Golden Gate DNA Assembly Simulator

This simulation walks through Golden Gate assembly, the modern one-pot method biotechnologists use to build a multi-part plasmid without hand-cloning each junction separately. Five DNA parts — backbone, promoter, ribosome-binding site, gene and terminator — each carry a Type IIS restriction site that cuts outside its own recognition sequence, leaving a custom 4-nucleotide overhang that fits only its intended neighbour. Adjust cut efficiency, ligase efficiency and the insert:vector molar ratio, then run 37°C/16°C thermocycles and watch the reaction tube fill with correctly closed circular plasmids while loose fragment sets dwindle. The live readouts track cycles run, the per-cycle success probability, and how many of the 60 fragment sets have assembled correctly — demonstrating the ratchet mechanism that makes Golden Gate converge toward completion far more reliably than a single restriction-and-ligation step.