Duplex DNA from sites of helicase-polymerase uncoupling links non-B DNA structure formation to replicative stress

Camille Amparo, Jarrod Clark, Victoria Bedell, Joyce L. Murata-Collins, Marianna Martella, Flavia Pichiorri, Emily F. Warner, Mahmoud A. S. Abdelhamid, Zoë A. E. Waller, Steven S. Smith

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BACKGROUND: Replication impediments can produce helicase-polymerase uncoupling allowing lagging strand synthesis to continue for as much as 6 kb from the site of the impediment.

MATERIALS AND METHODS: We developed a cloning procedure designed to recover fragments from lagging strand near the helicase halt site.

RESULTS: A total of 62% of clones from a p53-deficient tumor cell line (PC3) and 33% of the clones from a primary cell line (HPS-19I) were within 5 kb of a G-quadruplex forming sequence. Analyses of a RACK7 gene sequence, that was cloned multiple times from the PC3 line, revealed multiple deletions in region about 1 kb from the cloned region that was present in a non-B conformation. Sequences from the region formed G-quadruplex and i-motif structures under physiological conditions.

CONCLUSION: Defects in components of non-B structure suppression systems (e.g. p53 helicase targeting) promote replication-linked damage selectively targeted to sequences prone to G-quadruplex and i-motif formation.

Original languageEnglish
Pages (from-to)101-115
Number of pages15
JournalCancer Genomics & Proteomics
Issue number2
Publication statusPublished - Mar 2020


  • CMG helicase uncoupling
  • G-quadruplex
  • i-motif
  • replication stress

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