Dielectric study on hydration of B‐, A‐, and Z‐DNA

Umehara, Toshihiro; Kuwabara, Shinichi; Mashimo, Satoru; Yagihara, Shin

doi:10.1002/bip.360300702

Cited by 93 publications

(54 citation statements)

References 43 publications

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“…Time windows employed were 5 mad 20 ns for the shorter cell and 50, 100, 200, 500 ns, 1, 2, 5, and 10 Ixs for the longer cell. By using these cells, even very small relaxation with a relaxation strength of the magnitude of 0.1 may be measured in the frequency region of concern (Umehara et al, 1990). For the overlapping region of frequency between 100 MHz and 1 GHz, data obtained by the two cells were in agreement.…”

Section: Tdr Methodsmentioning

confidence: 74%

Dielectric-Relaxation Spectroscopy of Kaolinite, Montmorillonite, Allophane, and Imogolite under Moist Conditions

Ishida

Makino

Wang

2000

Clays and clay miner.

100

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Abstract--The dielectric behavior of kaolinite, montmorillonite, allophane, and imogolite samples adjusted to a water potential of 33 kPa was examined using a time-domain reflectometry method over a wide frequency range of 103-10 ~~ Hz. A dielectric relaxation peak owing to bound H20 was observed. The observation of this peak required the precise determination of the contributions of dc conductivity. The peak is located at 10 MHz, indicating that the relaxation time of the bound H20 is approximately ten times longer than the relaxation time of bound H20 with organic polymers, such as an aqueous globular-protein solution. The structure of bound H20 differs between phyllosilicates and amorphous phases, based on differences in relaxation strength and the pattern of distribution of the relaxation times. The dielectric process involving rotation of bulk H20 molecules was also observed at 20 GHz. The relaxation strength of bulk H20 increased with an increase in the water content. The interfacial polarization in the diffuse double layer occurred only in montmorillonite and kaolinite, indicating that mechanisms involving the Maxwell-Wagner and surface-polarization effects cannot be extended to include allophane and imogolite. Although these results suggest that additional work is required, a tentative conclusion is that a tangential migration of counter-ions along clay surfaces may be important.

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Section: Tdr Methodsmentioning

confidence: 74%

Dielectric-Relaxation Spectroscopy of Kaolinite, Montmorillonite, Allophane, and Imogolite under Moist Conditions

Ishida

Makino

Wang

2000

Clays and clay miner.

100

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“…X-ray crystallography, NMR, dielectric relaxation, and molecular dynamics simulation studies have shown that a significant amount of water molecules are bound to DNA (for reviews, see refs. [2][3][4][5][6]. For example, measurements of dielectric relaxation caused by water molecules bound to DNA in mixed water-ethanol solutions have found that 18-19 water molecules per nucleotide are present in B-DNA, but only 13-14 water molecules are bound in A-DNA (5).…”

mentioning

confidence: 99%

“…[2][3][4][5][6]. For example, measurements of dielectric relaxation caused by water molecules bound to DNA in mixed water-ethanol solutions have found that 18-19 water molecules per nucleotide are present in B-DNA, but only 13-14 water molecules are bound in A-DNA (5). The study also suggested that a structural transition of poly(dG-dC)⅐poly(dGdC) DNA from its B to Z form takes place on the removal of the bound water molecules, preferentially from the phosphate groups.…”

mentioning

confidence: 99%

Water at DNA surfaces: Ultrafast dynamics in minor groove recognition

Pal

Zhao

Zewail

2003

Proc. Natl. Acad. Sci. U.S.A.

233

296

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Water molecules at the surface of DNA are critical to its equilibrium structure, DNA-protein function, and DNA-ligand recognition. Here we report direct probing of the dynamics of hydration, with femtosecond resolution, at the surface of a DNA dodecamer duplex whose native structure remains unperturbed on recognition in minor groove binding with the bisbenzimide drug (Hoechst 33258). By following the temporal evolution of fluorescence, we observed two well separated hydration times, 1.4 and 19 ps, whereas in bulk water the same drug is hydrated with time constants of 0.2 and 1.2 ps. For comparison, we also studied calf thymus DNA for which the hydration exhibits similar time scales to that of dodecamer DNA. However, the time-resolved polarization anisotropy is very different for the two types of DNA and clearly elucidates the rigidity in drug binding and difference in DNA rotational motions. These results demonstrate that hydration at the surface of the groove is a dynamical process with two general types of trajectories; the slowest of them (Ϸ20 ps) are those describing dynamically ordered water. Because of their ultrafast time scale, the ''ordered'' water molecules are the most weakly bound and are accordingly involved in the entropic (hydration͞dehydration) process of recognition. H ydration of DNA plays important role in its structure, conformation, and function. Of significance to the function is the selective recognition by DNA of small molecules (ref. 1 and references therein). X-ray crystallography, NMR, dielectric relaxation, and molecular dynamics simulation studies have shown that a significant amount of water molecules are bound to DNA (for reviews, see refs. 2-6). For example, measurements of dielectric relaxation caused by water molecules bound to DNA in mixed water-ethanol solutions have found that 18-19 water molecules per nucleotide are present in B-DNA, but only 13-14 water molecules are bound in A-DNA (5). The study also suggested that a structural transition of poly(dG-dC)⅐poly(dGdC) DNA from its B to Z form takes place on the removal of the bound water molecules, preferentially from the phosphate groups.The molecular picture of hydration in the minor groove of B-DNA is unique. An x-ray crystallographic investigation (7) followed by solution NMR study (8) on a model dodecamer B-DNA duplex (for the sequence of A͞T tracts, CGCGAAT-TCGCG) showed that the minor groove is hydrated in an extensive and regular manner, with a zigzag ''spine'' of firstand second-shell hydration along the f loor of the groove. In contrast, hydration within the major groove is principally confined to a monolayer of water molecules. The conformational energy calculation suggested that the presence of the spine of hydration is the prime reason for the further narrowing of minor groove (9).The influence of drug binding on DNA hydration is striking. Acoustic and densimetric studies have shown that a fraction (not total) of the water molecules is released on recognition (10, 11). Hence, the balance between enthalpic and entr...

