Role of counterions in the gigahertz relaxation of wet DNA

Edwards, Glenn S.; Ying, Guangtao; Tribble, Jerri A.

doi:10.1103/physreva.45.r8344

Cited by 12 publications

(8 citation statements)

References 24 publications

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“…4,9,18,21 The damping of the Brillouin peaks is different in samples of Na-DNA and Li-DNA at the same relative humidity condition. 4,9,18,21 The damping of the Brillouin peaks is different in samples of Na-DNA and Li-DNA at the same relative humidity condition.…”

Section: Introductionmentioning

confidence: 98%

“…4,9,18,21 The damping of the Brillouin peaks is different in samples of Na-DNA and Li-DNA at the same relative humidity condition. 4 The low-frequency mode at ϳ20 cm −1 in the Raman spectra of wet DNA gels was studied at different temperatures. 4 The low-frequency mode at ϳ20 cm −1 in the Raman spectra of wet DNA gels was studied at different temperatures.…”

Section: Introductionmentioning

confidence: 98%

“…[1][2][3][4][5][6][7][8][9] Evidences from different kinds of experiments show that the internal dynamics of DNA molecules is closely coupled to that of the solvent molecules. [1][2][3][4][5][6][7][8][9] Evidences from different kinds of experiments show that the internal dynamics of DNA molecules is closely coupled to that of the solvent molecules.…”

Section: Introductionmentioning

confidence: 99%

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

Chen¹,

Berti²,

Baglioni³

et al. 2005

The Journal of Chemical Physics

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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.

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Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Chen¹,

Berti²,

Baglioni³

et al. 2005

The Journal of Chemical Physics

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“…"Manning shell" physically means that the counterions are massively condensed at some proper distance from the DNA surface, with the water of hydration filling the whole space between the DNA surface and the counterion condensate. Furthermore, this Manning shell is moving as a whole with respect to the DNA polyanion, activating the so-called "DNA acoustic plasmons" [91][92][93][94][95][96] . Hence, the very presence of the counterion-water shell, as well as the collective dynamics of the latter, should physically guarantee both static and dynamic screening of the phosphodiester electrostatics.…”

Section: Critical Assessment Of the Biopolymer Charge Transfer/transpmentioning

confidence: 99%

Electrical Conductance in Biological Molecules

Shinwari

Deen

Starikov

et al. 2010

Adv Funct Materials

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Nucleic acids and proteins are not only biologically important polymers: They have recently been recognized as novel functional materials surpassing in many aspects the conventional ones. Although Herculean efforts have been undertaken to unravel fine functioning mechanisms of the biopolymers in question, there is still much more to be done. This particular paper presents the topic of biomolecular charge transport, with a particular focus on charge transfer/transport in DNA and protein molecules. Here the experimentally revealed details, as well as the presently available theories, of charge transfer/transport along these biopolymers are critically reviewed and analyzed. A summary of the active research in this field is also given, along with a number of practical recommendations.)Received: ((will be filled in by the editorial staff))Revised: ((will be filled in by the editorial staff))

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“…Now, let us consider collective dynamics of the DNA-counterion-water system in solution -at first in the absence of the externally applied electrostatic field. It is long known [41][42][43][44][45][46] that such a system will allow acoustic plasmons with longitudinal vibrations of DNA duplexes as a whole with respect to their Manning clouds as a whole. However, this longitudinal degree of freedom has been obtained assuming that the charge density of the DNA duplex surface is uniform and homogeneous.…”

mentioning

confidence: 99%

Screw Motion of Dna Duplex During Translocation Through Pore I: Introduction of the Coarse-Grained Model

Starikov

Hennig

Yamada³

et al. 2009

Biophys. Rev. Lett.

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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.

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Role of counterions in the gigahertz relaxation of wet DNA

Cited by 12 publications

References 24 publications

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

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

Electrical Conductance in Biological Molecules

Screw Motion of Dna Duplex During Translocation Through Pore I: Introduction of the Coarse-Grained Model

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