Free Nucleic Acids

By incubating very small amounts of radioactively labeled nucleic acids (at least 100 times less than the amount of protein) with increasing concentrations of a target protein, the K- value can be calculated after quantification of the free nucleic acids (that is, those that are not bound to the filter) and the nucleic acid-target complexes that are retained on the filter. 

While most cells do not take up naked DNA in the absence of the physical or chemical treatments described above, muscle cells appear to be an exception. Direct injection of free nucleic acids in saline solutions into skeletal and cardiac muscles has been shown to result in prolonged expression (Wolff et al, 1991 Kitsis et al, 1991). By using this method, the 12 kilobase human dystrophin gene, defective in muscular dystrophy patients, has been introduced into the muscle cells of mice (Partridge, 1991 Ascadi et al, 1991). 

In 1891, Kossel reported the first study of the hydrolysis of a protein-free nucleic acid. Mainly as a result of his work, it was recognized that there are two nucleic acids, similarly constituted but differing in certain components. The nucleic acid readily isolated from yeast is of one type that from thymus gland and fish sperm is of the other. It is possible that other nucleic acids exist in fact, there have been indications from time to time that there are other nucleic acids, but only the two types under discussion have been adequately characterized. 

The first experimental solid-state O NMR and theoretical study of the 0 e.f.g. and chemical shielding tensors in a free nucleic acid base, thymine, has been reported. ... 

Jensen, R. H., and R. Chalkley. 1968. The physical state of nucleohistone under physiological ionic strength. The effect of interaction with free nucleic acids. Biochemistry (Wash.), 7 4388-4396. 

Two types of change are possible at C-7, epimerisation and modification of the substituent. Of the compounds tested to date, the 7,9-diepimer of 3-demethoxy-daunomydn is the compound most closely related to 7-epiadriamycin. This 7,9-diepimer stabilises the DNA helix to melting to a lesser degree than with dauno-mydn and consequently it is a less active inhibitor of cell-free nucleic acid synthesis than daunomycin [211]. It is impossible to conclude whether this is due to inversion of configuration at C-7 or at C-9 or at both centres. The only other compounds for which data are available are the 2 epimers of the simplified analogue discussed earlier, compound (71). Both epimers of (71) show equiv-... 

Ionic interactions are also used to associate genetic material with nanoparticulate carriers. Electrophoresis is perhaps the easiest way to assess the association efficiency of nucleic acids to a nanostructure. The associated genetic material will not migrate in an electrophoresis gel as would happen with free nucleic acids. It is also useful to visually determine the conformation of the plasmid DNA, supercoiled being the most effective form in comparison to circular and open forms. The association efficiency can be quantitatively determined using commercial kits and fluorescence techniques or, directly but with a lower sensitivity, by UV determination. For this purpose, the free nucleic acid needs to have been previously separated and subsequently quantified. 

Various phosphodiester backbone substates can be found in X-ray crystal structmes of free nucleic acids and in complexes with proteins (Djuranovic and Hartmann 2004 Vamai et al. 2002). In particular, the coupled e (rotation around C3 -03 bond in C4 -C3 -03 -P) and ( (rotation around 03 -P bond in C3 -03 -P-05 ) in gauche-/trans and in trans/gauche-regimes, termed Bj and Bjj substates, respectively, are frequent in crystal structures of free DNA (Varnai et al. 2002). 

---