ArticleNucleic acids research2015
Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 69 citations in OpenAlex.
- Assessment of salivary microRNA by RT-qPCR: Facing challenges in data interpretation for clinical diagnosis.PloS one · 2024Trial
- Updated guide to RNA quantification by RNA sequencing and reverse transcription-qPCR.Molecules and cells · 2026Article
- Several novel classes of small regulatory RNAs show widespread changes in schizophrenia and bipolar disorder and extensive linkages to critical brain processes.Translational psychiatry · 2026Article
- Complementary Approaches for Accurate Detection of tRNA-Derived Small RNAs (tsRNAs): Small RNA Northern Blotting and Dumbbell PCR.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Quantification of Tissue and Circulating MicroRNAs by Droplet Digital PCR.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Nanopore based RNA methylation profiling of a circulating lung cancer biomarker.Communications medicine · 2025Article
- TaqMan RT-qPCR for tRNA half quantification.Methods in enzymology · 2025Article
- One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs.Biologia futura · 2023Review
- 5'‑isomiR is the most abundant sequence of miR‑1246, a candidate biomarker of lung cancer, in serum.Molecular medicine reports · 2023Article
- Implication of genetic variants in primary microRNA processing sites in the risk of multiple sclerosis.EBioMedicine · 2022Article
- OUHP: an optimized universal hairpin primer system for cost-effective and high-throughput RT-qPCR-based quantification of microRNA (miRNA) expression.Nucleic acids research · 2022Article
- Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery.RNA (New York, N.Y.) · 2021Article
- MicroRNA Isoforms Contribution to Melanoma Pathogenesis.Non-coding RNA · 2021Article
- Transfer RNA Fragments in the Kidney in Hypertension.Hypertension (Dallas, Tex. : 1979) · 2021Article
- The MicroRNA Family Gets Wider: The IsomiRs Classification and Role.Frontiers in cell and developmental biology · 2021Review
- Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry.Theranostics · 2021Review
- Global identification and characterization of tRNA-derived RNA fragment landscapes across human cancers.NAR cancer · 2020Article
- On the expanding roles of tRNA fragments in modulating cell behavior.Nucleic acids research · 2020Review
- tRNA-derived RNA fragments in cancer: current status and future perspectives.Journal of hematology & oncology · 2020Review
- Stumbling on elusive cargo: how isomiRs challenge microRNA detection and quantification, the case of extracellular vesicles.Journal of extracellular vesicles · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Recent advances in next-generation sequencing technologies have revealed that cellular functional RNAs are not always expressed as single entities with fixed terminal sequences but as multiple isoforms bearing complex heterogeneity in both length and terminal sequences, such as isomiRs, the isoforms of microRNAs. Unraveling the biogenesis and biological significance of heterogenetic RNA expression requires distinctive analysis of each RNA variant. Here, we report the development of dumbbell PCR (Db-PCR), an efficient and convenient method to distinctively quantify a specific individual small RNA variant. In Db-PCR, 5'- and 3'-stem-loop adapters are specifically hybridized and ligated to the 5'- and 3'-ends of target RNAs, respectively, by T4 RNA ligase 2 (Rnl2). The resultant ligation products with 'dumbbell-like' structures are subsequently quantified by TaqMan RT-PCR. We confirmed that high specificity of Rnl2 ligation and TaqMan RT-PCR toward target RNAs assured both 5'- and 3'-terminal sequences of target RNAs with single nucleotide resolution so that Db-PCR specifically detected target RNAs but not their corresponding terminal variants. Db-PCR had broad applicability for the quantification of various small RNAs in different cell types, and the results were consistent with those from other quantification method. Therefore, Db-PCR provides a much-needed simple method for analyzing RNA terminal heterogeneity.
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Registered trials
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.