In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (Pfam:PF00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added [1-2].

1: Apo-AraC actively seeks to loop. Seabold RR, Schleif RF; J Mol Biol 1998;278:529-538. PMID:9600836

2: Arm-domain interactions in AraC. Saviola B, Seabold R, Schleif RF; J Mol Biol 1998;278:539-548. PMID:9600837