siRNA Design Calculator

Target mRNA Sequence (5' → 3', without UTRs):

Preferred Target Region:

GC Content Preference:

About the siRNA Design Calculator

The siRNA Design Calculator is a scientifically validated, peer-reviewed tool that automatically designs highly effective small interfering RNAs (siRNAs) based on the latest published algorithms (Reynolds et al., 2004; Ui-Tei et al., 2004; Amarzguioui et al.). It follows Thermo Fisher/Ambion and Dharmacon guidelines to maximize silencing efficiency (>80% knockdown) while minimizing off-target effects. Learn more at siRNA Design Calculator. Proudly supported by Agri Care Hub.

Why Proper siRNA Design Matters

Poorly designed siRNAs cause weak or no knockdown, high off-target effects, and immune activation. The siRNA Design Calculator uses eight proven criteria (Reynolds rules) and additional filters (GC content, thermodynamic asymmetry, seed region analysis) to deliver only the top-performing candidates — saving weeks of trial-and-error in the lab.

How to Use the Calculator

Paste your target mRNA sequence (DNA or RNA format accepted)
Choose preferred region (default: any — gives best results)
Select GC range (30–52% is optimal)
Click “Design Optimal siRNAs”

Scientific Rules Applied

Reynolds et al. (2004) 8-point scoring system:

GC content 30–52%
At least 3 A/U at positions 15–19 (sense strand)
No internal repeats or hairpins
A at position 19, A at position 3
U at position 10
No G/C at position 19
No G at position 13

Output Includes

Top 3–5 high-scoring siRNAs
Sense & antisense sequences
Target position
Efficiency score (0–10)
GC content & thermodynamic stability

Applications

Gene knockdown studies
Functional genomics
Therapeutic siRNA development
Plant & agricultural RNAi
Teaching molecular biology

Best Practices

Always validate top candidates experimentally. Use at least two independent siRNAs per gene. BLAST sequences to check specificity.

Conclusion

The siRNA Design Calculator brings gold-standard RNAi design to your browser — free, fast, and fully compliant with published guidelines. Design better siRNAs in seconds.

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