Replication‐induced DNA secondary structures drive fork uncoupling and breakage

Abstract: Sequences that form DNA secondary structures, such as G‐quadruplexes (G4s) and intercalated‐Motifs (iMs), are abundant in the human genome and play various physiological roles. However, they can also interfere with replication and threaten genome stability. Multiple lines of evidence suggest G4s inhibit replication, but the underlying mechanism remains unclear. Moreover, evidence of how iMs affect the replisome is lacking. Here, we reconstitute replication of physiologically derived structure‐forming sequences to find that a single G4 or iM arrest DNA replication. Direct single‐molecule structure detection within solid‐state nanopores reveals structures form as a consequence of replication. Combined genetic and biophysical characterisation establishes that structure stability and probability of structure formation are key determinants of replisome arrest. Mechanistically, replication arrest is caused by impaired synthesis, resulting in helicase‐polymerase uncoupling. Significantly, iMs also induce breakage of nascent DNA. Finally, stalled forks are only rescued by a specialised helicase, Pif1, but not Rrm3, Sgs1, Chl1 or Hrq1. Altogether, we provide a mechanism for quadruplex structure formation and resolution during replication and highlight G4s and iMs as endogenous sources of replication stress.

Object Details

• Location: Deutsche Nationalbibliothek Frankfurt am Main
• Extent: Online-Ressource
• Language: Englisch

References and Relationships

• Bibliographic citation: Replication‐induced DNA secondary structures drive fork uncoupling and breakage ; day:02 ; month:10 ; year:2023 ; extent:30 ; The EMBO journal / European Molecular Biology Organization ; (02.10.2023) (gesamt 30)

Contributors, Places and Time

• Creator: Williams, Sophie L. ; Casas Delucchi, Corella Susana ; Raguseo, Federica ; Guneri, Dilek ; Li, Yunxuan ; Minamino, Masashi ; Fletcher, Emma E. ; Yeeles, Joseph TP ; Keyser, Ulrich F. ; Waller, Zoë AE ; Di Antonio, Marco ; Coster, Gideon

Further information

• DOI: 10.15252/embj.2023114334
• URN: urn:nbn:de:101:1-2023100215023019221052
• Rights: Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
• Last update: 14.08.2025, 10:56 AM CEST