The Zuo1 C-terminal domain stabilizes the DNA guanosine quadruplex (G4) structures located on Chromosome IX in Saccharomyces cerevisiae

Deoxyguanosine quadruplexes (G4s) are stable non-B-DNA structures that can affect transcription, replication, and genome stability. Depending on various factors including cation binding, G4s can fold into different topologies, which can be linked to distinct function. In cells, G4 folding, function, and unfolding is affected by proteins that specifically target G4s. Zuo1 is a G4-binding protein in yeast. To investigate Zuo1 binding and its consequences on G4 formation and topology, we characterized Zuo1’s interaction with G4s, both in vitro and in vivo. The main domain of Zuo1 interacting with the G4 structures is the C-terminus (Zuo1348-433). We characterized this interaction by combining NMR, smFRET, and in vivo experiments with a G4 located on yeast chromosome IX (G4IX). The Zuo1-G4IX interaction stabilizes this G4 structure and triggers conformational shifts depending on the cation environment. The data presented here demonstrates that Zuo1 is targeted to a specific conformational state of G4IX, where it modulates G4 topology and stabilizes the G4IX, ultimately contributing positively to genome stability.