Mg²⁺ recognizes the sequence of DNA through its hydration shell

We have studied the interaction of Mg²⁺ with six deoxyoctanucleotide duplexes of known sequence. Specifically, we have measured the resulting hydration changes by following the change in the concentration increment of ultrasonic velocity, δA, of each of these six duplexes, in their Cs⁺ salt at 1.2 °C, during a course of a titration with Mg²⁺. The addition of Mg²⁺ results in the initial lowering of δA that levels off at [Mg²⁺]/[P_i] molar ratios ranging from 12 to 30, depending on the duplex, and corresponds to a dehydration event from the exchange of Cs⁺ counterions by Mg²⁺in the ionic atmosphere of the duplexes. This is followed by a further lowering of SA at higher [Mg²⁺]/[P_i] ratios that may result from DNA aggregation and/or conformational change. We obtained a change in the molar concentration increment of ultrasonic velocity per mole of bound Mg²⁺, Δ∆ Mg²⁺ and binding affinities, K_app, ranging from -4.4 cm³mol^-1 and 150 M^-1 for d(A)₈·d(T)₈ to-18 cm³ mol^-1 and 40 M^-1 for [d(CG)₄]₂, respectively, by fitting the first portion of each titration curve and assuming an overall binding of 0.5 Mg²⁺ per phosphate. Thus, the overall magnitude of the dehydration effect, which is determined by the structure of the Mg²⁺-DNA complex, and the K_app are functions of the DNA sequence. Furthermore, the dehydration effect of Mg²⁺ binding correlates with the hydration state of the DNA: the higher its hydration state, the lower the dehydration effect of Mg²⁺ binding is. Mg²⁺ recognizes the sequence of DNA through its overall hydration state, probably by forming mostly outer-sphere complexes with oligomers containing exclusively dA-dT base pairs and inner-sphere complexes with dG·dC oligomers.