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

TL;DR

This study shows how DNA Ligase 3α binds to nucleosomes using an arginine anchor, improving understanding of DNA repair mechanisms.

Contribution

The discovery of a novel arginine anchor in LIG3α that enables binding to nucleosomes.

Findings

LIG3α has higher affinity for nicks than XRCC1.

LIG3α binds more strongly to undamaged nucleosomes than to single strand breaks in naked DNA.

Binding to nucleosomes depends on two arginine residues in the N-terminal zinc finger.

Abstract

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 utilized a real time single molecule approach to quantify DNA binding kinetics of Halo-tagged LIG3α and XRCC1-YFP from nuclear extracts on long DNA substrates containing nicks, nucleosomes or nicks embedded in nucleosomes. LIG3α displayed 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 bound 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 the role of a novel arginine anchor in LIG3α for engaging nucleosomes.

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