Probing the mechanism of nick searching by LIG1 at the single-molecule level

DNA ligase 1 (LIG1) joins Okazaki fragments during the nuclear replication and completes DNA repair pathways by joining 3′-OH and 5′-PO4 ends of nick at the final step. Yet, the mechanism of how LIG1 searches for a nick at single-molecule level is unknown. Here, we combine single-molecule fluorescence microscopy approaches, C-Trap and total internal reflection fluorescence (TIRF), to investigate the dynamics of LIG1-nick DNA binding. Our C-Trap data reveal that DNA binding by LIG1 full-length is enriched near the nick sites and the protein exhibits diffusive behavior to form a long-lived ligase/nick complex after binding to a non-nick region. However, LIG1 C-terminal mutant, containing the catalytic core and DNA-binding domain, predominantly binds throughout DNA non-specifically to the regions lacking nick site for shorter time. These results are further supported by TIRF data for LIG1 binding to DNA with a single nick site and demonstrate that a fraction of LIG1 full-length binds significantly longer period compared to the C-terminal mutant. Overall comparison of DNA binding modes provides a mechanistic model where the N-terminal domain promotes 1D diffusion and the enrichment of LIG1 binding at nick sites with longer binding lifetime, thereby facilitating an efficient nick search process.