ArticleBMC molecular biology2011
The effects of stem length and core placement on shRNA activity.
Article in BMC molecular biology, 2011. 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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Who cites it
27 citing papers in PubMed.
- Nitro Reduction-Based RNA Control and Ultrafast Release.Angewandte Chemie (International ed. in English) · 2026Article
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- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
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- Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase.American journal of physiology. Cell physiology · 2024Article
- Current State of Human Gene Therapy: Approved Products and Vectors.Pharmaceuticals (Basel, Switzerland) · 2023Review
- miR-AB, a miRNA-based shRNA viral toolkit for multicolor-barcoded multiplex RNAi at a single-cell level.EMBO reports · 2022Article
- Article
- Lentivirus expressing shRNAs inhibit the replication of contagious ecthyma virus by targeting DNA polymerase gene.BMC biotechnology · 2020Article
- Efficient Knockdown and Lack of Passenger Strand Activity by Dicer-Independent shRNAs Expressed from Pol II-Driven MicroRNA Scaffolds.Molecular therapy. Nucleic acids · 2019Article
- RNA Interference Therapies for an HIV-1 Functional Cure.Viruses · 2017Review
- Preclinical Evaluation of a Lentiviral Vector for Huntingtin Silencing.Molecular therapy. Methods & clinical development · 2017Article
- Quantitative evaluation of first, second, and third generation hairpin systems reveals the limit of mammalian vector-based RNAi.RNA biology · 2016Article
- Ribozyme-enhanced single-stranded Ago2-processed interfering RNA triggers efficient gene silencing with fewer off-target effects.Nature communications · 2015Article
- Effective inhibition of HIV-1 production by short hairpin RNAs and small interfering RNAs targeting a highly conserved site in HIV-1 Gag RNA is optimized by evaluating alternative length formats.Antimicrobial agents and chemotherapy · 2015Article
- Alleviation of off-target effects from vector-encoded shRNAs via codelivered RNA decoys.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Molecular Properties, Functional Mechanisms, and Applications of Sliced siRNA.Molecular therapy. Nucleic acids · 2015Article
- RNA interference approaches for treatment of HIV-1 infection.Genome medicine · 2015Article
- Toward optimization of AgoshRNA molecules that use a non-canonical RNAi pathway: variations in the top and bottom base pairs.RNA biology · 2015Article
- Designing Ago2-specific siRNA/shRNA to Avoid Competition with Endogenous miRNAs.Molecular therapy. Nucleic acids · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExpressed short hairpin RNAs (shRNA) used in mammalian RNA interference (RNAi) are often designed around a specific short interfering RNA (siRNA) core. Whilst there are algorithms to aid siRNA design, hairpin-specific characteristics such as stem-length and siRNA core placement within the stem are not well defined.
resultsUsing more than 91 hairpins designed against HIV-1 Tat and Vpu, we investigated the influence of both of these factors on suppressive activity, and found that stem length does not correspond with predictable changes in suppressive activity. We also detected multiple processed products for all stem lengths tested. However, the entire length of the hairpin stem was not equally processed into active products. As such, the placement of the siRNA core at the base terminus was critical for activity.
conclusionWe conclude that there is no fixed correlation between stem length and suppressive activity. Instead, core selection and placement likely have a greater influence on the effectiveness of shRNA-based silencing.
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