dorsal/arxiv
View SchemaSingle DNA conformations and biological function
| Authors | Ralf Metzler, Tobias Ambjoernsson, Andreas Hanke, Yongli Zhang, Stephen Levene |
|---|---|
| Categories | |
| ArXiv ID | physics/0609139 |
| URL | https://arxiv.org/abs/physics/0609139 |
Abstract
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.
{
"annotation_id": "4aa78018-6f29-49b7-b869-4bac61d045c1",
"date_created": "2026-03-02T18:01:10.863000Z",
"date_modified": "2026-03-02T18:01:10.863000Z",
"file_hash": "496f96b6d4da4b87e3a6805d915398959eeec97996cf28df91225334ca267b5d",
"private": false,
"record": {
"abstract": "From a nanoscience perspective, cellular processes and their reduced in vitro\nimitations provide extraordinary examples for highly robust few or single\nmolecule reaction pathways. A prime example are biochemical reactions involving\nDNA molecules, and the coupling of these reactions to the physical\nconformations of DNA. In this review, we summarise recent results on the\nfollowing phenomena: We investigate the biophysical properties of DNA-looping\nand the equilibrium configurations of DNA-knots, whose relevance to biological\nprocesses are increasingly appreciated. We discuss how random DNA-looping may\nbe related to the efficiency of the target search process of proteins for their\nspecific binding site on the DNA molecule. And we dwell on the spontaneous\nformation of intermittent DNA nanobubbles and their importance for biological\nprocesses, such as transcription initiation. The physical properties of DNA may\nindeed turn out to be particularly suitable for the use of DNA in nanosensing\napplications.",
"arxiv_id": "physics/0609139",
"authors": [
"Ralf Metzler",
"Tobias Ambjoernsson",
"Andreas Hanke",
"Yongli Zhang",
"Stephen Levene"
],
"categories": [
"physics.bio-ph",
"cond-mat.soft",
"q-bio.BM"
],
"title": "Single DNA conformations and biological function",
"url": "https://arxiv.org/abs/physics/0609139"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "7875bac2-d212-477b-a0a8-e9ba04dc9407",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}