Hydration of DNA

Fig. 7. Hydration of DNA, and with a drug recognized in the minor groove. Time scales are indicated for bulk water, dynamically ordered water, configurational changes and structured water...

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]. 

Fig. 24.2. IWo plots describing the net hydration of DNA, r. Tbp water activity aw is changed by different Cs+ salts. With about 20 water molecules per nucleotide, the hydration is complete for the Cs+ salt of DNA (after [859]). Bottom dependence of B-DNA content on net hydration r which was adjusted with different alkali chloride concentrations, r values for B-DNA = 0% and 100% indicate that minimum hydration of double helical DNA is 3.6 water molecules per nucleotide, and formation of B-DNA is complete with about 20 water molecules per nucleotide ([522] after [857,...

Because the addition of salt or organic solvents to aqueous solutions affects the water activity, we can expect a direct correlation between water activity and DNA conformation. Water activity, on the other hand, will influence the hydration of DNA, and therefore a connection between hydration and DNA structure can be expected. A few suggestions have been made concerning this correlation. 

TUnis M-JB, Hearst JE (1968) On the hydration of DNA. I. Preferential hydration and stability of DNA in concentrated trifluoracetate solution. Biopolymers 6 1325 -1344 II. Base composition dependence of net hydration of DNA. Biopolymers 6 1345-1353... 

Clementi (1985) described ab initio computational chemistry as a global approach to simulations of complex chemical systems, derived directly from theory without recourse to empirical parametrizations. The intent is to break the computation into steps quantum mechanical computations for the elements of the system, construction of two-body potentials for the interactions between them, statistical mechanical simulations using the above potentials, and, finally, the treatment of higher levels of chemical complexity (e.g., dissipative behavior). This program has been followed for analysis of the hydration of DNA. Early work by Clementi et al. (1977) established intermolecular potentials for the interaction of lysozyme with water, given as maps of the energy of interaction of solvent water with the lysozyme surface. 

Stanley CB, Rau DC. Preferential hydration of DNA the magnitude and distance dependence of alcohol and polyol interactions. Biophys. J. 2006 91 912-920. 

Liepinsh E, Leupin W, Otting G. Hydration of DNA in aqueous solution NMR evidence for a kinetic destabilization of the minor 50. groove hydration of d(TTAA)2 versus d(AATT)2 segments. Nucl. 

Jacobson A, Leupin W, Liepinsh E, Otting F. Minor groove hydration of DNA in aqueous solution sequence-dependent next neighbor effect of the hydration lifetimes in d(TTAA)2 segments 52. measured by NMR spectroscopy. Nucl. Acids Res. 1996 24 2911-2918. 

Elcock AH, Mccammon JA. Sequence-dependent hydration of DNA. Theoretical Results. J. Am. Chem. Soc. 1995 117 10161-10162. 

That hydration of DNA affects its conformation is also evident from the fact that dehydration stabilizes the A phase. Rather remarkably, quantum effects might be largely responsible for this. The zero-point motions of protons are entirely responsible for the binding of water to A-DNA, and in more hydrated conditions a change in the zero-point kinetic energy is sufficient in itself to motivate the transition to B-DNA [104]. Whether the protons concerned are those of water molecules in the hydration shell or those in the DNA s H-bonds (or perhaps a bit of both) is not yet clear. 

The above evidence means that the hydration shell has to be included in some way in the realistic study of the electronic structure and properties of DNA and DNA fragments. The review which follows is devoted to the current status of the quantum-chemical investigations of the hydration of DNA bases. It is subdivided into two parts. In the first one we describe the two most popular and currently the most reliable schemes to model solvent influence. They are the continuum approximation of the different levels of the complexity and the supermolecular approach. For the purposes of our chapter, we describe the current results in modeling the hydration of DNA based on the continuum... 

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