dorsal/arxiv
View SchemaInferring the in vivo looping properties of DNA
| Authors | Leonor Saiz, J. Miguel Rubi, Jose M. G. Vilar |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0512036 |
| URL | https://arxiv.org/abs/q-bio/0512036 |
| DOI | 10.1073/pnas.0505693102 |
| Journal | Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005) |
Abstract
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of the loop and found that, in addition to the intrinsic periodicity of the DNA double helix, the free energy has an oscillatory component with about half the helical period. Moreover, the oscillations have such an amplitude that the effects of regulatory molecules become strongly dependent on their precise DNA positioning and yet easily tunable by their cooperative interactions. These unexpected results can confer to the physical properties of DNA a more prominent role at shaping the properties of gene regulation than previously thought.
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"abstract": "The free energy of looping DNA by proteins and protein complexes determines\nto what extent distal DNA sites can affect each other. We inferred its in vivo\nvalue through a combined computational-experimental approach for different\nlengths of the loop and found that, in addition to the intrinsic periodicity of\nthe DNA double helix, the free energy has an oscillatory component with about\nhalf the helical period. Moreover, the oscillations have such an amplitude that\nthe effects of regulatory molecules become strongly dependent on their precise\nDNA positioning and yet easily tunable by their cooperative interactions. These\nunexpected results can confer to the physical properties of DNA a more\nprominent role at shaping the properties of gene regulation than previously\nthought.",
"arxiv_id": "q-bio/0512036",
"authors": [
"Leonor Saiz",
"J. Miguel Rubi",
"Jose M. G. Vilar"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"physics.bio-ph",
"q-bio.QM",
"q-bio.SC"
],
"doi": "10.1073/pnas.0505693102",
"journal_ref": "Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005)",
"title": "Inferring the in vivo looping properties of DNA",
"url": "https://arxiv.org/abs/q-bio/0512036"
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