1. What is PCR Product Size?

PCR product size refers to the length in base pairs (bp) of the DNA fragment amplified by polymerase chain reaction (PCR). It's calculated as the difference between the end and start positions of the primers plus one.

2. How Does the Calculator Work?

The calculator uses the simple formula:

Where:

• Start Position - The 5' position of the forward primer on the template DNA
• End Position - The 5' position of the reverse primer on the template DNA
• +1 - Accounts for inclusion of both terminal nucleotides

Explanation: The formula calculates the length of DNA that will be amplified between the two primer binding sites.

3. Importance of PCR Product Size

Details: Knowing the expected product size is crucial for PCR design, gel electrophoresis analysis, and downstream applications like cloning or sequencing.

4. Using the Calculator

Tips: Enter the start and end positions in base pairs (bp). The end position must be greater than or equal to the start position.

5. Frequently Asked Questions (FAQ)

Q1: Why add 1 to the difference?
A: The +1 accounts for the fact that both the start and end nucleotides are included in the product.

Q2: What's a typical PCR product size?
A: Most PCR products range from 100-3000 bp, though sizes outside this range are possible with optimized protocols.

Q3: How does product size affect PCR?
A: Larger products require longer extension times and may amplify less efficiently. Very small products (<100 bp) may require special considerations.

Q4: Does this work for qPCR?
A: Yes, the same calculation applies to qPCR products, though qPCR products are typically shorter (80-200 bp).

Q5: What if my primers overlap?
A: If the end position is before the start position (reverse orientation), you'll need to adjust your calculation based on your specific application.