dorsal/arxiv
View SchemaGeneralized Poland-Scheraga model for supercoiled DNA
| Authors | Thomas Garel, Henri Orland, Edouard Yeramian |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0407036 |
| URL | https://arxiv.org/abs/q-bio/0407036 |
Abstract
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is applied to the extremities of DNA: We propose a simple model for the energy of twisted DNA and compute the entropy of a loop, subject to angular constraints (supercoiling). The denaturation curves are shifted towards lower or higher temperatures depending on the sign of the torque, and the UV absorption peaks are softened. The properties of supercoiled DNA can be deduced through the use of a numerical Legendre transform. In the homogeneous case, we find that for weak supercoiling, the phenomenological quadratic law relating the torsional energy to the number of unpaired bases is recovered.
{
"annotation_id": "f686d6cc-dcbb-4854-841a-7caac55cac90",
"date_created": "2026-03-02T18:01:31.872000Z",
"date_modified": "2026-03-02T18:01:31.872000Z",
"file_hash": "44be526a4d4ad4d8b7aebac431c31b5f7f0a54be3d209d38098fddb3f28a7e29",
"private": false,
"record": {
"abstract": "The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers\nthe statistical mechanics of the thermally induced binding of two complementary\nstrands of DNA. In this paper, we show how to modify the PS model when a torque\nis applied to the extremities of DNA: We propose a simple model for the energy\nof twisted DNA and compute the entropy of a loop, subject to angular\nconstraints (supercoiling). The denaturation curves are shifted towards lower\nor higher temperatures depending on the sign of the torque, and the UV\nabsorption peaks are softened. The properties of supercoiled DNA can be deduced\nthrough the use of a numerical Legendre transform. In the homogeneous case, we\nfind that for weak supercoiling, the phenomenological quadratic law relating\nthe torsional energy to the number of unpaired bases is recovered.",
"arxiv_id": "q-bio/0407036",
"authors": [
"Thomas Garel",
"Henri Orland",
"Edouard Yeramian"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"title": "Generalized Poland-Scheraga model for supercoiled DNA",
"url": "https://arxiv.org/abs/q-bio/0407036"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "4307cbfe-bbe7-4f67-97cf-a6c456ba6efe",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}