1. What is PCR Size Calculation?

PCR (Polymerase Chain Reaction) size calculation determines the length of the DNA fragment amplified between two primers. It is a fundamental parameter in molecular biology experiments and primer design.

2. How Does the Calculator Work?

The calculator uses the PCR size formula:

Where:

• \( Primer2\ Start \) — The starting position of the reverse primer (in base pairs)
• \( Primer1\ End \) — The ending position of the forward primer (in base pairs)

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 calculation is essential for experimental design, gel electrophoresis analysis, product verification, and ensuring proper amplification efficiency.

4. Using the Calculator

Tips: Enter Primer2 Start and Primer1 End positions in base pairs. Both values must be positive integers, and Primer2 Start should be greater than Primer1 End for valid amplification.

5. Frequently Asked Questions (FAQ)

Q1: Why add +1 in the formula?
A: The +1 accounts for inclusive counting of both the end position of Primer1 and the start position of Primer2.

Q2: What are typical PCR product sizes?
A: PCR products typically range from 100-3000 bp, though optimal sizes are usually between 150-1000 bp for efficient amplification.

Q3: Can this calculator be used for any DNA template?
A: Yes, the formula applies to any linear DNA template when primer positions are known relative to a reference sequence.

Q4: What if Primer2 Start is less than Primer1 End?
A: This would result in a negative size, indicating invalid primer design where primers are oriented incorrectly or overlap improperly.

Q5: Does this account for primer lengths?
A: No, this calculation gives the amplified product size between primer binding sites. The actual amplified fragment includes the primer sequences themselves.