Na₂CO₃ Influence on DNA Double Helix Stability: Strong Anion Destabilizing Effect

Abstract

Addition of Na₂CO₃ to almost salt-free DNA solution (5·10⁻⁵M EDTA, pH=5.7, Tm=26.5 °C) elevates both pH and the DNA melting temperature (Tm) if Na₂CO₃ concentration is less than 0.004M. For 0.004M Na₂CO₃, Tm=58 °C is maximal and pH=10.56. Further increase in concentration gives rise to a monotonous decrease in Tm to 37 °C for 1M N₂CO₃ (pH=10.57). Increase in pH is also not monotonous. The highest pH=10.87 is reached at 0.04M Na₂CO₃ (Tm=48.3 °C). To reveal the cause of this DNA destabilization, which happens in a narrow pH interval (10.56÷10.87) and a wide Na₂CO₃ concentration interval (0.004÷1M), a procedure has been developed for determining the separate influences on Tm of Na⁺, pH, and anions formed by Na₂CO₃ (HCO₃ ⁻ and CO₃ ^2-). Comparison of influence of anions formed by Na₂CO₃ on DNA stability with Cl⁻ (anion inert to DNA stability), ClO₄ ⁻ (strong DNA destabilizing “chaotropic” anion) and OH⁻ has been carried out. It has been shown that only Na⁺ and pH influence Tm in Na₂CO₃ solution at concentrations lower than 0.001M. However, the Tm decrease with concentration for [Na₂CO₃]≥0.004M is only partly caused by high pH≈10.7. Na₂CO₃ anions also exert a strong destabilizing influence at these concentrations. For 0.1M Na₂CO₃ (pH=10.84, [Na⁺]=0.2M, Tm=42.7 °C), the anion destabilizing effect is higher 20 °C. For NaClO₄ (ClO₄ ⁻ is a strong “chaotropic” anion), an equal anion effect occurs at much higher concentrations ∼3M. This means that Na₂CO₃ gives rise to a much stronger anion effect than other salts. The effect is pH dependent. It decreases fivefold at neutral pH after addition of HCl to 0.1M Na₂CO₃ as well as after addition of NaOH for pH>11.2.