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“…Studies of water vapour adsorption of DNA films by IR spectroscopy have shown that the hydrogen bonded water peak maxima shifted from 3473 to 3583 cm -1 as moisture content increases. This was attributed to the formation of a thin liquid water film on the surface of DNA [6].The interaction between DNA and water were described by quantum mechanical methods [2] and by molecular dynamics [7]. Water network around simulated duplexes was more conformation specific rather than sequence specific [7].…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Water vapour adsorption on DNA

Balköse

Alp

Ülkü

2008

J Therm Anal Calorim

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DNA is a molecule which is present in the nucleus of each living cell. It is the molecule which synthesizes proteins. DNA conformation [1], electrical conductivity [2] and density [3] depend on the amount of water it contains. The phosphate groups, nitrogen and oxygen atoms of the base pairs in DNA bind to water molecules by hydrogen bonding. DNA adsorbs moisture from atmosphere and it is a water soluble macromolecule. The state of water in DNA has been investigated by X-ray diffraction, by inelastic neutron scattering [4] and melting of frozen water in DNA [5] by previous workers. The bound water in frozen DNA does not show ice melting endotherm. This is due to distribution of electric charges around phosphate groups. Dielectric study on hydration of DNA in water-ethanol solutions showed that 19 and 13 molecules of water per nucleotide are required for B-DNA and A-DNA respectively to keep the double helix. Studies of water vapour adsorption of DNA films by IR spectroscopy have shown that the hydrogen bonded water peak maxima shifted from 3473 to 3583 cm -1 as moisture content increases. This was attributed to the formation of a thin liquid water film on the surface of DNA [6].The interaction between DNA and water were described by quantum mechanical methods [2] and by molecular dynamics [7]. Water network around simulated duplexes was more conformation specific rather than sequence specific [7]. Water influences DNA stability and the contribution of water molecules to the energy of DNA helical structure was found from the energy spectrum of the bound water and enthalpy of helix-coil transformation [8]. Energy change was inversely proportional to amount of bound water per nucleotide.In studying DNA by IR spectroscopy diffuse reflectance The state of the sample could change during sample preparation, handling and measurement stages using these techniques.This research aims studying water vapour adsorption of DNA in situ. Outgassing the samples in vacuum and sending water vapour at controlled rate and pressure prevented any change in state of the sample between outgassing and measuring stages. No change in state of the sample occurs since the sample was not transferred from preparation environment to measuring environment. While water vapour was sent continuously at a low rate in gravimetric system, water vapour at different pressures was sent in steps in FTIR Drift cell and microcalorimeter cell. ExperimentalIn the present study sodium salt DNA obtained from calf tymus (Sigma) was used.The morphology of the fibres was investigated by scanning electron microscopy using Philips VL30 SFEG SEM.Equilibrium and kinetics of water vapour adsorption on calf thymus DNA was studied by Cahn gravimetric adsorption system described in a previous paper [11]. The system has Edwards ultra high vacuum system and all vacuum glass valves were from Scientific Glass Company. Adsorption isotherm of water vapour on DNA at 25°C was determined after Analysis and Calorimetry, Vol. 94 (2008)

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Dielectric study on hydration of B‐, A‐, and Z‐DNA

Cited by 93 publications

References 43 publications

Dielectric-Relaxation Spectroscopy of Kaolinite, Montmorillonite, Allophane, and Imogolite under Moist Conditions

Dielectric-Relaxation Spectroscopy of Kaolinite, Montmorillonite, Allophane, and Imogolite under Moist Conditions

Water at DNA surfaces: Ultrafast dynamics in minor groove recognition

Water vapour adsorption on DNA

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