dorsal/arxiv
View SchemaSimulated and Experimental Bending Dynamics in DNA with and without A-Tracts
| Authors | Alexey K. Mazur, Dimitri E. Kamashev |
|---|---|
| Categories | |
| ArXiv ID | physics/0108038 |
| URL | https://arxiv.org/abs/physics/0108038 |
Abstract
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of DNA structure. We report here the results of comparative theoretical and experimental studies of bending dynamics in 35-mer DNA fragments. This length appears large enough for the curvature to be distinguished by gel electrophoresis. Two DNA fragments, with identical base pair composition, but different sequences are compared. In the first one, a single A-tract motif was four times repeated in phase with the helical screw whereas the second sequence was "random". Both calculations and experiments indicate that the A-tract DNA is distinguished by the large static curvature and characteristic bending dynamics, suggesting that the computed effect corresponds to the experimental phenomenon. The results poorly agree with earlier views that attributed a decisive role in DNA bending to sequence specific base pair stacking or binding of solvent counterions, but lend additional support to the hypothesis of a compressed frustrated state of the backbone as the principal physical cause of the static curvature. We discuss the possible ways of experimental verification of this hypothesis.
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"abstract": "The macroscopic curvature of double helical DNA induced by regularly repeated\nadenine tracts is well-known but still puzzling. Its physical origin remains\ncontroversial even though it is perhaps the best-documented sequence modulation\nof DNA structure. We report here the results of comparative theoretical and\nexperimental studies of bending dynamics in 35-mer DNA fragments. This length\nappears large enough for the curvature to be distinguished by gel\nelectrophoresis. Two DNA fragments, with identical base pair composition, but\ndifferent sequences are compared. In the first one, a single A-tract motif was\nfour times repeated in phase with the helical screw whereas the second sequence\nwas \"random\". Both calculations and experiments indicate that the A-tract DNA\nis distinguished by the large static curvature and characteristic bending\ndynamics, suggesting that the computed effect corresponds to the experimental\nphenomenon. The results poorly agree with earlier views that attributed a\ndecisive role in DNA bending to sequence specific base pair stacking or binding\nof solvent counterions, but lend additional support to the hypothesis of a\ncompressed frustrated state of the backbone as the principal physical cause of\nthe static curvature. We discuss the possible ways of experimental verification\nof this hypothesis.",
"arxiv_id": "physics/0108038",
"authors": [
"Alexey K. Mazur",
"Dimitri E. Kamashev"
],
"categories": [
"physics.bio-ph",
"physics.chem-ph",
"q-bio.BM"
],
"title": "Simulated and Experimental Bending Dynamics in DNA with and without A-Tracts",
"url": "https://arxiv.org/abs/physics/0108038"
},
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