Atomic force microscopy study of the effects of Mg²⁺ and other divalent cations on the end-to-end DNA interactions

Atomic force microscopy (AFM) was applied to directly visualize the end-to-end DNA interaction mediated by magnesium cations. We took advantage of the APS-mica, allowing the preparation of samples in a broad range of monovalent and divalent cations to separate the effects of Mg²⁺ and Na⁺ cations on the interaction of restriction DNA fragments with cohesive end. The AFM data clearly show that DNA restriction fragments with cohesive ends form substantial amount of circles in the presence of Mg²⁺ cations, suggesting that Mg²⁺ cations stabilize the interaction of cohesive ends. This effect depends on the MgCl₂ concentration, so that the yield of circles approaches 18% in the presence of 50 mM MgCl₂. Furthermore, we demonstrate that this conferred cohesive end stability is specific for divalent cations, as substitution of MgCl₂ with NaCl leads to a near complete loss of cohesive end stability. We further demonstrate that cohesive end stabilization is achieved by substituting Mg²⁺ with Ca²⁺, Mn²⁺, or Zn²⁺. The data obtained suggest that the end stabilization mediated by divalent cations is primarily the result of inter-base interactions rather than bridging of phosphate moieties.