The zinc finger of DNA ligase 3α binds to nucleosomes via an arginine anchor

Ligation of DNA single strand breaks is critical for maintaining genome integrity during DNA replication and repair. DNA Ligase III (LIG3α) forms an important complex with X-ray cross complementing protein 1 (XRCC1) during single strand break and base excision repair. We utilize a real time single molecule approach to quantify DNA binding kinetics of HaloTag-LIG3α and XRCC1-YFP from nuclear extracts on long DNA substrates containing nicks, nucleosomes or nicks embedded in nucleosomes. LIG3α displays higher affinity for nicks than XRCC1 with the LIG3α catalytic core and N-terminal zinc finger (ZnF) competing for nick engagement. Surprisingly, compared to single strand breaks in naked DNA, LIG3α binds even more avidly to an undamaged nucleosome reconstituted on the 601-sequence, with binding dependent on two arginine residues in the N-terminal ZnF. These studies reveal insights into nick detection and identify an arginine anchor mechanism for LIG3α engagement with nucleosomes. LIG3α forms a complex with XRCC1 during single strand break and base excision repair. Here, the authors show that LIG3α displays higher affinity for nicks than XRCC1 and binds with its N-terminal ZnF domain more avidly to an undamaged nucleosome.