{
  "annotation_id": "9617fc56-ad1c-4942-ab7a-9c0cde94d8a0",
  "date_created": "2026-03-02T18:01:10.920000Z",
  "date_modified": "2026-03-02T18:01:10.920000Z",
  "file_hash": "12e8c02982a89b3644aa477979f24ffe26862f91c309f20d54f261c61a4253b5",
  "private": false,
  "record": {
    "abstract": "Many proteins interact with and deform double-stranded DNA in cells.\nSingle-molecule experiments have studied the elasticity of DNA with\nhelix-deforming proteins, including proteins that bend DNA. These experiments\nincrease the need for theories of DNA elasticity which include helix-deforming\nproteins. Previous theoretical work on bent DNA has examined a long DNA\nmolecule with many nonspecifically binding proteins. However, recent\nexperiments used relatively short DNA molecules with a single, well-defined\nbend site. Here we develop a simple theoretical description of the effect of a\nsingle bend. We then include the description of the bend in the finite worm\nlike chain model (FWLC) of short DNA molecules attached to beads. We predict\nhow the DNA force-extension relation changes due to formation of a single\npermanent kink, at all values of the applied stretching force. Our predictions\nshow that high-resolution single-molecule experiments could determine the bend\nangle induced upon protein binding.",
    "arxiv_id": "physics/0607267",
    "authors": [
      "Jinyu Li",
      "Philip C. Nelson",
      "M. D. Betterton"
    ],
    "categories": [
      "physics.bio-ph"
    ],
    "doi": "10.1021/ma0609533",
    "journal_ref": "Macromolecules 39 (25), 8816 - 8821 (2006)",
    "title": "Entropic elasticity of DNA with a permanent kink",
    "url": "https://arxiv.org/abs/physics/0607267"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "899a39f4-96db-44e4-81ff-1c4b3b719592",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}