The non-specific atmosphere around nucleic acids, often termed the “ion atmosphere,” encompasses a collection of weak ion-nucleic acid interactions. Although non-specific, the ion atmosphere has shown to influence nucleic acid folding and structural stability. Studies investigating the composition of the ion atmosphere have shown competitive occupancy between metal ions in the same solution. Many studies have investigated single ion effects on nucleic acid secondary structure stability. However, there have been no comprehensive studies investigating how the competitive occupancy of mixed ions in the ion atmosphere influences nucleic acid secondary structure stability. Here, six nucleic acid sequences were optically melted in buffers containing molar quantities, or mixtures, of either XCl (X=Li, K, Rb, or Cs) or NaCl (standard conditions). For each sequence, the stability in solutions containing mixed metal ions and standard conditions were compared. The identity of metal ions in solutions appeared to have less of an effect on DNA duplex stability when compared to their RNA counterparts. The LiCl solutions always stabilized the duplex compared to standard conditions, regardless of duplex composition. Solutions containing a 1:1 mixture of XCl: NaCl suggested one alkali metal chloride contributed more to the duplex stability than the other.

Competitive influence of alkali metals in the ion atmosphere on nucleic acid duplex stability

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