The nic site or nick region is found within the origin of transfer (oriT) site and is key in starting bacterial conjugation.[1]

Purpose

A single strand of DNA, called the T-strand, is cut at nic by an enzyme called relaxase.[1] This single strand is eventually transferred to the recipient cell during the process of bacterial conjugation. Before this cleavage can occur, however, it is necessary for a group of proteins to attach to the oriT site. This group of proteins is called the relaxosome.[1] It is thought that portions of the oriT site are bent in a way that creates interaction between the relaxosome proteins and the nic site.[1]

Cleaving the T-strand involves relaxase cutting a phosphodiester bond at the nic site.[1] Interestingly, the cleaved strand is left with a hydroxyl group at the 3' end, which may allow for the strand to form a circular plasmid after moving into the recipient cell.[2,3]

[1] Lanka Erich, Wilkins Brian M (1995). “DNA Processing Reactions in Bacterial Conjugation.” Annu. Rev. Biochem. 64: 141-69.

[2] Matson S W, Nelson W C, Morton B S (1993). "Characterization of the Reaction Product of the oriT Nicking Reaction Catalyzed by Escherichia coli DNA helicase I." Journal of Bacteriology. 175(9): 2599-2606.

[3] Grohmann E, Muth G, Espinosa M (2003). "Conjugative Plasmid Transfer in Gram-positive Bacteria." Microbiol Mol Biol Rev. 67(2):277-301.