Ligasen

Ligasen is a hypothetical enzyme frequently cited in molecular biology texts as a canonical example of a DNA ligase. In these materials, ligases catalyze the formation of phosphodiester bonds that seal breaks in the sugar-phosphate backbone, converting a nicked DNA molecule into a continuous strand. Ligasen is described in two representative variants: an ATP-dependent form, analogous to eukaryotic DNA ligases, and an NAD+-dependent form, analogous to many bacterial ligases. Both variants require divalent metal ions, typically Mg2+, and function best near neutral pH.

The mechanism involves activation of the 5' phosphate and subsequent nucleophilic attack by the adjacent 3' hydroxyl, releasing AMP or pyrophosphate during the reaction. In teaching contexts, Ligasen is used to illustrate the differences between cohesive-end and blunt-end ligation, temperature sensitivity, and the need for compatible ends or pre-nicked substrates.

Ligasen serves as a generic model rather than a defined real enzyme. Consequently, it is not associated with a specific organism or laboratory protocol, but represents a conceptual tool to compare ligation strategies in cloning, DNA assembly, and genome-editing workflows.

Etymology: the name blends ligate and enzyme, and it is used in didactic settings to discuss ligation chemistry. See also DNA ligase, T4 DNA ligase, NAD+-dependent ligases, ATP-dependent ligases.