DNA hydration

A possible explanation of the hysteresis could be the non-equilibrium of the DNA hydration. In that case the value of hysteresis has to depend on the size of the experimental sample. However, such a dependence is not observed in the wide range of DNA film thicknesses (0.05-0.2 fmi) [14], [12]. Thus, hysteresis cannot be a macroscopic phenomenon and does reflect the molecular interaction of water and the biopolymer. 

Since there is such an imprecise division between direct and indirect effects in the literature, some experimental results are presented to clarify this classification. Basically, one cannot detect HO radicals at low DNA hydrations (ca. 10 water molecules per nucleotide) [12]. This means that in the first step of ionization, the hole produced in the DNA hydration shell transfers to the DNA. It is impossible to distinguish the products from the hole or electron initially formed in the water from the direct-effect damage products. For this discussion, direct-type damage will be considered to arise from direct ionization of DNA or from the transfer of electrons and holes from the DNA solvation shell to the DNA itself. 

The DNA solvation shell consists of about 20-22 water molecules per nucleotide of these, — 15-17 waters associate with the nucleoside and —5 waters associate with the phosphate group [13,14]. Water outside the solvation layer is termed bulk water. Upon freezing, the DNA solvation water forms two primary phases the ice phase, consisting of one or more of the crystalline forms of ice, and a DNA-associated phase, consisting of ordered water which comes in direct contact with the DNA (primary layer) and disordered water in the secondary layer. DNA hydration is expressed in terms of F, the number of water molecules per nucleotide. 

From the yields of 5,6-dihydropyrimidine radicals, we predict reduction product yields of 0.04-0.06 pmol/J for 5,6-dihydrouracil and 0.03-0.05 pmol/J for 5,6-dihydro-thymine for B-form DNA hydrated to 9 waters per nucleotide. With respect to oxidation products, we predict strand-break yields —0.10 pmol/J. A very surprising prediction of this model is that the yield of damaged guanine is nil. Half the damage is oxidized sugar products and the other half is reduced pyrimidines. 

Hydroxyl radicals formed in the DNA hydration shell have a high probability for reaction with the DNA and will result in DNA lesions, including base damage and strand breaks [3, 18, 19]. In this respect hole transfer from water to DNA would prevent formation of the hydroxyl radical, and may act... 

Cai et al. [7d] studied the effect of the level of DNA hydration on electron and hole transfer in the MX-DNA system. ESR spectra show that MX radicals decrease relative to the DNA radicals with increasing hydration levels up to r=22 D20/nucleotide. The results further indicate that, as the hydration level increases up to F=22 D20/nucleotide, the interduplex distance D s increases. This results in a substantial decrease in the apparent transfer distances as well as electron and hole transfer rates. Figure 9 shows plots of the transfer rates of electrons, holes, and overall DNA radicals at 77 K vs hydration levels (lower axis) as well as vs the distance between DNA ds s (upper axis). Please note that at hydration levels higher than 22 D20/nucleotide, a... 

DNA Hydration and Structural Transitions Are Correlated Some Hypotheses... 

This technique was employed to monitor the B —> A transition of DNA as a function of the relative humidity (Pilet and Brahms, 1973 Pohle et al., 1984). The investigated bands are those which reflect the vibrations of the phosphate groups. As shown by Fig. 4.7-3, which presents the polarized infrared spectra of a salmon sperm DNA hydrated film with 93% RH (top, B form) and 58% RH (bottom, A form), the dichroism of the two phosphate bands changes. The B form of the antisymmetric PO2 stretching vibration around 1230 cm is non-dichroic, while that of the A form is perpendicular. The B form of the symmetric PO2 stretching vibration around 1090 cm is perpendicular, while that of the A form is parallel. A simple computation, for instance for the latter band, shows that the value of the angle between the transition dipole moment of this vibration and the double helical axis varies between 68 ° (B form) and 49 ° (A form). This parameter is an extremely sensitive indicator of a B A transition and may also be employed to show the inhibition of a B —> A transition by various classes of molecules, such as proteins (Liquier et al., 1977 Taillandier et al., 1979) or drugs (Fritzsche and Rupprecht, 1990). 

Ion-beam irradiation (77 K) of DNA hydrated to T = 18 DjO/ nucleotide resulted in a DNA-phosphorus-centered radical. Samples were irradiated with 60 MeV/u, or 100 Mev/u Ar +. The ESR results showed the presence of an axially symmetric spectrum with large phosphorus couplings (Aj = 77.5 mT and = 61.0 mT, = 2.000,= 2.001), from a radical that constituted ca. 0.1% to 0.2% of the total radical concentration. Earlier literature regarding the origin and ESR spectra of such radicals existed and it was concluded that the radical was a phosphoryl radical (ROPOj, Scheme 6), formed from the electron gain path. In DNA, such a radical could result only from P-O bond cleavage at either the C3 or C5 of the deoxyribose sugar... 

Structural Aspects of DNA Hydration Dynamics of DNA Hydration Computer Simulations Protein-DNA Recognition Concluding Remarks... 

Water of hydration is chemically identical to water in the bnlk. The differences between these two popnlations of water involve only their physical properties. Conseqnently, many physical methods have been employed to characterize water of DNA hydration. 

In summary, the picture emerging from these studies suggests that DNA is an extensively hydrated macromolecule the very stmcture of DNA is dictated by its interactions with water. The aggregate results suggest that 10 to 30 waters per phosphate interact with DNA and that these waters can be distinguished from bulk water by various physical observables. DNA hydration, as characterized by physical methods, has been shown to be sequence-, composition-, and conformation-dependent. However, different physical parameters are sensitive to different subpopulations of waters of hydration. As such, different parameters may be complementary but not directly comparable with each parameter providing its own unique window into a particular aspect of DNA-solvent interactions. 

Mrevlishvili GM. Dependence of natural DNA hydration on the GC content, (in Russian). Dokl. Akad. Nauk USSR 1981 260 761-764. 

Feig M, Pettitt BM. A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers 1998 48 199-209. 

Faraone A, Mamontov E. Experimental evidence of fragile-to- 96. strong dynamic crossover in DNA hydration water. J. Chem. 

Perhaps the first indication of the dependence of DNA damage on hydration was reported for frozen aqueous solutions [85], where the radical yield in wet DNA was reported to be twice the yield obtained in dry DNA. Additionally, the yield of radical ions at 77 K was found to increase by a factor of four upon inclusion of the primary DNA hydration layer [86]. In lyophilized DNA, it was instead noted that radical yield increases with hydration to a certain extent, but then a plateau is reached that cannot be surmounted by increasing the level of hydration [73]. The absolute yields of the individual ion radicals have also been determined to vary with hydration, where for example T predominates in dry DNA and predominates when the hydration layer is included [75,77]. Alternatively, evidence exists which indicates that DNA damage does not increase with consideration of the primary hydration layer, but increases upon inclusion of the secondary layer. These studies include investigations of the release of unaltered bases [87], the production of base damage products (14 detected in total) [70], and the efficiency of strand breaks [88]. 

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