DNA, solvation shell

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. 

The alternative noncovalent functionalization does not rely on chemical bonds but on weaker Coulomb, van der Waals or n-n interactions to connect CNTs to surface-active molecules such as surfactants, aromatics, biomolecules (e.g. DNA), polyelectrolytes and polymers. In most cases, this approach is used to improve the dispersion properties of CNTs [116], for example via charge repulsion between micelles of sodium dodecylsulfate [65] adsorbed on the CNT surface or a large solvation shell formed by neutral molecule (e.g. polyvinylpyrrolidone) [117] around the CNTs. 

Sevilla et al. [49] have simulated the EPR spectrum of whole DNA equilibrated with D2O irradiated and observed at 77 K. The results were 77% Cyt and 23% Thy for the anions and >90% Gua for the cations. The analysis produced a small imbalance in the cations (44%) and anions (56%). It was suggested that some holes remain trapped in the solvation shell. It is also possible that this reflects small errors in the treatment of the basis spectra, or that some DNA radicals are not accounted for because their EPR signal is too broad and poorly resolved. 

Studies of the direct effect have been largely confined to DNA samples in the solid state. This is done in order to maximize direct-type damage and minimize indirect-type damage. In addition, low temperatures are often employed both as a means of sequestering the DNA from the bulk water and as a means of stabilizing free radical intermediates. In frozen DNA samples, the mobility of holes and excess electrons differs for the different sample components ice, solvation shell, DNA backbone, and base stacks. We start with the ice phase. 

In an aqueous solution of DNA, the water outside of the solvation shell is referred to as bulk water. When DNA solutions are frozen, the bulk water crystallizes as a separate phase—ice. Ice does not form if the concentration of DNA is brought to a level where only the solvation shell remains, about 20-22 waters/nucleotide. If brought to this concentration slowly, a film is formed. Freezing a film does not create ice. Another type of sample is prepared by first lyophilizing DNA and then letting it sit at a preselected humidity that determines the level of hydration, typically 2.5 < F < 22. Subsequent freezing of these cotton-like samples does not yield ice. 

Ionization of DNA s solvation shell produces water radical cations (H20 ) and fast electrons. The fate of the hole is dictated by two competing reactions hole transfer to DNA and formation of HO via proton transfer. If the ionized water is in direct contact with the DNA (F < 10), hole transfer dominates. If the ionized water is in the next layer out (9 < r < 22), HO formation dominates [67,89,90]. The thermalized excess electrons attach preferentially to bases, regardless of their origin. Thus the yield of one-electron reduced bases per DNA mass increases in lockstep with increasing F, up to an F of 20-25. This means that when F exceeds 9, there will be an imbalance between holes and electrons trapped on DNA, the balance of the holes being trapped as HO . At F = 17, an example where the water and DNA masses are about equal, the solvation shell doubles the number of electron adducts, increasing the DNA-centered holes by a bit over 50% [91-93]. 

DNA waters of solvation play a significant role in the DNA damage process from ionizing radiation. In fiilly hydrated DNA, approximately 8-10 water molecules per nucleotide (T = 8-10 H2O/ nucleotide) form a primary solvation shell of molecules directly in contact with the DNA and its coimtetion. When these molecules are ionized, hole transfer to the DNA molecule is faster than deprotonation... 

Soon the excitement to see for the first time graphical representations of computed solvation shells for solvated ions from Monte Carlo simulations [81]. The next step was to go to even more complex systems, like enzymes, proteins, and particularly nucleic acids, A-DNA [82], B-DNA [83], without and with counterions [84] and in solution. The quantum biology community was taken by surprise, but soon accepted the new path as a new but necessary computational standard. I was proud to have forcefully recalled that the correct dictionary of quantum biology must contain terms like temperature, volume and free energy eventually, I was elected president of the International Society of Quantum Biology. 

The crystal structures of protein-DNA complexes reveal the presence of several ordered water molecules at protein-DNA interfaces. Such water molecules may reside in the solvation shells of the protein before their binding to DNA, and they may serve to fill all the gaps arising from imperfect matches of protein and DNA surfaces to maintain a suitable packing density for the system, or they may act as mediators of the protein-DNA recognition process. Some water molecules are also found in the interior cavities of such macromolecules. 

A special reaction is the eleetron-attaehment-indueed proton transfer in the guanine-cytosine base pair, which is considered to be relevant in radiation damage of DNA. Therefore, Chen and eo-workers investigated this reaction by means of density-functional theory revealing that the proton-transfer is endothermie in base-pair staeks, while it is exothermie in the isolated guanine-cytosine base pair itself. Moreover, the transfer is supported by water moleeules from the first solvation shell of the base pair. 

Since limited results are available to date, we have started a comprehensive investigation of the stepwise hydration of the DNA bases. An interesting result that has been obtained from this investigation is the predicted difference between the arrangement of water molecules in the first solvation shell of the thymine and uracil molecules [129]. Most gas phase properties of these species... 

It should be noted that DNA can hardly be totally freed from water. Commonly, a certain number of water molecules (about 8-12 per nucleotide) are tightly associated with the different parts of the macromolecule, forming a primary solvation shell. However, when the water molecules are ionized, hole transfer to the DNA molecules can occur and electrons ejected from the water molecules can be scavenged by DNA molecules (Scheme 5.17). In fact, the existence of a primary solvation shell can cause an increase in the radiation-induced damage to DNA by about 50% [90]. 

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