Water around RNA

Several studies have explored the possible role of water in the biological activities of RNA. Local stmctures of nucleic acids result from interplay between the solvent and nucleic acid molecules so that both together constitute a functional and structural 

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Being a single strand, RNA is more open to the interaction of water. Unfortunately there exist fewer studies of water dynamics around RNA. Here the structure is relatively less rigid and also more open, allowing water molecules to sustain stronger interactions with the nucleic acids. 

Nucleic acids, DNA and RNA, are attractive biopolymers that can be used for biomedical applications [175,176], nanostructure fabrication [177,178], computing [179,180], and materials for electron-conduction [181,182]. Immobilization of DNA and RNA in well-defined nanostructures would be one of the most unique subjects in current nanotechnology. Unfortunately, a silica surface cannot usually adsorb duplex DNA in aqueous solution due to the electrostatic repulsion between the silica surface and polyanionic DNA. However, Fujiwara et al. recently found that duplex DNA in protonated phosphoric acid form can adsorb on mesoporous silicates, even in low-salt aqueous solution [183]. The DNA adsorption behavior depended much on the pore size of the mesoporous silica. Plausible models of DNA accommodation in mesopore silica channels are depicted in Figure 4.20. Inclusion of duplex DNA in mesoporous silicates with larger pores, around 3.8 nm diameter, would be accompanied by the formation of four water monolayers on the silica surface of the mesoporous inner channel (Figure 4.20A), where sufficient quantities of Si—OH groups remained after solvent extraction of the template (not by calcination). 

Chapter 2). However, AH is distinctly negative for association of heterocyclic bases. This has also been attributed to a decrease in the ordering of solvent around the bases as a result of exclusion of water. Attraction or repulsion of partial charges on the polar groups comprising the purine and pyrimidine bases may also be an important factor.43 46 8 For addition of a base pair to an RNA helix, the change in aithalpy, AH, varies from about -24 to -60 kj/mol.44,45... 

Figure 20.6 Comparative cumulative distribution functions to assess the amount of counterion accumulation around the Tar—Tar complex, A-form RNA, and B-form DNA, respectively. Data were obtained from molecular dynamics simulations with explicit representations of water molecules and ions. The ordinate quantifies the number of counterions accumulated around the macroions within contours that have AG less than or equal to the value on the abscissa.

RNA and DNA are poly anions at pH 7. The pk of the phosphate OH group is close to 1. DNA is a double helix in which a large purine base is always paired with a small pyrimidine base. Only AT and CG pairs occur. AT and GC pairing are favored by optimal hydrogen bonds, which connect the base pairs in the hydrophobic center (Fig. 8.2.5a). Monomeric AT and GC bases do not pair in water but they do pair in organic solvents. The double helices are destroyed reversibly (they melt ) if the hydrogen bonds are thermally disrupted at temperatures between 70 and 80°C. In UV spectra one then observes a loss of intensity of the bands around 270 nm and a small short-wavelength shift. Each DNA has a characteristic ratio (G+C) (A+T), called the coefficient of specifity, which varies... 

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