Hydration of nucleic acids

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. 

Berman HM (1986) Hydration of nucleic acid crystals. Ann NY Acad Sci 482 166-178... 

Beveridge DL, Maye PV, Jayaram B, Ravishanker G, Mezei M (1984) Aqueous hydration of nucleic acid constituents Monte Carlo computer simulation studies. J Biomol Struct Dynam 2 261-270... 

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

E. Westhof and D.L. Beveridge, Hydration of Nucleic Acids, in Water Science Reviews 5, edited by F. Franks (Cambridge University Press, Cambridge, 1990), pp. 24—136. 

G. Hummer, A. E. Garcia, and D. M. Soumpasis, Hydration of nucleic acid fragments comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes, Biophys. J. 68, 1639-1652 (1995). 

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... 

Molecular dynamics simulations of DNA duplexes go back nearly 15 years and useful insights into the structure, dynamics and hydration of nucleic acids has emerged from these studies. Nonetheless, the increase in computer power, dlowing one to simulate into the nanosecond time range, with die inclusion of explicit solvent and coimterions and improvements in the simulation protocols (force fields and efficient ways to include long range electrostatic effects) has made the last few years particularly fruitfiil. 

The application of Monte Carlo method for the study of hydration of nucleic acids, their components [77-80], and hydration of the DNA-ligand complexes (for example, dCpG with proflavine [81] and DNA with azinomycin B [82] intercalated complexes) was described in literature in detail. Monte Carlo simulations enable to evaluate the low energy conformations of various complexes of DNA fragments. 

Shestopalova AV (2002) Hydration of nucleic acids components in dependence of nucleotide eomposition and relative humidity a Monte Carlo simulation. Europ Phys J D 20(l) 331-337... 

Hydration of nucleic acids has a number of distinctions due to their polyionic character and uneven nonspherical shapes [487]. In physiological conditions, the double-helical DNA directly interacts with solvent ions in several water layers from its surface therefore, the functional DNA hydration shell is very thick. Under limited hydration, there is a strict relationship between the state of DNA and hydration number F measured as the number of water molecules per nucleotide (or phosphate). When r is reduced below 30, the common B-form of DNA is already perturbed, but it is maintained until F 20 [487,488]. Below this hydration, DNA undergoes different conformational transitions, among which the transition from B- to A-form [489] with a midpoint at about F = 15 is the most studied (see Section 6). 

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