Cloning Wizards

PlasmidStudio includes simulation wizards for four cloning methods. Each wizard walks you through the method-specific steps with visual previews and validation.

Access the wizards from the "Clone" button in the viewer header, or click "Suggest Cloning Strategy" to have the AI recommend the best method for your construct.

Steps: Select Method → Pick Constructs → Enzymes & Digest → Fragments & Ligate → Review

The wizard suggests enzyme pairs based on unique cut sites in your source and destination vectors. A gel simulation shows the expected fragment pattern. Select compatible fragments and ligate them to create the new construct.

Steps: Select Method → Define Fragments (2–6) → Validate Overlaps → Assemble Preview → Review

Define your fragments with 20–40 bp overlaps between adjacent pieces. The wizard validates overlap Tm (traffic-light indicators: green/yellow/red) and uniqueness. Auto-generated Gibson primers include the overlap extensions.

Steps: Select Method → Select Type IIS Enzyme (BsaI/BsmBI/BbsI) → Define Parts → Validate Overhangs → Review

Choose a Type IIS enzyme, then define your parts with custom 4-bp overhangs. The wizard checks for internal Type IIS sites (with silent mutation domestication), validates overhang uniqueness, and shows a junction map with colored overhang pills.

Steps: Select Method → Reaction Type (BP/LR) → Define Entry → Destination Vector → Review

BP reactions move an insert into an entry vector (attB × attP). LR reactions move it into a destination vector (attL × attR). The wizard auto-detects att sites and shows a recombination preview diagram. Pre-populated destination vectors include pDEST15, pDEST17, pDEST26, and pLenti-CMV.

Not sure which method to use? Click "Suggest Cloning Strategy" in the viewer header. The AI analyzes your construct based on: - Unique cutter count - Number of inserts/fragments - Construct size - GC content - Internal Type IIS sites

It provides a qualitative rating for each method (Excellent fit / Good fit / Possible but not ideal / Not recommended) with a detailed comparison table. When two methods score within 10 points, both are presented with a tradeoff explanation.