1. What is PCR Product Length?

PCR product length is the size in base pairs (bp) of the DNA fragment amplified between two primers. It's a fundamental parameter in PCR experiment design, affecting amplification efficiency and downstream applications.

2. How to Calculate PCR Product Length

The calculation is simple:

Where:

• Primer 1 Position — The 5' end position of the forward primer on the template DNA
• Primer 2 Position — The 5' end position of the reverse primer on the template DNA

Note: This calculation assumes standard primers binding to opposite strands. For primers binding to the same strand, the calculation would be different.

3. Importance of PCR Product Length

Details: Optimal PCR product lengths (typically 100-1000 bp) ensure efficient amplification. Shorter products amplify more efficiently but may be harder to visualize, while longer products may have lower yield.

4. Using the Calculator

Tips: Enter the positions of both primers in base pairs (bp). Primer 2 position must be greater than Primer 1 position for a valid product length.

5. Frequently Asked Questions (FAQ)

Q1: What's the ideal PCR product length?
A: Most applications work best with products between 100-1000 bp. For qPCR, 75-200 bp is ideal.

Q2: Does this include primer lengths?
A: No, this calculates the distance between primer binding sites. The actual amplified product will be slightly longer (by the length of the primers themselves).

Q3: What if my primers are on the same strand?
A: Then the product length would be the distance between 3' ends plus the length of both primers.

Q4: How does product length affect PCR conditions?
A: Longer products may require longer extension times and specialized polymerases.

Q5: Can I amplify very long products?
A: Standard PCR typically works up to 5kb. For longer products, consider long-range PCR with specialized enzymes.