enzymatic conversion of RNA sequence information into DNA by squaramide ligation for accurate RNA quantification.Communications chemistry · 2026Article
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- Co-mapping clonal and transcriptional heterogeneity in somatic evolution via GoT-Multi.Cell genomics · 2026Article
- Co-allosteric hairpin probe for detecting microRNA with high specificity.RSC advances · 2025Article
- Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq).Nucleic acids research · 2025Article
- A platform for multimodalbioRxiv : the preprint server for biology · 2025Article
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- Advances in Genotyping Detection of Fragmented Nucleic Acids.Biosensors · 2024Review
- Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.Nature biomedical engineering · 2024Article
- Quantification of tRNA mRNA (New York, N.Y.) · 2024Article
- Multiplex Detection of RNA Viruses Based on Ligation Reaction and Universal PCR Amplification.Current microbiology · 2024Article
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- An instrument-free, programmable approach for nucleic acid detection.Nature biomedical engineering · 2023Article
- Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.Nature biomedical engineering · 2023Article
- RT-IVT method allows multiplex real-time quantification of in vitro transcriptional mRNA production.Communications biology · 2023Article
- Quantitative analysis of miRNAs using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER)-qPCR.Molecular therapy. Nucleic acids · 2023Article
- Giant Viruses as a Source of Novel Enzymes for Biotechnological Application.Pathogens (Basel, Switzerland) · 2022Review
- Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.Scientific reports · 2022Article
- Functional Genomic Analyses Reveal an Open Pan-genome for the Chloroviruses and a Potential for Genetic Innovation in New Isolates.Journal of virology · 2022Article
- Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.Accounts of chemical research · 2021Review
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ligation-based nucleic acid detection methods are primarily limited to DNA, since they exhibit poor performance on RNA. This is attributed to reduced end-joining efficiency and/or fidelity of ligases. Interestingly, chlorella virus DNA ligase (PBCV-1 DNA ligase) has recently been shown to possess high RNA-templated DNA end-joining activity; however, its fidelity has not yet been systematically evaluated. Herein, we characterized PBCV-1 ligase for its RNA-templated end-joining fidelity at single base mismatches in 3' and 5' DNA probe termini and found an overall limited end-joining fidelity. To improve the specificity in PBCV-1 ligase-driven RNA detection assays, we utilized structure-specific 5' exonucleolytic activity of Thermus aquaticus DNA polymerase, used in the invader assay. In the iLock (invader padLock) probe assay, padlock probe molecules are activated prior ligation thus the base at the probe ligation junction is read twice in order to aid successful DNA ligation: first, during structure-specific invader cleavage and then during sequence-specific DNA ligation. We report two distinct iLock probe activation mechanisms and systematically evaluate the assay specificity, including single nucleotide polymorphisms on RNA, mRNA and miRNA. We show significant increase in PBCV-1 ligation fidelity in the iLock probe assay configuration for RNA detection.
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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.