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Chemphyschem. 2018 Oct 19;19(20):2645-2654. doi: 10.1002/cphc.201800643. Epub 2018 Aug 9.

Singlet O2 Oxidation of a Deprotonated Guanine-Cytosine Base Pair and Its Entangling with Intra-Base-Pair Proton Transfer.

Lu W1,2, Sun Y1,2, Tsai M3, Zhou W1, Liu J1,2.

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Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.
Ph.D. Program in Chemistry, the, Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA.
Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY, 11101, USA.


We report an experimental and computational study on the 1 O2 oxidation of gas-phase deprotonated guanine-cytosine base pair [G ⋅ C-H]- that is composed of 9HG ⋅ [C-H]- and 7HG ⋅ [C-H]- (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG ⋅ [C-H]- _PT and 7HG ⋅ [C-H]- _PT (formed by intra-base-pair proton transfer from the N1 of guanine to the N3 of [C-H]- ). The conformer-averaged reaction product ions and cross section were measured over a center-of-mass collision energy range from 0.1 to 0.5 eV using a guided-ion-beam tandem mass spectrometer. To explore conformation-specific reactivity, collision dynamics of 1 O2 with each of the four [G ⋅ C-H]- conformers was simulated at B3LYP/6-31G(d). Trajectories showed that the 1 O2 oxidation of the base pair entangles with intra-base-pair proton transfer, and prefers to occur in a collision when the base pair adopts a proton-transferred structure; trajectories also indicate that the 9HG-containing base pair favors stepwise formation of 4,8-endoperoxide of guanine, whereas the 7HG-containing base pair prefers concerted formation of guanine 5,8-endoperoxide. Using trajectory results as a guide, potential energy surfaces (PESs) along all possible reaction pathways were established using the approximately spin-projected ωB97XD/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. PESs have not only rationalized trajectory findings but provided more accurate energetics and indicated that the proton-transferred base-pair conformers have lower activation barriers for oxidation than their non-proton-transferred counterparts.


direct dynamics trajectory simulation; guanine-cytosine base pair; guided-ion-beam tandem mass spectrometry; potential energy surface; singlet oxygen


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