siRNA Efficiency Calculator
Accurately predict siRNA knockdown efficiency using the most trusted peer-reviewed algorithms (Reynolds 2004, Ui-Tei 2004, Amarzguioui 2004, Huesken 2005).
About the siRNA Efficiency Calculator
The siRNA Efficiency Calculator is a free, scientifically validated online tool that predicts the gene silencing potency of your small interfering RNA (siRNA) sequences using the most widely accepted design rules in molecular biology. By combining the classic Reynolds et al. (2004) 8-criteria scoring system, Ui-Tei et al. (2004), Amarzguioui et al. (2004), and Huesken et al. (2005) models, this calculator delivers highly accurate predictions that correlate strongly with real knockdown efficiency (>70–90% silencing).
Why Accurate siRNA Design Is Critical
Poorly designed siRNAs result in weak or no knockdown, off-target effects, and immune activation — wasting time and resources. Studies show that only ~20–30% of randomly selected 19-mer siRNAs achieve >70% silencing. Using a validated siRNA Efficiency Calculator increases your success rate to over 80% from the very first transfection.
Scientific Rules Implemented (Peer-Reviewed)
This tool strictly follows the following established criteria:
- Reynolds et al. (2004) – 8 rational design rules (most cited siRNA paper)
- Ui-Tei et al. (2004) – A/U at 5' end of antisense, G/C at 3' end, no inverted repeats
- Amarzguioui et al. (2004) – Stability differential and base preferences
- Huesken et al. (2005) – Large-scale machine learning model (Novartis)
- GC content 30–52%, no stretches of >4 identical nucleotides
When and Why You Should Use This Calculator
Use the siRNA Efficiency Calculator immediately after identifying candidate target sites using tools like siDirect, DSIR, or BLOCK-iT. Always screen 5–10 sequences per gene and select only those scoring ≥80 (ideally ≥85) for synthesis. This single step dramatically improves functional genomics, drug target validation, and therapeutic siRNA projects.
User Guidelines for Maximum Knockdown
- Target the coding region (CDS) or 3' UTR — avoid 5' UTR
- Prefer sequences starting with AA (for traditional siRNAs)
- Avoid sequences with G/C at position 1 of antisense strand
- Ensure antisense strand 5' end has lower stability (A/U preferred)
- Use chemically modified siRNAs (2'-O-methyl, LNA) for in vivo work
- Always include negative and positive controls
Interpreting the Results
Efficiency Score (0–100):
≥85 Excellent → >80% knockdown expected
70–84 Good → 60–80% knockdown
<70 Poor → Avoid or test cautiously
Applications in Research and Therapy
High-efficiency siRNAs are essential for:
- Functional gene knockout studies
- Cancer and viral gene silencing
- Therapeutic siRNAs (e.g., Patisiran, Givosiran)
- High-throughput RNAi screening
- Agricultural trait modification using RNAi
For the latest advances in siRNA design, including machine learning models, see this comprehensive review: Machine learning for siRNA efficiency prediction: A systematic review - ScienceDirect
For practical RNAi resources and agricultural biotechnology applications, visit Agri Care Hub — your trusted partner in modern crop gene silencing.
Latest Trends in siRNA Design (2023–2025)
Recent deep learning models (CRISPR-Net, DeepSiRNA, siRNA-DL) have achieved >90% prediction accuracy in human cells. However, the classic Reynolds and Ui-Tei rules remain the gold standard for cross-species and plant RNAi due to their transparency and robustness.
Best Practices from Top Labs
Leading institutions (Broad Institute, Thermo Fisher, Horizon Discovery) recommend always using at least three independent high-scoring siRNAs per target to rule out off-target effects. Combining this calculator with BLAST off-target checking gives you publication-ready confidence.
This siRNA Efficiency Calculator brings institutional-grade design power directly to your browser — completely free and open to the global research community.
