dorsal/arxiv
View SchemaIn vivo evidence of alternative loop geometries in DNA-protein complexes
| Authors | Leonor Saiz, Jose M. G. Vilar |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0602012 |
| URL | https://arxiv.org/abs/q-bio/0602012 |
Abstract
The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an oscillatory component of about half the helical period and oscillates asymmetrically with an amplitude significantly smaller than predicted by current theories. Here, we show that the in vivo behavior is accurately accounted for by the simultaneous presence of two distinct conformations of looped DNA. Our analysis reveals that these two conformations have different optimal free energies and phases and that they behave distinctly in the presence of key architectural proteins.
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"abstract": "The in vivo free energy of looping double-stranded DNA by the lac repressor\nhas a remarkable behavior whose origins are not fully understood. In addition\nto the intrinsic periodicity of the DNA double helix, the in vivo free energy\nhas an oscillatory component of about half the helical period and oscillates\nasymmetrically with an amplitude significantly smaller than predicted by\ncurrent theories. Here, we show that the in vivo behavior is accurately\naccounted for by the simultaneous presence of two distinct conformations of\nlooped DNA. Our analysis reveals that these two conformations have different\noptimal free energies and phases and that they behave distinctly in the\npresence of key architectural proteins.",
"arxiv_id": "q-bio/0602012",
"authors": [
"Leonor Saiz",
"Jose M. G. Vilar"
],
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"q-bio.BM",
"cond-mat.soft",
"physics.bio-ph"
],
"title": "In vivo evidence of alternative loop geometries in DNA-protein complexes",
"url": "https://arxiv.org/abs/q-bio/0602012"
},
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