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: 7.51). 08/2011; 107(8):088102. DOI: 10.1103/PhysRevLett.107.088102
Source: PubMed


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.

Download full-text


Available from: Jacques Ollivier,
  • Source
    • "In this context it has been proposed that the denaturation is a sharp, first order like, transition driven by the entropic gain associated to the reduced stacking coupling which renders the bases motion more disordered [54]. While the precise value of the melting entropy may depend on the sequence specificities [55], recent neutron scattering investigations have suggested that DNA maintains the helical order almost up to the melting [56] and that denaturation is rather a continuous transition, albeit occurring in a narrow temperature range as shown by renormalization group analysis of the DPB model [57]. Similar trends have been found in simulations of DNA denaturation based on Langevin dynamics [58] and in the path integral method developed both for homogeneous [40] and heterogeneous [41] sequences, although in the latter the denaturation takes place in multiple steps due to the fact that the AT rich regions generally open at lower temperatures than the GC rich ones "
    [Show abstract] [Hide abstract]
    ABSTRACT: The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous short sequences of DNA, i.e. ∼100 base pairs, in the framework of a mesoscopic Hamiltonian model which accounts for the helicoidal geometry of the molecule. The theoretical background for the application of the path integral formalism to predictive analysis of the molecule thermodynamical properties is discussed. The base pair displacements with respect to the ground state are treated as paths whose temperature dependent amplitudes are governed by the thermal wavelength. The ensemble of base pairs paths is selected, at any temperature, consistently with both the model potential and the second law of thermodynamics. The partition function incorporates the effects of the base pair thermal fluctuations which become stronger close to the denaturation. The transition appears as a gradual phenomenon starting from the molecule segments rich in adenine-thymine base pairs. Computing the equilibrium thermodynamics, we focus on the interplay between twisting of the complementary strands around the molecule axis and nonlinear stacking potential: it is shown that the latter affects the melting profiles only if the rotational degrees of freedom are included in the Hamiltonian. The use of ladder Hamiltonian models for the DNA complementary strands in the pre-melting regime is questioned.
    Journal of Theoretical Biology 03/2014; 354. DOI:10.1016/j.jtbi.2014.03.031 · 2.12 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: C60 fullerenes confined inside single-walled carbon nanotubes form an archetypal one-dimensional system. X-ray diffraction experiments, from room temperature to 1073 K, reveal an increasing melting phenomenon. Detailed analysis of the sawtooth peak characteristic of the fullerene organization allows the quantitative determination of fluctuations in intermolecular distances. The present results validate the predictions of one-dimensional statistical models.
    Physical Review B 02/2012; 86:045446. DOI:10.1103/PhysRevB.86.045446 · 3.74 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Fullerenes inserted in single-walled carbon nanotubes, the so-called “peapods,” provide scientists with an exceptional molecular model system to study one-dimensional physics and confinement. In this communication, we present recent inelastic neutron scattering measurements concerning the translational dynamics of this one-dimensional system. The recent synthesis of a large amount of two-dimensional oriented samples allows us to extract the sole contribution of the inserted C60 chains. The related quasi-elastic-like peak evolves with the temperature but never shows an additional inelastic contribution when lowering temperature, indicating that carbon peapod is a true one-dimensional system down to low temperatures.
    Fullerenes Nanotubes and Carbon Nanostructures 05/2012; 20(4-7):395-400. DOI:10.1080/1536383X.2012.655209 · 0.84 Impact Factor
Show more