Faculty Publications and Presentations

The Deprotonated Guanine-Cytosine Base Pair

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This article was published in Proceedings of the National Academy of Sciences of the United States of America, vol. 103, issue 20, pgs. 7554-7559.


Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26–27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine–cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal·mol−1, vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal·mol−1 lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H···O2 distance dramatically reduced from 1.88 to 1.58 Å, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a “reverse wobble” incorporating two N-H···N hydrogen bonds. Three different types of relaxation energies (4.3–54 kcal·mol−1) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.