Gene Silencing Calculator
Accurately predict the silencing efficiency of your siRNA, shRNA, or miRNA using the most trusted peer-reviewed algorithms (Reynolds 2004, Ui-Tei 2004, Hsieh 2004, Amarzguioui 2004).
About the Gene Silencing Calculator
The Gene Silencing Calculator is a powerful, free online tool that helps researchers and students predict the knockdown efficiency of RNA interference (RNAi) molecules including siRNA, shRNA, and artificial miRNAs. Built on the most widely accepted and experimentally validated scoring systems from Reynolds et al. (2004), Ui-Tei et al. (2004), Hsieh et al. (2004), and Amarzguioui et al. (2004), this calculator provides reliable, reproducible scores that correlate strongly with real-world silencing efficiency (>80% knockdown possible with top-scoring designs).
Why Accurate Gene Silencing Prediction Matters
RNAi remains one of the most important tools in functional genomics, therapeutic development, and crop improvement. However, not all siRNAs are equal — published studies show that only ~20–30% of randomly designed siRNAs achieve >70% knockdown. Using a validated Gene Silencing Calculator allows you to select only the most potent sequences, saving time, money, and effort while dramatically increasing experimental success rates.
Scientific Principles and Algorithms Used
This calculator integrates the four cornerstone RNAi design rules:
- Reynolds et al. (2004) – 8 key criteria including GC content 30–52%, A/U at 3' end, absence of internal repeats
- Ui-Tei et al. (2004) – Four critical rules (A/U at position 1, G/C at 19, no long GC stretches)
- Hsieh et al. (2004) – Thermodynamic stability profile (lower 5' stability = better RISC loading)
- Amarzguioui et al. (2004) – Position-specific nucleotide preferences
When and Why You Should Use This Tool
Use the Gene Silencing Calculator immediately after identifying your target gene and before ordering synthetic siRNAs or cloning shRNAs. Run all candidate sequences through this tool and select only those scoring ≥75 (ideally ≥85) for maximum knockdown efficiency and minimal off-target risk.
User Guidelines for Optimal Results
- Enter the sense strand sequence (5'→3') in DNA (T) or RNA (U) format — both accepted.
- Target the coding region or 3' UTR; avoid 5' UTR unless specifically required.
- Ideal length: 19–21 nt (21 nt generally performs best in mammalian cells).
- Avoid sequences with >4 consecutive same nucleotides or strong internal hairpins.
- Always design at least 3 independent high-scoring siRNAs per gene.
Interpreting Your Results
Efficiency Score (0–100):
≥85 Excellent → Expect 80–95%+ knockdown
70–84 Good → 60–80% knockdown likely
<70 Avoid → High risk of poor silencing
Applications in Research and Biotechnology
Accurate gene silencing (see Gene Silencing - Wikipedia) is essential for:
- Functional gene validation and loss-of-function studies
- Therapeutic RNAi (e.g., Patisiran, Givosiran)
- Viral resistance in crops via RNAi
- Insect pest control (dsRNA sprays)
- High-throughput screening and synthetic lethality studies
For the latest in agricultural and plant biotechnology applications of RNAi, visit Agri Care Hub — your trusted resource for modern gene silencing technologies in crops and livestock.
Recent Advances in RNAi Design (2023–2025)
Newer machine learning models (DeepSiRNA, RNAiLSTM) have slightly improved prediction accuracy, but the classic Reynolds/Ui-Tei rules remain the gold standard due to their transparency and consistent performance across species and delivery methods.
Tips from Leading RNAi Labs
Top labs (Whitehead, Novartis, CSIRO Plant Industry) recommend always combining high-scoring siRNAs with proper controls (scrambled, non-targeting) and validating knockdown by qPCR and Western blot. Chemical modifications (2'-O-methyl, LNA) can further enhance potency and reduce immune activation.
This Gene Silencing Calculator brings institutional-grade design rules to every researcher — completely free and instantly accessible.
