Dynamics and structure of water bound to DNA

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

doi:10.1021/j100328a009

Cited by 29 publications

(19 citation statements)

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“…They show up peaks between 50 and 80 MHz, 0.9 and 1.2 GHz and 15 and 18 GHz for the b-, d-and g-relaxations, respectively, which slightly shi towards lower frequencies with decreasing temperature. Similar kinds of peaks have been observed previously for rigid biopolymers such as DNA and collagen, which show a dielectric relaxation peak around 100 MHz independently of bulk water relaxation observed around 20 GHz, [56][57][58] and it was concluded that the observed peak was due to the orientation of water molecules bound to these polymers.…”

Section: Resultssupporting

confidence: 85%

Relaxation dynamics in lens crystallin proteins: a dielectric and thermodynamic approach using TDR

2014

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Dielectric relaxation of water in biological systems, such as proteins and DNA, can often be described by two different time constants, one in the picosecond and the other in the nanosecond regime. In the present work, we report the temperature dependence of the relaxation dynamics, dielectric permittivity (3 0 ) and loss (3 00 ) of aqueous lens proteins (crystalline) in the goat eye lens. The measurements have been carried out in the frequency range from 10 MHz to 20 GHz using TDR and in the temperature region from 298.15 K to 278.15 K. We analyse the three dispersion regions commonly found in protein solutions, usually termed b-, g-and d-relaxation. The b-relaxation, occurring in the frequency range between 70 and 100 MHz, and the g-relaxation between 15 and 18 GHz can be attributed to the rotation of the polar protein molecules in their aqueous medium and the reorientational motion of the free water molecules respectively. The nature of d-relaxation, which is often ascribed to the motion of bound water molecules, is not yet fully understood. Here, we provide data on the temperature dependence of dielectric and thermodynamic parameters of all three detected processes, b-, g-and d-relaxation. We found significant temperature dependence of the dielectric and thermodynamic parameters of the aqueous proteins, indicating conformational changes.

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Section: Resultssupporting

confidence: 85%

Relaxation dynamics in lens crystallin proteins: a dielectric and thermodynamic approach using TDR

2014

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“…Recently we used the time‐domain reflectometry (TDR) to disclose dynamic features of this system, particularly the characteristic structures and properties of water 19, 20. This is because TDR is a method developed by Cole and Mashimo21–25 for measuring dielectric dispersion in the 1 MHz to 10 GHz and used effectively for aqueous biopolymer solutions 25–34. So far heat capacity measurements have been made on H 2 O and D 2 O solutions of relatively low concentrations (below 21.1 wt %)9, 10, 13, 19 and TDR measurements on 14.7, 17.8, and 20 wt % solutions 19, 20.…”

Section: Introductionmentioning

confidence: 99%

Ordering in aqueous polysaccharide solutions. I. Dielectric relaxation in aqueous solutions of a triple‐helical polysaccharide schizophyllan

Hayashi¹,

Shinyashiki²,

Yagihara³

et al. 2001

Biopolymers

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Deuterium oxide solutions of a triple-helical polysaccharide schizophyllan, undergoing an order-disorder transition centered around 17 degrees C, were studied by the time-domain reflectometry (TDR) to obtain dielectric dispersions in the solution and frozen states. In the solution state, the dispersion below the transition temperature is resolved in three dispersions (relaxation times at 0 degrees C) ascribed to side chain glucose residue (1; 102 ns), structured water (s; 2.0 ns) and bulk water (h), respectively, from low to high frequencies. Bulk water is divided into slow water (h2; 0.04 ns) and free or pure water (h1; 0.02 ns). Above the transition temperature structured water almost disappears and is compensated by slow water. Structured water is similar to bound water for proteins but different from it because of this transition behavior. Another dispersion (l) seen at the lowest frequency is assigned to the rotation of side-chain glucose residue coupled with hydrated water. Parts of this dispersion and structured water are suggested to constitute bound water. In the frozen state were observed a major dispersion (h; 0.14 ns) and a minor one (m; 28 ns), which were ascribed to considerably mobile and less mobile waters. They are similar to but not exactly the same as that for unfreezable water in bovine serum albumin solutions argued by Miura et al. (Biopolymers, 1995, Vol. 36, p. 9). Water is molded into different structures by the triple helix.

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“…Recently we have found the dielectric relaxation peak due to the bound water around 100 MHz. 11,12 The measurements were performed a t temperatures higher than 0°C and in dilute aqueous solutions with appropriate buffer. The results obtained offer what information is available on hydration of DNA in vivo.…”

Section: Introductionmentioning

confidence: 99%

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

Umehara¹,

Kuwabara²,

Mashimo³

et al. 1990

Biopolymers

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Dielectric relaxation peak due to bound water was found around 100 MHz in poly(dG-dC).poly(dG-dC) and calf thymus DNA in water-ethanol mixtures with NaCl buffer. Relaxation time and strength show a transition for poly(dG-dC).poly(dG-dC) at an ethanol composition Cw = 0.45 (w/w) where the structural transition from B- to Z-DNA takes place. It has been suggested that the transition is caused by removal of the bound water molecules preferentially from the phosphate groups. If the bound water molecules are removed equally from the phosphate groups and the grooves, the structural transition from B to A takes place. By analogy with hydration of tropocollagen, it was found that 19 water molecules per one nucleotide are at least necessary to keep B-DNA. Thirteen molecules are bound to A-DNA and 9 molecules to Z-DNA. Stringlike multimers are proposed as available structures of the bound water.

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Dynamics and structure of water bound to DNA

Cited by 29 publications

References 1 publication

Relaxation dynamics in lens crystallin proteins: a dielectric and thermodynamic approach using TDR

Relaxation dynamics in lens crystallin proteins: a dielectric and thermodynamic approach using TDR

Ordering in aqueous polysaccharide solutions. I. Dielectric relaxation in aqueous solutions of a triple‐helical polysaccharide schizophyllan

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

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