ArticleRNA (New York, N.Y.)2018
miPrimer: an empirical-based qPCR primer design method for small noncoding microRNA.
Article in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Non-coding RNA profiles associated with equine osteoarthritis: a systematic review.Frontiers in veterinary science · 2026Pooled it
- Application of RNA markers in forensic body fluid analysis: from specificity and stability to polymorphism.International journal of legal medicine · 2026Review
- MicroRNA Profiling as a Novel Predictive Tool for Operational Tolerance in Pediatric Liver Transplantation: A Single-center Study.Transplantation direct · 2026Article
- Analyzing qPCR data: Better practices to facilitate rigor and reproducibility.Biochemistry and biophysics reports · 2025Article
- Development of a Novel Endometrial Signature Based on Endometrial microRNA for Determining the Optimal Timing for Embryo Transfer.Biomedicines · 2024Article
- Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer.Scientific reports · 2021Article
- TRPM7 Induces Mechanistic Target of Rap1b Through the Downregulation of miR-28-5p in Glioma Proliferation and Invasion.Frontiers in oncology · 2019Article
- A Novel Multi-Gene Detection Platform for the Analysis of miRNA Expression.Scientific reports · 2018Article
- Evaluation of digital real-time PCR assay as a molecular diagnostic tool for single-cell analysis.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are 18-25 nucleotides (nt) of highly conserved, noncoding RNAs involved in gene regulation. Because of miRNAs' short length, the design of miRNA primers for PCR amplification remains a significant challenge. Adding to the challenge are miRNAs similar in sequence and miRNA family members that often only differ in sequences by 1 nt. Here, we describe a novel empirical-based method, miPrimer, which greatly reduces primer dimerization and increases primer specificity by factoring various intrinsic primer properties and employing four primer design strategies. The resulting primer pairs displayed an acceptable qPCR efficiency of between 90% and 110%. When tested on miRNA families, miPrimer-designed primers are capable of discriminating among members of miRNA families, as validated by qPCR assays using Quark Biosciences' platform. Of the 120 miRNA primer pairs tested, 95.6% and 93.3% were successful in amplifying specifically non-family and family miRNA members, respectively, after only one design trial. In summary, miPrimer provides a cost-effective and valuable tool for designing miRNA primers.
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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.