The ccdB gene encodes a toxic protein that inhibits cell proliferation. Bacteria that do not encode a ccdA gene (inhibitor of ccdB protein) die upon uptake of a plasmid containing a ccdB gene. This positive selection is a useful tool for molecular cloning.

ccdB genes are used for the Gateway cloning technique and 3A-assembly. The ccdB gene is usually used in the backbone vector which conveys the antibiotic resistance to the transformed cells if the ccdB gene was replaced by the cloned construct.