Nucleic acid ionic strength

The theory and application of this fluorescence method have been discussed in detail by LePecq and others (3,8). The assay requires that there is sufficient ionic strength to minimize ionic binding (e.g., O.IM sodium chloride), that the pH is 4-10, that no heavy metals are present, that the fluorescence is not enhanced on binding to other excipients (e.g., proteins) and that at least portions of the nucleic acids are not complexed. These requirements can usually he met when dealing with recombinant products in some cases the samples must he manipulated to create the appropriate conditions. In the intercalative method of dye binding, proteins rarely interfere with the assay, and procedures have been developed to remove the few interferences they may cause (e.g., the use of heparin or enzymatic digestion of the protein 9). 

The UV absorption of nucleic acids depends strongly on their nature and solvent conditions as pH, ionic strength, and temperature. Approximate absorption coefficients are given in Tables 1.8 and 1.9. Using these coefficients, yield is calculated during chromatography, ultracentrifugation, and other preparative processes with sufficient precision. 

Ionic strength influences are well known with respect to the rate and energetics of nucleic acid hybridization [17]. Charge and ionic radius are both important in terms of stabilizing the structure of the duplex as well as stabilizing the stem portion of the molecular beacon [17]. The stem structure stability was increased when a divalent cation was incorporated into the hybridization buffer solution [17]. It was reported that cations were best at stabilizing the duplex formed upon hybridization in the order Ca2+ > Mg2+ K+ > Na+. The ultimate detection limit of the sensor configuration was calculated to be 1.1 nM [17]. 

Ion pair interactions are also present in natural supramolecular systems (e.g. DNA-peptides, polyamine-nucleic acids and among proteins or enzymes). Such kinds of attractive forces are strongly dependent on the ionic strength (I) of the solution if extrapolated to I = 0 the average value for the free energy of association for one cation-anion pair is about 8 KJ/mol, and... 

Polyphosphates in aqueous solutions of low ionic strength are capable of forming complexes with other polymers, especially proteins (Katchman and Van Wazer, 1954), basic polypeptides (Singh, 1964), arid nucleic acids (Kulaev and Belozersky, 1958 Ebel et al, 1958c). This ability increases as the chain length of the polyphosphate molecule increases. In acidic solution, these complexes separate as precipitates. The ability of condensed... 

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