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 determined by the positions of the forward and reverse primers on the template DNA.

2. How Does the Calculator Work?

The calculator uses the PCR product size formula:

Where:

• Reverse Primer Position — The 5' position of the reverse primer on the template DNA
• Forward Primer Position — The 5' position of the forward primer on the template DNA

Explanation: The formula calculates the distance between primer binding sites and adds 1 to account for inclusive counting of both terminal nucleotides.

3. Importance of PCR Product Size

Details: Knowing the expected PCR product size is crucial for designing experiments, selecting appropriate electrophoresis conditions, and verifying successful amplification.

4. Using the Calculator

Tips: Enter primer positions in base pairs (bp). The reverse primer position must be greater than or equal to the forward primer position for valid results.

5. Frequently Asked Questions (FAQ)

Q1: Why add 1 to the difference?
A: The +1 accounts for inclusive counting of both the first and last nucleotides in the amplified fragment.

Q2: What if my reverse primer is before my forward primer?
A: This would indicate incorrect primer orientation. Primers must face each other (forward 5'→3', reverse 3'←5') for successful PCR.

Q3: What are typical PCR product sizes?
A: Most PCR products range from 100-3000 bp, though this depends on the application. qPCR typically uses 50-150 bp products.

Q4: Does this work for genomic DNA and plasmids?
A: Yes, the calculation works for any DNA template as long as you know the exact primer binding positions.

Q5: How does primer length affect product size?
A: Primer length doesn't affect product size calculation, as size is determined by primer binding positions, not primer lengths.