{
  "abstract": "We are interested in DNA stiffness in vitro and in vivo. Classical approaches for measuring this parameter in vitro involve tedious T4 DNA ligase-mediated cyclization kinetics experiments performed for one DNA fragment length at a time to establish effective local end-end concentrations (J-factors). Protein-mediated DNA looping is a more relevant biological reaction. An efficient approach to determine length-dependent protein-mediated DNA J-loop values in vitro has been lacking. We describe LOOP-TAG, a massively-parallel method. We leverage intramolecular DNA looping and tagmentation catalyzed by Tn5 transposase (Tnp) tethered to the terminus of a ~1,000-bp bead-bound duplex DNA. We detected loops terminating with Tnp. Counts of the resulting DNA looping-dependent bead-bound tagmentation products from deep sequencing determine DNA loop length probabilities at single-base pair resolution for all bead-bound fragments. When normalized to DNA fragment length probabilities from tagmentation using known concentrations of free Tnp, length-dependent J-loop values are directly determined. We demonstrate LOOP-TAG for Tnp tethered in two ways and in the presence of DNA-kinking architectural DNA binding protein Nhp6A. Intermediate length J-loop values are consistent with expectations of wormlike chain theory after accounting for strong sequence-dependence of Tnp. DNA loops are shifted to smaller sizes in the presence of Nhp6A, as predicted.",
  "abstract_shown": true,
  "affiliations": [
    "Mayo Clinic College of Medicine and Science"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "N. R. Kennel"
    },
    {
      "name": "N. A. Becker"
    },
    {
      "name": "J. P. Peters"
    },
    {
      "affs": [
        0
      ],
      "name": "L. J. Maher"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ddvh0jtq5rdp9.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.21.753159",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753159v1.full",
  "id": "ddvh0jtq5rdp9",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753159v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "1312|Diffusion and Search Dynamics"
    ]
  ],
  "openalex": "W7214242975",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753159v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/ddvh0jtq5rdp9.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:23Z",
      "native_id": "10.64898/2026.09.21.753159",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753159v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "LOOP-TAG: massively-parallel measurement of length-dependent protein-mediated DNA looping probabilities by tagmentation in vitro",
  "title_text": "LOOP-TAG: massively-parallel measurement of length-dependent protein-mediated DNA looping probabilities by tagmentation in vitro",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:23Z",
  "url": "https://research.draconitic.com/paper/ddvh0jtq5rdp9",
  "venue": "bioRxiv",
  "versions": []
}