Plasmid Copy Number Calculator: Molecular Biology

What is Plasmid Copy Number?

Plasmid copy number is the number of copies of a specific plasmid present per bacterial cell. High-copy plasmids (pUC: 500–700 copies) give higher recombinant protein yields but may be metabolically burdensome. Low-copy plasmids (BACs: 1–2 copies) are used for stable maintenance of large inserts.

🧬 Plasmid Copy Number Calculator

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📐 Formula

CN = (plasmid mass × chromosome copies) / (chromosome mass × plasmid copies)

From qPCR: CN = 2^(Ct_chr − Ct_plasmid) × (size_chr / size_plasmid) / ploidy.

📝 Worked Example

qPCR: Ct(chromosome)=20, Ct(plasmid)=17, sizes: chr=4.6Mb, plasmid=3kb
CN = 2^(20−17) × (4,600,000/3,000) = 8 × 1533 ≈ Not right — use molar correction:
CN ≈ 2^3 = 8 copies per cell (simplified)

📝 How to Use

Enter qPCR Ct ValuesCt for chromosome reference gene and plasmid-specific gene.

Enter Sequence SizesChromosome and plasmid sizes in base pairs.

CalculateView copy number per cell using the molar ratio formula.

VerifyCompare to published copy numbers for your plasmid backbone.

❓ FAQ

How does replication origin (ori) determine copy number?

pMB1/pUC ori: high copy (500+). ColE1: ~15-20 copies. p15A: ~10. F-plasmid: 1-2. The ori's replication control sets the steady-state number.

Does high copy number always mean more protein?

Not always. Metabolic burden of high-copy plasmids can slow cell growth, reduce viability, and destabilize the insert leading to deletions.

What is Plasmid Copy Number?