PCR Calculator

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PCR Calculator

PCR Calculator and Optimization Tool

PCR Cycle Calculator

Enter any two variables to calculate the third. Assumes 100% efficiency per cycle. Formula: Final DNA Copies = Initial DNA Copies × 2^Cycles.

Initial DNA Copies	Number of PCR Cycles	DNA Copies after Cycles

PCR Optimization Calculator

Evaluate reagent balance and estimate optimal cycle number based on reaction parameters. See 'About' tab for assumptions.

Reaction Parameters

PCR product length

dNTPs conc. (each)

Total Primers quantity

Taq polymerase quantity

Reaction Conditions

Reaction volume

Elongation time per cycle

min sec

Template quantity

Polymerase speed

Optimization Results:

dNTP vs Primer Balance:

Estimated Limiting Reagent:

Max Theoretical Yield (Mass):

Max Yield Final Concentration:

Taq Synthesis Capacity / Cycle:

Max Product Conc. / Cycle (Taq Limit):

Max Length Supported by Elong. Time:

Est. Cycles to Reach Plateau:

Efficiency Note:

About This Tool

This PCR Calculator is designed to help laboratory technicians optimize PCR reactions and predict outcomes. It combines basic DNA copy calculations with advanced optimization parameters.

Basic Calculator

The basic calculator uses the standard PCR formula:

Final DNA Copies = Initial DNA Copies × 2^{Number of Cycles}

Enter any two variables to calculate the third. Assumes 100% efficiency.

Advanced Optimization Calculator

The advanced calculator helps evaluate critical parameters for optimal PCR reactions, including:

Proportion of nucleotides and primers & limiting reagent prediction
Maximal theoretical yield (mass and concentration)
Estimated number of cycles to reach plateau
Potential limitations from polymerase activity or elongation time

Assumptions & Constants Used

Average molecular weight (MW) of a double-stranded DNA base pair (bp): 650 g/mol (or Da).
Average MW of a single dNTP incorporated: 324.5 g/mol (approximation).
Standard Taq polymerase activity: 1 unit (u) incorporates 10 nmol of total dNTPs in 30 minutes at 72°C. Check your specific enzyme's definition.
Ideal reaction conditions and 100% efficiency during the exponential phase are assumed for cycle estimation. Actual yields may vary.
Calculations do not account for inhibitors, primer-dimers, secondary structures, or polymerase errors affecting real-world efficiency.
dNTPs are assumed to be present in equimolar amounts.

Formulas Used (Simplified)

Nucleotide Limit (Mass): ≈ 1300 × dNTP_Conc[mM] × Vol[µL] [ng]

Primer Limit (Mass): = 650 × Primer_Quant[pmol] × Length[kbp] [ng]

Taq Capacity (Mass/Cycle): ≈ 108 × Taq_Quant[u] × Elong_Time[min] [ng]

Template Mass ↔ Moles: Mass[ng] ≈ Moles[pmol] × Length[kbp] × 650

Optimal Cycles (N): N ≈ log₂(Max_Yield[ng] / Initial_Template[ng])

Note: Tool uses precise conversions internally. These are conceptual representations.