Algorithmic Primer Design

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  Main UI

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  Generated DNA sequence

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  More DNA sequence

• Automatic Primer Design: Generates forward and reverse primers based on DNA sequence, mutation position, and desired amino acid
• Constraint Validation: Ensures primers meet all requirements:
• GC content: 50-70%
• Melting temperature (T_m): 60-70°C
• T_m difference between primers: ≤2°C
• Tail length: 15-25 bp on each side of mutation
• G/C clamps: At least 2 at each end
• User-Friendly Interface: Clean, modern web interface with real-time validation
• Detailed Results: Shows primer sequences, properties, and validation status

Usage

1. Enter DNA Sequence: Paste your DNA sequence (A, T, C, G only)
2. Specify Mutation Position: Enter the 1-based position of the amino acid you want to mutate
3. Select New Amino Acid: Choose the desired amino acid from the dropdown
4. Design Primers: Click "Design Primers" to generate forward and reverse primers
5. Review Results: Check the primer sequences, properties, and validation status

Technical Details

Primer Design Algorithm

The algorithm:

1. Converts the amino acid to its most common codon
2. Identifies the mutation position in the DNA sequence
3. Generates forward primer with upstream tail + mutation codon
4. Generates reverse primer (reverse complement) with downstream tail
5. Adjusts primer lengths to match T_m within tolerance
6. Validates all constraints (GC%, T_m, G/C clamps, tail length)

T_m Calculation

Uses a simplified formula:

$$T_m = 64.9 + 41 * (G + C - 16.4) / (A + T + G + C)$$

G/C Clamp Detection

Checks the last 3 nucleotides at each end for G or C bases, ensuring at least 2 are present.

Technologies

• Next.js
• TypeScript
• Tailwind CSS
• React

License

MIT

Built With

• claude
• cursor
• nextjs