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Plasmid & Selectable Marker Explorer

Build and explore circular plasmid maps for common cloning and expression vectors. Toggle restriction enzyme cut sites, test selectable marker outcomes, and calculate transformation efficiency with an interactive visual editor.

Plasmid MappUC19 (2,686 bp)

2,686 bpori (ColE1)ampRampR promoterlacZαlac promoterMCS

Plasmid Presets

High-copy cloning vector with ampicillin resistance and blue-white screening (lacZα).

Restriction Enzymes

Selectable Markers

Inhibits cell wall synthesis by blocking transpeptidase (PBP)

Gene Insert

Transformation Efficiency

Colony count150
DNA amount0.050 μg
Dilution factor10 ×
Plated volume0.10 mL
Total volume1.0 mL

Transformation Efficiency

Efficiency=colonies×vol. correction×dilutionμg DNA\mathrm{Efficiency} = \frac{\text{colonies} \times \text{vol. correction} \times \text{dilution}}{\mu\mathrm{g\,DNA}}
=150×10.1×100.05=300,000  transformants/μg= \frac{150 \times \frac{1}{0.1} \times 10}{0.05} = 300,000\;\text{transformants/}\mu\text{g}
Efficiency
300,000 /μg
Total transformants
15,000
Moderate efficiency. Typical chemical transformation yields 10⁶ to 10⁸ transformants/μg. Electroporation can achieve 10⁹ to 10¹⁰.

Selection Outcome

Transformed cells
Survive
Non-transformed cells
Killed
Bacteria that took up the plasmid express the ampR gene, making them resistant to ampicillin. Non-transformed cells lack this gene and are killed by the antibiotic. Only transformants form colonies.
Resistance gene: ampR

Restriction Fragments

Uncut plasmid: 2,686 bp (circular)

Reference Guide

Plasmid Structure

A plasmid is a small, circular, double-stranded DNA molecule found naturally in bacteria. Engineered plasmids serve as vectors to carry foreign genes into host cells.

Every functional cloning vector needs at minimum an origin of replication (ori) for autonomous replication, a selectable marker (usually an antibiotic resistance gene), and a multiple cloning site (MCS) where foreign DNA can be inserted.

Selectable Markers

Selectable markers allow researchers to identify which bacteria successfully took up the plasmid. The most common markers are antibiotic resistance genes.

When bacteria are plated on media containing the antibiotic, only cells carrying the plasmid (with the resistance gene) survive and form colonies. Non-transformed cells are killed.

Common markers include ampR (ampicillin resistance via beta-lactamase), kanR (kanamycin resistance), and tetR (tetracycline resistance).

Transformation Efficiency

Transformation efficiency measures how well bacteria take up foreign DNA. It is expressed as the number of transformants (colony-forming units) per microgram of DNA.

Efficiency=colonies×VtotalVplated×dilutionμg DNA\mathrm{Efficiency} = \frac{\text{colonies} \times \frac{V_{\text{total}}}{V_{\text{plated}}} \times \text{dilution}}{\mu\mathrm{g\,DNA}}

Chemical (CaCl₂) transformation typically yields 10⁶ to 10⁸ transformants/μg. Electroporation can achieve 10⁹ to 10¹⁰ transformants/μg.

Restriction Enzymes

Restriction endonucleases cut DNA at specific palindromic recognition sequences. They are essential tools for molecular cloning, used to cut both the vector and the insert DNA at compatible sites.

For example, EcoRI recognizes the sequence GAATTC and produces sticky (cohesive) ends. SmaI recognizes CCCGGG and produces blunt ends.

The multiple cloning site (MCS) of a plasmid contains many unique restriction sites clustered together, giving researchers flexibility in choosing which enzymes to use for cloning.