Divalent metal ions such as magnesium play key roles in formation and maintenance of DNA double-helical structures. The ions neutralize and screen the highly-charged phosphate backbone of the DNA. Recent studies by X-ray crystallography, NMR and molecular dynamics have also suggested that the binding of divalent metal ions to DNA is sequence-specific, and may contribute to the bending of the DNA double helix.

In the present work, we have used proton exchange and NMR spectroscopy to define the effects of magnesium ions upon the dynamics and energetics of individual base pairs in double-helical DNA. The DNA molecule investigated is the dodecamer [5'-d(CGCAGATCTGCG)-3']₂. The effects of the metal ion on the DNA structure were probed in ¹H-¹H NOESY experiments. The results show that magnesium does not induce a significant change in the DNA structure, except for small changes at the ends of the helix. The rates of exchange of the imino protons with solvent were measured as a function of the concentration of the exchange catalyst (Tris-base), in the absence and in the presence of magnesium. The results reveal that magnesium ions affect the exchange rates and their dependence on exchange catalyst concentration. The effects depend on the nature of the base and its near neighbors, and on the location of the base pair in the DNA structure. The largest effects are observed for the two central G-C base pairs. A model is proposed to explain these effects in terms of base-specific magnesium binding and magnesium-induced changes in the protonation equilibria of each base.

Acknowledgement

Supported by a grant from the NIH, GM65159.