Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

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. DOI: 10.1103/PhysRevLett.107.088102 PACS numbers: 87.14.gk, 63.22.Àm, 78.70.Nx, 87.10.Tf DNA stores the genetic code of all living organisms. Its principle biological functions of DNA are therefore transcription and replication. These processes take place in cells where DNA undergoes protein-mediated, mechanical manipulation resulting in folding, coiling and denaturing of the DNA molecule. The elasticity of DNA also underpins cleavage by enzymes [1] and the formation of 'bubbles' of locally denatured zones along the helix [2,3]. Models describing biologically relevant processes depend on the mechanical properties of DNA expressed as parameters, such as the base-pair force constant, which is crucial in the process of denaturing of DNA [4,5]. All measurements of DNA elasticity are therefore important in understanding the biological function of DNA and here we focus on stretching elasticity and the underlying base-pair stacking interaction.Recently considerable progress has been made in measuring the flexibility of the DNA helix although one concern is the extent to which the experimental or theoretical approaches themselves influence the results [6]. From well-defined oligomers of DNA, the stretch-torsion coupling can be obtained via magnetic tweezers and measuring the consequent over-or under-winding of the helix by tracking an attached rotor bead. In the work of Gore et al.[7], a stretching elastic modulus is reported, which equates to an inter base-pair force constant of 3 N=m. Another example of a molecular sculpturing approach involves DNA oligomers capped with gold nanoparticles, which allow the end-to-end distance to be measured by small angle x-ray scattering [8]. This work reported corresponding values 10 times smaller: 0:3 N=m. Similarly, Wiggins et al.[9] extracted bending force constants from single DNA molecule conformations on a substrate. They too found that the corresponding force constants are much smaller on a local length scale than predicted by classical elasticity models. A more theoretical approach [10] uses the well-known melting temperatures of DNA to calculate the flexibility on a local length scale via the Peyrard-Bishop model [11], assuming ...

Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures

“…These apparent discrepancies between macroscopic and microscopic flexibilities are not unexpected. Even for DNA, it has been difficult to reconcile microscopic flexibility with mesoscopic persistence length measurements (9,10). …”

Progressive melting in confined one-dimensional C60chains

“…This interest exceeds the domain of physics and extends to biological structures such as DNA. 5,6 However, none of the existing 1D systems was stable at high temperature. This is why the discovery of single-walled carbon nanotube (SWNT) inclusion compounds has once again highlighted 1D systems and their particular thermodynamics.…”

Translational Dynamics of One-Dimensional Fullerene Chains Encapsulated Inside Single-Walled Carbon Nanotubes

“…The dynamical structure factor of such a system can be 396 C. Bousige et al calculated exactly (8)(9)(10). Inelastic neutron scattering (INS) experiments were successfully performed with Hg 3-δ AsF 6 single crystals where long 1D mercury chains were shown to be 1D harmonic liquid above the critical temperature of 120 K (11), and the same type of study was also performed on water chains in DNA (12,13). Nevertheless, the common problem of these compounds is that they are not stable at high temperature, and that when lowering the temperature a long range order establishes due to the interaction with the three-dimensional (3D) network (14)(15)(16), preventing one from studying 1D properties on a wide temperature range.…”