Direct determination of the base-pair force constant of DNA from the acoustic phonon dispersion of the double helix.

Reactor Institute Delft, Delft University of Technology, Mekelweg 15, 2629JB, Delft, The Netherlands.
Physical Review Letters (Impact Factor: 7.73). 08/2011; 107(8):088102. DOI: 10.1103/PhysRevLett.107.088102
Source: PubMed

ABSTRACT Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Information about molecular interactions in DNA can be obtained from experimental melting temperature data by using mesoscopic statistical physics models. Here, we extend the technique to RNA and show that the new parameters correctly reproduce known properties such as the stronger hydrogen bonds of AU base pairs. We also were able to calculate a complete set of elastic constants for all 10 irreducible combinations of nearest neighbours (NNs). We believe that this is particularly useful as experimentally derived information about RNA elasticity is relatively scarce. The melting temperature prediction using the present model improves over those from traditional NN model, providing thus an alternative way to calculate these temperatures for RNA. Additionally, we calculated the site-dependent base pair oscillation to explain why RNA shows larger oscillation amplitudes despite having stronger AU hydrogen bonds.
    Nucleic Acids Research 10/2012; · 8.81 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The paper proposes a new modeling approach for the prediction and analysis of the mechanical properties in DNA molecules based on a hybrid atomistic-finite element continuum representation. The model takes into account of the complex geometry of the DNA strands, a structural mechanics representation of the atomic bonds existing in the molecules and the mass distribution of the atoms by using a lumped parameter model. A thirteen-base-pair DNA model is used to illustrate the proposed approach. The properties of the equivalent bond elements used to represent the DNA model have been derived. The natural frequencies, vibration mode shapes and equivalent continuum mechanical properties of the DNA strand are obtained. The results from our model compare well with a high-fidelity Molecular Mechanics simulation and existing MD and experimental data from open literature.
    Journal of Nanotechnology in Engineering and Medicine. 01/2014;
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: This work is dedicated to the study of the structural and dynamical behavior of a model one-dimensional system over a wide temperature range : carbon nano-peapods. This compound is constituted of fullerenes (C60, in our case) inserted inside single-walled carbon nanotubes. The perfect match between the inner diameter of the tubes and the diameter of the fullerenes results in a chain organization of the C60 molecules. The synthesis of these peapods is described in the first part of this manuscript. The two next chapters are aimed to the description of the different experimental and simulation methods that are used to monitor the structural and dynamical behavior of the C60 molecules. In the three last chapters, we describe the behavior of the C60 molecules over three tempe- rature ranges, labeled high (500–1100 K), low (0–200 K), and intermediary (200–500 K) ranges. By comparing experimental results to analytical models for both monomer and polymer pea- pods (the rotational degree of freedom being hindered in the latter), we highlight three different behaviors of the molecules in these three ranges.
    11/2012, Degree: PhD, Supervisor: Stéphane Rols and Pascale Launois

Full-text (2 Sources)

Available from
May 31, 2014