dorsal/arxiv
View SchemaRelaxation of DNA curvature by single stranded breaks: Simulations and experiments
| Authors | Dimitri E. Kamashev, Alexey K. Mazur |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0311003 |
| URL | https://arxiv.org/abs/q-bio/0311003 |
Abstract
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature in A-tract repeats can be relaxed by introducing single stranded breaks (nicks). This effect has not been tested earlier and it would not be accounted for by alternative models of DNA bending. Here the curvature in a specifically designed series of nicked DNA fragments is tested experimentally by gel mobility assays and, simultaneously, by free molecular dynamics simulations. Single stranded breaks produce virtually no effect upon the gel mobility of the random sequence DNA. In contrast, nicked A-tract fragments reveal a regular modulation of curvature depending upon the position of the strand break with respect to the overall bend. Maximal relaxation is observed when nicks occur inside A-tracts. The results are partially reproduced in simulations. Analysis of computed curved DNA conformations reveals a group of sugar atoms that exhibit reduced backbone length within A-tracts, which can correspond to the compression hypothesis.
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"abstract": "The recently proposed compressed backbone theory suggested that the intrinsic\ncurvature in DNA can result from a geometric mismatch between the specific\nbackbone length and optimal base stacking orientations. It predicted that the\ncurvature in A-tract repeats can be relaxed by introducing single stranded\nbreaks (nicks). This effect has not been tested earlier and it would not be\naccounted for by alternative models of DNA bending. Here the curvature in a\nspecifically designed series of nicked DNA fragments is tested experimentally\nby gel mobility assays and, simultaneously, by free molecular dynamics\nsimulations. Single stranded breaks produce virtually no effect upon the gel\nmobility of the random sequence DNA. In contrast, nicked A-tract fragments\nreveal a regular modulation of curvature depending upon the position of the\nstrand break with respect to the overall bend. Maximal relaxation is observed\nwhen nicks occur inside A-tracts. The results are partially reproduced in\nsimulations. Analysis of computed curved DNA conformations reveals a group of\nsugar atoms that exhibit reduced backbone length within A-tracts, which can\ncorrespond to the compression hypothesis.",
"arxiv_id": "q-bio/0311003",
"authors": [
"Dimitri E. Kamashev",
"Alexey K. Mazur"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"physics.bio-ph"
],
"title": "Relaxation of DNA curvature by single stranded breaks: Simulations and experiments",
"url": "https://arxiv.org/abs/q-bio/0311003"
},
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