{
  "abstract": "Single-stranded DNA breaks (SSBs) at repetitive elements promote internal loops (i-loops), precursors of extrachromosomal circular DNA (eccDNA). Here, we present a protocol for inducing targeted breaks at human telomeric or alpha-satellite repeats using doxycycline-inducible Cas9 nickase variants and repeat-specific sgRNAs. We describe steps for verifying strand-specific nicking by alkaline-gel Southern blotting and detecting i-loop accumulation by two-dimensional agarose gel electrophoresis (2D gel). In this protocol, DNase I treatment of isolated nuclei is employed as a Cas9-independent control. For complete details on the use and execution of this protocol, please refer to Zanella et al.¹.",
  "abstract_shown": true,
  "affiliations": [
    "IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy. Electronic address: elia.zanella@ifom.eu.",
    "IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.",
    "IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy. Electronic address: ylli.doksani@ifom.eu."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Elia Zanella"
    },
    {
      "affs": [
        1
      ],
      "name": "Flavia Bruno"
    },
    {
      "affs": [
        2
      ],
      "name": "Ylli Doksani",
      "orcid": "0000-0002-2392-5722"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1tbnptbekj9dn.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104888",
  "fulltext_url": "https://europepmc.org/articles/PMC13675476",
  "id": "1tbnptbekj9dn",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://europepmc.org/article/MED/42837263",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|CRISPR and Genetic Engineering"
    ]
  ],
  "openalex": "W7220727856",
  "pdf_url": "https://europepmc.org/articles/PMC13675476?pdf=render",
  "pmcid": "PMC13675476",
  "pmid": "42837263",
  "published": "2026-10-06",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/1tbnptbekj9dn.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:02Z",
      "native_id": "MED:42837263",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42837263"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|CRISPR and Genetic Engineering",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol for Cas9 nickase-mediated induction and two-dimensional gel detection of i-loops at human telomeric and alpha satellite repeats.",
  "title_text": "Protocol for Cas9 nickase-mediated induction and two-dimensional gel detection of i-loops at human telomeric and alpha satellite repeats.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:02Z",
  "url": "https://research.draconitic.com/paper/1tbnptbekj9dn",
  "venue": "STAR protocols",
  "versions": []
}