1. What Is Expected PCR Size Calculation?

Expected PCR size calculation determines the length of the DNA fragment that will be amplified during polymerase chain reaction (PCR) based on the positions of the forward and reverse primers on the template DNA.

2. How Does The Calculator Work?

The calculator uses the PCR size formula:

Where:

• \( Primer2\ Start \) — Starting position of the reverse primer (bp)
• \( Primer1\ End \) — Ending position of the forward primer (bp)

Explanation: The formula calculates the distance between the end of the forward primer and the start of the reverse primer, adding 1 to include both terminal bases.

3. Importance Of PCR Size Calculation

Details: Accurate PCR size prediction is essential for experimental design, gel electrophoresis analysis, product verification, and ensuring amplification of the correct target fragment.

4. Using The Calculator

Tips: Enter primer positions in base pairs (bp). Both values must be non-negative integers, and Primer2 Start should be greater than Primer1 End for a valid positive size.

5. Frequently Asked Questions (FAQ)

Q1: Why add +1 in the formula?
A: The +1 accounts for inclusive counting of both the start and end positions in the amplified fragment.

Q2: What if the calculated size is negative?
A: A negative size indicates invalid primer positions where the reverse primer starts before the forward primer ends, which is not feasible for PCR amplification.

Q3: How accurate is this calculation?
A: This provides the theoretical minimum size. Actual PCR product size may be slightly larger due to primer overhangs or specific experimental conditions.

Q4: Does this work for all types of PCR?
A: This formula works for standard PCR. Specialized PCR methods like overlap extension PCR may require different calculations.

Q5: How do I determine primer positions?
A: Primer positions are typically determined using sequence analysis software that maps primers to the target DNA template.