Role of counterions in the gigahertz relaxation of wet DNA

SCREW MOTION OF DNA DUPLEX DURING TRANSLOCATION THROUGH PORE I: INTRODUCTION OF THE COARSE-GRAINED MODEL

Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion–hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion–hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA–protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA–protein molecular machines via symmetry breaking in DNA–protein friction.

Effects of counterion valency on the damping of phonons propagating along the axial direction of liquid-crystalline DNA

The phonon propagation and damping along the axial direction of films of aligned 40 wt % calf-thymus DNA rods are studied by inelastic x-ray scattering (IXS). The IXS spectra are analyzed with the generalized three effective eigenmode theory, from which we extract the dynamic structure factor S(Q,E) as a function of transferred energy E=variant Planck's over 2piomega, and the magnitude of the transferred wave vector Q. S(Q,E) of a DNA sample typically consists of three peaks, one central Rayleigh scattering peak, and two symmetric Stokes and anti-Stokes Brillouin side peaks. By analyzing the Brillouin peaks, the phonon excitation energy and damping can be extracted at different Q values from about 4 to 30 nm(-1). A high-frequency sound speed is obtained from the initial slope of the linear portion of the dispersion relation below Q=4 nm(-1). The high-frequency sound speed obtained in this Q range is 3100 ms, which is about twice faster than the ultrasound speed of 1800 ms, measured by Brillouin light scattering at Q approximately 0.01 nm(-1) at the similar hydration level. Our observations provide further evidence of the strong coupling between the internal dynamics of a DNA molecule and the dynamics of the solvent. The effect on damping and propagation of phonons along the axial direction of DNA rods due to divalent and trivalent counterions has been studied. It is found that the added multivalent counterions introduce stronger phonon damping. The phonons at the range between approximately 12.5 and approximately 22.5 nm(-1) are overdamped by the added counterions according to our model analyses. The intermediate scattering function is extracted and it shows a clear two-step relaxation with the fast relaxation time ranging from 0.1 to 4 ps.

Low doses of alpha- and gamma-radiation enhance DNA thermal stability

Isolated calf thymus DNA in buffered solutions has been exposed to 0-150 Gy of alpha- and gamma-radiation. The effects of alpha- and gamma-radiation on the thermal stability and electrophoretic mobility of the DNA molecules have been studied by UV spectroscopic 'melting' and Pulsed Field Gel Electrophoresis (PFGE), respectively. The observed thermal denaturation parameters were fitted to the energy propagation descriptive model. The experimental results for the samples exposed to relatively low (low) doses indicate an increased thermal stability and a reduced mobility over that of the controls. The expected overall degradation of the DNA molecules was confirmed for the samples exposed to high doses. Our results are in good agreement with the predictions of the energy propagation model, which now is also tested in the low dose region and for an additional type of ionising radiation (alpha-particles). Our findings are consistent with conformational changes at low doses resulting in a DNA form characterised by localised alterations, which affect the energy flow along the DNA molecule.