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<p>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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月21日

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  • Ashna Nagpal,
  • Matthew A. Schaich,
  • Tyler M. Weaver,
  • Vera Roginskaya,
  • Annahita Sallmyr,
  • Liam P. Leary,
  • Bret D. Freudenthal,
  • Alan E. Tomkinson,
  • Bennett Van Houten

摘要

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.