Enter PCR Inputs
This calculator estimates theoretical PCR copy growth, DNA mass, concentration, and target-reaching cycles using a constant-efficiency model.
Example Data Table
| Initial Copies | Cycles | Efficiency | Amplicon Length | Volume | Final Copies | Mass | Cycles to Target |
|---|---|---|---|---|---|---|---|
| 500 | 32 | 90% | 180 bp | 25 µL | 4.1599e+11 | 82.0636 ng | 22.6043 |
This sample uses 500 starting copies, 32 cycles, 90% efficiency, a 180 bp amplicon, and a 25 µL reaction volume.
Formula Used
1. Copy number after n cycles
Final Copies = Initial Copies × (1 + Efficiency)Cycles
2. DNA mass estimate
DNA Mass (g) = Copies × Amplicon Length × 660 ÷ Avogadro’s Number
3. Concentration estimate
Concentration (ng/µL) = Total DNA Mass (ng) ÷ Reaction Volume (µL)
4. Cycles needed for a target
Cycles to Target = ln(Target ÷ Initial) ÷ ln(1 + Efficiency)
These equations represent an idealized exponential phase. Real PCR often deviates because of primer depletion, polymerase limits, inhibitors, nonspecific products, and plateau effects.
How to Use This Calculator
- Enter the starting number of amplifiable DNA copies.
- Set the planned cycle count for the reaction.
- Enter expected amplification efficiency as a percentage.
- Provide the amplicon length in base pairs.
- Add the final reaction volume in microliters.
- Optionally enter a target copy threshold.
- Click the calculate button to view summary metrics.
- Review the graph, cycle table, and export the report as CSV or PDF.
FAQs
1. What does PCR efficiency mean here?
Efficiency describes how much the amplicon increases each cycle. At 100%, DNA doubles every cycle. At 90%, growth is 1.9 times per cycle instead of 2 times.
2. Why are real PCR yields often lower than this estimate?
Real reactions lose efficiency as cycles progress. Primer depletion, enzyme fatigue, inhibitors, secondary structures, and plateau behavior reduce actual yield below the ideal exponential model.
3. Can I use this for qPCR planning?
Yes. The target copy field helps estimate how many cycles may be needed to reach a threshold. It is useful for planning, though it does not replace instrument-derived Ct analysis.
4. Why does amplicon length matter?
Amplicon length does not change copy growth directly, but it affects estimated DNA mass. Longer products weigh more, so identical copy numbers produce higher total mass.
5. Why is the graph logarithmic?
PCR growth spans many orders of magnitude. A logarithmic axis keeps early cycles visible while still showing very large late-cycle copy counts clearly.
6. Does reaction volume change copy number?
No. Volume does not change total copies in this model. It changes concentration outputs, including copies per microliter and estimated ng per microliter.
7. Should I enter molecules, templates, or copies?
Enter the effective number of amplifiable template copies. If you estimate molecules from mass, convert them to copies first for a more meaningful prediction.
8. Is this suitable for endpoint PCR and cloning workflows?
Yes. It is helpful for endpoint PCR planning, cloning preparation, and rough yield checks. Treat results as theoretical guidance rather than guaranteed bench output.