ArticleRNA (New York, N.Y.)2019
Chimeric padlock and iLock probes for increased efficiency of targeted RNA detection.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Microfluidic toolbox using padlock probes and rolling circle amplification for direct detection and genotyping of viral RNA.RSC advances · 2026Article
- Establishment of a Padlock Probe-Based Fluorescence Quantitative PCR Method for the Detection of the SARS-CoV-2 Omicron S371L Mutation.Journal of fluorescence · 2026Article
- Probing neuropsychiatric disorders through in vivo CRISPR screening.Current opinion in genetics & development · 2026Review
- Article
- Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.Development (Cambridge, England) · 2024Article
- Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.Nature biomedical engineering · 2024Article
- Mapping cancer biology in space: applications and perspectives on spatial omics for oncology.Molecular cancer · 2024Review
- The use of RNA-based treatments in the field of cancer immunotherapy.Molecular cancer · 2023Review
- Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.Scientific reports · 2022Article
- Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.Accounts of chemical research · 2021Review
- Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets.Russian journal of bioorganic chemistry · 2021Article
- SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution.PLoS biology · 2020Article
- Squaramides and Ureas: A Flexible Approach to Polymerase-Compatible Nucleic Acid Assembly.Angewandte Chemie (International ed. in English) · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many approaches exist to detect RNA using complementary oligonucleotides. DNA ligation-based techniques can improve discrimination of subtle sequence variations, but they have been difficult to implement for direct RNA analysis due to the infidelity and inefficiency of most DNA ligases on RNA. In this report, we have systematically studied if ribonucleotide substitutions in padlock probes can provide higher catalytic efficiencies for Chlorella virus DNA ligase (PBCV-1 DNA ligase) and T4 RNA ligase 2 (T4Rnl2) on RNA. We provide broad characterization of end-joining fidelity for both enzymes in RNA-templated 3'-OH RNA/5'-pDNA chimeric probe ligation. Both ligases showed increased ligation efficiency toward chimeric substrates on RNA. However, end-joining fidelity of PBCV-1 DNA ligase remained poor, while T4Rnl2 showed a somewhat better end-joining fidelity compared to PBCV-1 DNA ligase. The recently presented invader padlock (iLock) probes overcome the poor end-joining fidelity of PBCV-1 DNA ligase by the requirement of target-dependent 5' flap removal prior to ligation. Here we show that two particular ribonucleotide substitutions greatly improve the activation and ligation rate of chimeric iLock probes on RNA. We characterized the end-joining efficiency and fidelity of PBCV-1 DNA ligase and T4Rnl2 with chimeric iLock probes on RNA and found that both enzymes exhibit high ligation fidelities for single nucleotide polymorphisms on RNA. Finally, we applied the chimeric probe concept to directly differentiate between human and mouse
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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.