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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.

Author information

1
Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.
2
Ph.D. Program in Chemistry, the, Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA.
3
Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY, 11101, USA.

Abstract

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.

KEYWORDS:

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

PMID:
30047606
DOI:
10.1002/cphc.201800643

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