1. What is PCR Product Size Calculation?

PCR product size calculation determines the length of the DNA fragment amplified by polymerase chain reaction. It is calculated by subtracting the upstream primer position from the downstream primer position on the DNA template.

2. How Does the Calculator Work?

The calculator uses the simple formula:

Where:

• \( Downstream \) — Position of the downstream primer in base pairs (bp)
• \( Upstream \) — Position of the upstream primer in base pairs (bp)

Explanation: The difference between the two primer positions gives the length of the amplified DNA fragment.

3. Importance of PCR Product Size

Details: Knowing the expected product size is crucial for PCR optimization, gel electrophoresis analysis, and ensuring specific amplification of the target sequence.

4. Using the Calculator

Tips: Enter the positions of both primers in base pairs. Ensure downstream position is greater than upstream position for valid calculation.

5. Frequently Asked Questions (FAQ)

Q1: What if my downstream position is smaller than upstream?
A: This would result in a negative product size, which is not biologically possible. Please check your primer positions.

Q2: Does this calculation account for primer length?
A: No, this calculation only considers the positions of the primers on the template DNA, not the length of the primers themselves.

Q3: What are typical PCR product sizes?
A: PCR products typically range from 100-3000 bp, though this can vary depending on the application and polymerase used.

Q4: Why is accurate product size important?
A: Accurate size prediction helps in gel electrophoresis analysis, cloning strategies, and verifying specific amplification.

Q5: Can I use this for qPCR applications?
A: Yes, the same calculation applies for qPCR, though optimal product sizes for qPCR are typically shorter (80-200 bp).