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- W2110102010 abstract "The overstretching transition in torsionally unconstrained DNA is studied by means of atomistic molecular dynamics simulations. The free-energy profile as a function of the length of the molecule is determined through the umbrella sampling technique providing both a thermodynamic and a structural characterization of the transition pathway. The zero-force free-energy profile is monotonic but, in accordance with recent experimental evidence, becomes two-state at high forces. A number of experimental results are satisfactorily predicted: (i) the entropic and enthalpic contributions to the free-energy difference between the basic (B) state and the extended (S) state; (ii) the longitudinal extension of the transition state and (iii) the enthalpic contribution to the transition barrier. A structural explanation of the experimental finding that overstretching is a cooperative reaction characterized by elementary units of approximately 22 base pairs is found in the average distance between adenine/thymine-rich regions along the molecule. The overstretched DNA adopts a highly dynamical and structurally disordered double-stranded conformation which is characterized by residual base pairing, formation of non-native intra-strand hydrogen bonds and effective hydrophobic screening of apolar regions." @default.
- W2110102010 created "2016-06-24" @default.
- W2110102010 creator A5025730785 @default.
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- W2110102010 date "2014-08-06" @default.
- W2110102010 modified "2023-10-17" @default.
- W2110102010 title "The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics" @default.
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- W2110102010 doi "https://doi.org/10.1098/rsif.2014.0399" @default.
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