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 evidences, 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; (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 22 base-pairs is found in the average distance between AT 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.
The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics / L. Bongini; V. Lombardi; P. Bianco. - In: JOURNAL OF THE ROYAL SOCIETY INTERFACE. - ISSN 1742-5689. - STAMPA. - 11:(2014), pp. non si applica-non si applica. [10.1098/rsif.2014.0399]
The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics.
BONGINI, LORENZO;LOMBARDI, VINCENZO;BIANCO, PASQUALE
2014
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 evidences, 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; (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 22 base-pairs is found in the average distance between AT 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.File | Dimensione | Formato | |
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