PCR Product Size Calculation

PCR Product Size Formula:

\[ PS = (EP - SP) + 1 \]

PCR Product Size (PS):

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1. What Is PCR Product Size Calculation?

PCR Product Size Calculation determines the length of the DNA fragment amplified by polymerase chain reaction (PCR). It is calculated using the start and end positions of the primers on the target DNA sequence.

2. How Does The Calculator Work?

The calculator uses the PCR product size formula:

\[ PS = (EP - SP) + 1 \]

Where:

\( PS \) — PCR Product Size (base pairs)
\( EP \) — End Position of the primer
\( SP \) — Start Position of the primer

Explanation: The formula calculates the length of the amplified DNA fragment by subtracting the start position from the end position and adding 1 to include both terminal bases.

3. Importance Of PCR Product Size Calculation

Details: Accurate PCR product size calculation is essential for experimental design, primer validation, gel electrophoresis analysis, and ensuring specific amplification of target DNA sequences.

4. Using The Calculator

Tips: Enter the start position and end position in base pairs. Both values must be positive integers, and 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 between EP and SP?
A: Adding 1 ensures that both the start and end bases are included in the count, providing the correct length of the amplified fragment.

Q2: What are typical PCR product sizes?
A: PCR product sizes typically range from 100-3000 bp, though this can vary based on the application and polymerase used.

Q3: Can this calculator be used for any PCR application?
A: Yes, this calculation applies to standard PCR, qPCR, RT-PCR, and other PCR-based techniques that involve DNA amplification.

Q4: What if my end position is smaller than my start position?
A: The end position must be equal to or greater than the start position. If primers are designed in reverse orientation, their positions should be swapped before calculation.

Q5: How does product size affect PCR efficiency?
A: Smaller products (100-500 bp) generally amplify more efficiently than larger products due to faster extension times and reduced polymerase errors.