Isoschizomers

Isoschizomers are restriction endonucleases that recognize the same DNA sequence. They may differ in where they cleave within that sequence, which can result in different ends being generated. If two enzymes cut at exactly the same position within the recognition site and produce identical fragments, they are called strict (or true) isoschizomers. If they recognize the same sequence but cut at different positions, creating different ends, they are referred to as neoisoschizomers.

The recognition sequences involved are typically short and often palindromic, ranging from about four to eight base pairs. Isoschizomer pairs are derived from different bacterial sources and can be distinguished by comparing their digestion patterns on the same DNA substrate or by mapping their cut sites. In practice, choosing between isoschizomers can influence cloning strategies, for example by selecting an enzyme that yields a preferred end type or by enabling alternative ligation options.

Isoschizomers are cataloged in restriction enzyme databases such as REBASE, which lists pairs and their properties. The concept highlights how enzymes with the same recognition sequence can differ in cleavage position and end configuration, offering flexibility in experimental design.

Isoschizomers should not be confused with isocaudomers, which refer to restriction enzymes that produce compatible cohesive ends regardless of the recognition sequence. Understanding the relationship among isoschizomers, neoisoschizomers, and related terms helps in planning digestion and ligation steps in molecular cloning and DNA mapping.