Edited by Norma Allewellc-Myc-interacting zinc finger protein-1 (Miz-1) is a polyCys2His2 zinc finger (ZF) transcriptional regulator of many cell cycle genes. A Miz-1 DNA sequence consensus has recently been identified and has also unveiled Miz-1 functions in other cellular processes, underscoring its importance in the cell. Miz-1 contains 13 ZFs, but it is unknown why Miz-1 has so many ZFs and whether they recognize and bind DNA sequences in a typical fashion. Here, we used NMR to deduce the role of Miz-1 ZFs 1-4 in detecting the Miz-1 consensus sequence and preventing nonspecific DNA binding. In the construct containing the first 4 ZFs, we observed that ZFs 3 and 4 form an unusual compact and stable structure that restricts their motions. Disruption of this compact structure by an electrostatically mismatched A86K mutation profoundly affected the DNA binding properties of the WT construct. On the one hand, Miz1-4 WT was found to bind the Miz-1 DNA consensus sequence weakly and through ZFs 1-3 only. On the other hand, the four ZFs in the structurally destabilized Miz1-4 A86K mutant bound to the DNA consensus with a 30-fold increase in affinity (100 nM). The formation of such a thermodynamically stable but nonspecific complex is expected to slow down the rate of DNA scanning by Miz-1 during the search for its consensus sequence. Interestingly, we found that the motif stabilizing the compact structure between ZFs 3 and 4 is conserved and enriched in other long poly-ZF proteins. As discussed in detail, our findings support a general role of compact inter-ZF structures in minimizing the formation of off-target DNA complexes.Miz-1 (c-Myc-interacting zinc finger protein-1) is an 88-kDa protein that contains a BTB (Broad complex, Tramtrack, and Bric-a-brac)-POZ (poxvirus and zinc finger) (POZ) 3 domain at its N terminus followed by 13 ZFs. It was first identified as a direct interactor of the oncogenic protein c-Myc by yeast twohybrid screening (1). Miz-1 is an activator of cell cycle regulator genes, such as the cyclin-dependent kinase inhibitors p15CIP1 (p21), and p57 KIP2 (p57) (2-5). Miz-1 activates the transcription of those genes by recruiting different co-activators, such as the histone acetyltransferase p300 and the nucleophosmin (3, 6). Moreover, it was shown that in response to TGF-, Miz-1 forms a complex with the Smad 2/3/4 proteins to activate the expression of p15. This interaction was shown to involve a region located within the first four ZFs of Miz-1 and the MH1 domain of Smad 3 (7). Whereas the role of Miz-1 in cell cycle regulation is well established, recent studies have underlined its implication in other cell cycle-independent processes, such as autophagy, endocytosis, vesicular trafficking, inflammation and DNA repair (8 -11). Moreover, some cytoplasmic functions of Miz-1, such as its implication in the regulation of the Wnt pathway, are emerging, revealing the multifunctional nature of this transcription factor (12).c-Myc can directly bind Miz-1 and repress the expression of p15, p21, and p57, ...