The C6 zinc cluster dictates asymmetric binding by HAP1.

Unlike other C6 zinc cluster proteins such as GAL4 and PPR1, HAP1 binds selectively to asymmetric DNA sites containing a direct repeat of two CGG triplets. Here, we show that the HAP1 zinc cluster is solely responsible for asymmetric binding by HAP1. An asymmetric interaction between two zinc clusters of a HAP1 dimer must position the zinc clusters in a directly repeated orientation, and enable them to recognize two CGG triplets in a direct repeat. Further, our data suggest that this asymmetric interaction acts cooperatively with the interaction between dimerization elements to promote HAP1 dimerization, and locks HAP1-DNA complexes in a stable, dimeric conformation.