Hydration of nucleic acid bases

Kim SK, Lee W, Herschbach DR (1996) Cluster beam chemistry Hydration of nucleic acid bases ionization potentials of hydrated adenine and thymine. Journal of Physical Chemistry 100 7933-7937. 

Sukhodub LF. Interaction and hydration of nucleic acid bases in a vacuum. Experimental study. Chem. Rev. 1987 87 589-606. 

Poltev VI, Grokhhna TA, Malenkov GG (1984) Hydration of nucleic acid bases studied using novel atom-atom potential functions. J Biomol Struct Dyn 2 413-429 Pratt LR (2002) Introduction. Water Chem Rev 102 2625-2526 (and the other papers in this issue) Prendergast D, Galli G (2006) X-ray absorption spectra of water from first principles calculations. Phys Rev Lett 96 215502-1-215502-4... 

A. H. Elcock and W. G. Richards, Relative hydration free energies of nucleic acid bases,... 

We present experimental results on photophysical deactivation pathways of uracil and thymine bases in the gas phase and in solvent/solute complexes. After photoexcitation to the S2 state, a bare molecule is tunneled into and trapped in a dark state with a lifetime of tens to hundreds of nanoseconds. The nature of this dark state is most likely a low lying nn state. Solvent molecules affect the decay pathways by increasing IC from the S2 to the dark state and then further to the ground state, or directly from S2 to S0. The lifetimes of the S2 state and the dark state are both decreased with the addition of only one or two water molecules. When more than four water molecules are attached, the photophysics of these hydrated clusters rapidly approaches that in the condensed phase. This model is now confirmed from other gas phase and liquid phase experiments, as well as from theoretical calculations. This result offers a new interpretation on the origin of the photostability of nucleic acid bases. Although we believe photochemical stability is a major natural selective force, the reason that the nucleic acid bases have been chosen is not because of their intrinsic stability. Rather, it is the stability of the overall system, with a significant contribution from the environment, that has allowed the carriers of the genetic code to survive, accumulate, and eventually evolve into life s complicated form. 

Kabelac, M. Hobza, P. Hydration and stabiUty of nucleic acid bases and base pairs, Phys. Ghent. Ghent. Phys. 2007, 9,903-917. 

P. E. Young and I. H. Hillier, Chem. Phys. Lett., 215,405 (1993). Hydration Free Energies of Nucleic Acid Bases Using an Ab Initio Continuum Model. 

An interesting analysis of the solvation characteristics of nucleic acid bases can be obtained by inspection of fractional contribution to solvation (for details see ref. 105), which is defined as the contribution to the total free energy of solvation that can he assigned to a particular structural subunit of the molecule. Fractional contributions can be determined at the atomic or group level, which helps to understand the behaviour of complex solutes in solution. For instance, the results in Figure 4 represent fractional contributions to the free energy of hydration projected into atomic surfaces for selected nucleic acid bases. 

Since the aromatic core of nucleic acid bases has a high content in polar groups, their electron distribution is expected to be largely influenced by the water molecules upon hydration. This is reflected in the solvent-induced shifs... 

In this chapter we have revised basic concepts related to the physics of solvation and the main theoretical methods that can be used to represent the effect of solvent. As an application of the theoretical background, we have examined the sensitivity of chemical properties of nucleic acid bases and related compounds to hydration. We have shown that most of the chemical behavior of these compounds is largely determined by the solvent. 

Solvation, and particularly hydration, leads to very important and complex changes in the electronic distribution of nucleic acid bases. This changes are reflected in an enhancement of the molecular polarity, as well as in an alteration of the intrinsic electrophilic/nueleophilic properties. 

Even if It could be shown that RNA preceded both DNA and proteins in the march toward living things that doesn t automatically make RNA the first self replicating molecule Another possibility is that a self replicating polynucleotide based on some carbo hydrate other than o ribose was a precursor to RNA Over many generations natural selection could have led to the replacement of the other carbohydrate by D ribose giving RNA Recent research on unnatural polynucleotides by Professor Albert Eschenmoser of the Swiss Federal Institute of Technology (Zurich) has shown for example that nucleic acids based on L threose possess many of the properties of RNA and DNA... 

A number of studies on photochemistry of the nucleic acid bases in aqueous solutions demonstrated that while uracil undergoes reversible hydration under exposure to UV irradiation, the other bases (thymine, adenine, and guanine) were stable [41,42], However, the sensitivity of dissolved thymine to UV irradiation can be significantly increased if the solution is rapidly frozen [43]. In 1960 the thymine photoproduct was isolated from irradiated frozen aqueous solution of thymine. Elemental analysis, molecular weight measurements, powder X-ray diffraction, NMR and IR spectroscopy confirmed that the most likely photoproduct is a thymine dimer [20]. Similar photoproduct was obtained by hydrolysis of irradiated DNA. Its formation was attributed to reaction between two adjacent thymine groups on the same DNA chain [44], Independently an identical compound was isolated from DNA of UV-irradiated bacteria [45]. 

In polymeric nucleic acids, the Watson-Crick base pairs also have the potential to form additional hydrogen bonds. These will generally be saturated by water of hydration molecules. They are, in fact, necessary for specific recognition of a particular nucleic acid base sequence by a particular protein such as, for example,... 

RNA and DNA are in general very difficult to model with force-field based approaches. One major difficulty is to reproduce the backbone conformation (crucial for any modeling of nucleic acids), as the corresponding torsional energy barriers are very small [29]. First results from AIMD are encouraging the calculated structure of a hydrated GpG RNA duplex in laboratory realizable conditions (that is, in the crystal phase)[25] showed excellent agreement with experiment and provided the H-bond network postulated by the crystallographers. 

Water is an essential part in the biomacromolecular system, which is mainly responsible for the structure and functions of nucleic acids, proteins, and other constituents of cell [136-138]. Both proteins and DNA are generally hydrated. It is well known that the conformation of DNA is sensitive to hydration, and presence of salts and ligand molecules [112, 138]. The nucleic acids have three levels of water structure. About 12 water molecules per nucleotide are involved in the primary hydration shell [107, 112, 137, 138]. The water molecules present in the primary shell are impermeable to cations and do not form ice on freezing. The secondary level is permeable to cations and forms ice on freezing and third level is the completely disordered, so-called bulk water. Several theoretical studies have been carried out on the level of hydration on DNA bases, base pairs, base stacks, and double helical DNA [107, 121, 131, 139]. Both the experimental and molecular simulation studies have clearly brought out the importance of hydration in DNA and RNA structures [140-147]. 

In the fields of molecular associations, G. Port and A. Pullman have determined the location of the main hydration sites in the purinic and pyrimidinic bases of nucleic acids 77>. An expansion of the electrostatic potential somewhat different from those reported in Chap. VIII was employed 78>. The results show that association with a water molecule is preferred in every case on the ring plane, with well evidenced minima. 

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