Li+, Na+, and K+ Binding to the DNA and RNA Nucleobases. Bond Energies and Attachment Sites from the Dissociation of Metal Ion-Bound Heterodimers

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Abstract

The alkali metal ion (M+ = Li+, Na+, K+) affinities of the common DNA and RNA nucleobases are determined in the gas phase by investigating the dissociation of metal ion-bound heterodimers [nucleobase + B]M+, in which B represents a reference base of known affinity (kinetic method). The dimer ion decompositions are assessed at two different internal energies, namely from metastable precursor ions and after collisional activation. This approach makes it possible to deconvolute entropy from enthalpy and, therefore, leads to more accurate affinity (i.e. enthalpy or bond energy) values. For the nucleobases studied, viz. guanine, cytosine, adenine, thymine, and uracil, the corresponding M+−nucleobase bond energies are (kJ mol-1) as follows: 239, 232, 226, 215, and 211 with Li+; 182, 177, 172, 144, and 141 with Na+; and 117, 110, 106, 102, and 101 with K+. The method used also provides quantitative information about the overall entropy change occurring upon the dissociation of the heterodimers; this change is most significant when dissociation alters rotational degrees of freedom. The magnitude of the operating entropy effects gives information on the structures of both the metal ion-bound dimers and the metalated nucleobase monomers. It is found that Li+, Na+, and K+ bind very similarly to the nucleobases. Attachment sites that explain the observed entropic effects and metal ion affinity orders are suggested and discussed. A notable characteristic of several of the resulting structures is their ability to form stabilizing ion pairs (salt bridges).

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