Hydration shell of DNA

One of the most thoroughly investigated examples of polymeric biomolecules in regard to the stabilization of ordered structures by hydration are the DNAs. Only shortly after establishing the double-helix model by Watson and Crick 1953 it became clear, that the hydration shell of DNA plays an important role in stabilizing the native conformation. The data obtained by the authors working in this field up until 1977 are reviewed by Hopfinger155>. 

Falk M, Poole A-G, Goymour CG (1970) Infrared study of the state of water in the hydration shell of DNA. Can J Chem 48 1536-1542... 

One manifestation of strong solnte-solvent interactions is the inability of affected waters to freeze when the temperature falls well below the freezing point. Nnclear magnetic resonance (NMR), infrared spectroscopy, and low-temperatnre calorimetry have been employed to characterize the number of nonfreezing waters in the hydration shell of DNA (6-9). Based on their infrared measnrements of DNA films, Falk et al. (6) have concluded that about 10 water molecules per nucleotide are incapable of freezing with an additional 3 waters that show... 

At low temperatures, radiation-induced conductivity critically depends on the water content and appears only above the critical hydration levels 0.41 and 0.79 g/g for collagen and DNA, respectively [602, 603]. The critical hydration level for DNA corresponds to about 15 water molecules per phosphate group (F = 15). The effects of various additives on the conductivity evidence charge migration in the hydration shell of DNA [604]. At much lower hydrations (0.12 to 0.22g/g), conductivity of hydrated DNA shows exponential dependence on h [605], which may be attributed to the intrinsic semiconductivity of the DNA backbone. More detailed experimental studies of DNA hydration [606] show that radiation-induced conductivity starts not strictly atP =15 [602, 603] but via a sigmoid-like increase within hydration range from r = lltoF = 16 with subsequent stepwise increase at F 24. 

Diffusion of water in the hydration shell of DNA molecule depends on hydration F, similarly as at the lysozyme surface. The effective diffusion coefficient calculated by equation (27) shows a gradual increase with hydration, which is followed by a weak trend toward saturation (Fig. 118, left panel). The short-range mobility and long-range mobility calculated in the time intervals 5 ps short-range mobility are seen in the hydration range... 

Figure 122 Time dependence of the MSD (r ) of Na ions in the hydration shells of DNA in a double-logarithmic scale (symbols). Fits of the data in the range 1 < t(ps) < 1000 to equations (25) and (26) are shown by dashed and sohd lines, respectively (data from [642]).

Change of the fitting parameters in equation (26) with hydration is shown in Fig. 123. The exponent of a of anomalous diffusion of ions demonstrates sigmoid-like behavior with hydration. An inflection point of this dependence, which indicates transition between two regimes, is remarkably close to the percolation threshold of water at F = 15.5. Below and above this hydration level, different temporal/spatial disorder is probed by Na+ ions in the hydration shell of DNA. When the hydration shell is dispersed in a large number of small clusters below the percolation threshold, a is low (at about 0.65). When the hydrogen-bonded network of water exists above the percolation threshold, a approaches 0.80. So, spanning water network smooths a DNA surface for translational motion of ions. 

A. Oleinikova, I. Brovchenko, A. Krukau, A. Mazur, Anomalous diffusion in the hydration shell of DNA, to be published. 

Primary and secondary hydration shells around DNA. The hydration of DNA is not homogeneous. It can be described in terms of two shells, as suggested by sedimentation equilibrium studies [857-859, 861], isopiestic measurements [860], gravimetric and infrared spectroscopic investigations [853-855, 862]. 

With these notes of caution, X-ray crystallographic studies have provided important insights into the patterns of hydration of the A-, B-, and Z-conformations of DNA. In a seminal work, based on 15 B-DNA, 22 A-DNA, and 22 Z-DNA structures, Schneider et al. (17) have determined the average number of water molecules located in the first hydration shells of phosphates and bases of A-, B-, and Z-form DNAs. It has been found that the sum of the waters in the hydration shells of phosphates and bases coincides with the net number of ordered waters in A- and B-DNA. This agreement is consistent with a picture in which the hydration shells of phosphate groups and bases in DNA do not overlap. By contrast, the sum of phosphate and base waters in Z-DNA (6.8) is larger than the total number of ordered waters (5.3), which suggests an overlap between the hydration shells of the backbone and the bases. The latter... 

V, P. Chuprina, U. Heinemann, A. A. Nurislamov, P. Zielenkiewicz, and R. E. Dickerson, Proc. Natl. Acad. Set. USA, 88, 593 (1991). Molecular Dynamics Simulation of the Hydration Shell of a B-DNA Decamer Reveals Two Main Types of Minor-Groove Hydration Depending on Groove Width. 

Formation of a sparming network of hydration water at the DNA surface upon hydration was studied by computer simulations [200,621] using the water drop methods [622, 623]. Simulations were carried out for a rigid dodecamer fragment of double-helical DNA. The structures of the canonical B-DNA and A-DNA [624] were fixed in space. The system involved 24 bases and 22 phosphate groups in two DNA strands surrounded by a mobile hydration shell of 22 Na ions and 24F water molecules. Evolution of the cluster size distribution ns on the surface of B-DNA upon increasing hydration is shown in Fig. 104. At low hydrations (F = 12, 13, and 14), ns shows deviations upward from the power law (19) at the intermediate cluster sizes S. At high hydrations (F = 17, 18, 19, and... 

The hydration shell is formed with the increasing of the water content of the sample and the NA transforms from the unordered to A- and then to B form, in the case of DNA and DNA-like polynucleotides and salt concentrations similar to in vivo conditions. The reverse process, dehydration of NA, results in the reverse conformational transitions but they take place at the values of relative humidity (r.h.) less than the forward direction [12]. Thus, there is a conformational hysteresis over the hydration-dehydration loop. The adsorption isotherms of the NAs, i.e. the plots of the number of the adsorbed water molecules versus the r.h. of the sample at constant temperature, also demonstrate the hysteresis phenomena [13]. The hysteresis is i( producible and its value does not decrease for at least a week. 

The average DNA helix diameter used in modeling applications such as the ones described here includes the diameter of the atomic-scale B-DNA structure and— approximately—the thickness of the hydration shell and ion layer closest to the double helix [18]. Both for the calculation of the electrostatic potential and the hydrodynamic properties of DNA (i.e., the friction coefficient of the helix for viscous drag) a helix diameter of 2.4 nm describes the chain best [19-22]. The choice of this parameter was supported by the results of chain knotting [23] or catenation [24], as well as light scattering [25] and neutron scattering [26] experiments. 

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