mg2+ recognizes the sequence of DNA through its hydration shell

Buckin V.A., Kankiya B.I., Rentzeperis D. and Marky L.

J. Am. Chem. Soc., 116, pp. 9423-9429 (1994)

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 1.2C, during a course of a titration with Mg2+. The addition of Mg2+ results in the initial lowering of δA that levels off at [Mg2+]/[Pi] molar ratios ranging front 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 δA at higher [Mg2+]/[Pi] 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+, ΔAMg2+, and binding affinities, Kapp, ranging from 4.4 cm3 mol-1 and 150 M-1 for d(A)8d(T)8 to18 cm3 mo1-1 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 Kapp 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 dAdT base pairs and inner-sphere complexes with dGdC oligomers.

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