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Quantitative Biology > Biomolecules

arXiv:q-bio/0512036 (q-bio)
[Submitted on 20 Dec 2005]

Title:Inferring the in vivo looping properties of DNA

Authors:Leonor Saiz, J. Miguel Rubi, Jose M. G. Vilar
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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.
Comments: 20 pages, 4 figures
Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM); Subcellular Processes (q-bio.SC)
Cite as: arXiv:q-bio/0512036 [q-bio.BM]
  (or arXiv:q-bio/0512036v1 [q-bio.BM] for this version)
  https://doi.org/10.48550/arXiv.q-bio/0512036
Journal reference: Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005)
Related DOI: https://doi.org/10.1073/pnas.0505693102

Submission history

From: Jose Vilar [view email]
[v1] Tue, 20 Dec 2005 00:52:51 UTC (309 KB)
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