Research ArticlePHYSICAL SCIENCES

Capturing the radical ion-pair intermediate in DNA guanine oxidation

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Science Advances  02 Jun 2017:
Vol. 3, no. 6, e1700171
DOI: 10.1126/sciadv.1700171
  • Fig. 1 The ion-pair species formed in the oxidation process of guanine in the G base and in the GC base pair within dsDNA separately.
  • Fig. 2 Oxidation of G monomer.

    Transient absorption spectra obtained after 355-nm laser flash photolysis of Na2S2O8 + LiCl at 298 K (A) and at 230 K (B). OD, optical density. Transient absorption spectra obtained after 355-nm laser flash photolysis of Na2S2O8 + LiCl + dG at 298 K (C) and at 230 K (D). (E) Time slice (0.1 μs) of the transient absorption spectra obtained after 355-nm laser flash photolysis of Na2S2O8 + LiCl + dG at different temperatures. (F) Normalized absorption changes at 340 and 510 nm after laser flash photolysis of Na2S2O8 + LiCl + dG at 298 K. The concentration of Na2S2O8, LiCl, and dG used in above experiments is 150 mM, 7.0 M, and 4 mM, respectively.

  • Fig. 3 Computation results.

    (A) Geometry of the ion-pair G+•⋯Cl optimized at the CAM-B3LYP/6-311++G** level. Charge distribution analyzed through the natural bond orbital (NBO) scheme at the same level is indicated. (B) TD-CAM-B3LYP/6-311++G** calculated absorption spectrum of G+•⋯Cl. MOs corresponding to the transition at 584 nm are also shown. Spin density distributions of G+• (C) and G+•⋯Cl (D). NBO and spin density analysis confirms the ion-pair G+•⋯Cl nature, showing that, upon the complex formation, charge separation occurs between G (+0.4|e|) and Cl (−0.4|e|), and the spin density is transferred from Cl to G, with the unpaired spin being largely localized on the guanine moiety as that for G+•. Carbon, oxygen, nitrogen, chlorine, and hydrogen atoms are denoted with gray, red, blue, green, and white balls, respectively.

  • Fig. 4 Oxidation of G in dsDNA.

    Transient absorption spectra obtained at 298 K (A) and at 230 K (B) after 355-nm laser flash photolysis of Na2S2O8 + LiCl + dsDNA. (C) Time slice (0.1 μs) of the transient absorption spectra obtained after 355-nm laser flash photolysis of Na2S2O8 + LiCl + dsDNA at different temperatures. (D) Kinetic curves monitored at 480 and 610 nm after laser flash photolysis of Na2S2O8 + LiCl + dsDNA at 230 K, with the biexponential fits to the data (solid lines). The concentration of Na2S2O8, LiCl, and dsDNA used in above experiments is 150 mM, 7.0 M, and 0.1 mM, respectively.

  • Fig. 5 PT mechanism.

    Schematic diagram of the proton transfer (PT) along the central hydrogen bond from G+• to C within G:C base pair (A) and when a nearby Cl is attached (B).

  • Fig. 6 Activation energy.

    Arrhenius plots for the temperature dependence (240, 235, 230, and 225 K) of the rate constants (black circle dots, fast phase; blue circle dots, slow phase) obtained from the absorbance changes at 480 nm (A) and 610 nm (B), with the activation energy indicated. Solid red line is the fit.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/6/e1700171/DC1

    fig. S1. Oxidation of G by SO4−•.

    fig. S2. MOs mainly involved in the electronic transitions of G+•⋯Cl computed at the TD-CAM-B3LYP/6-311++G**//CAM-B3LYP/6-311++G** level.

    fig. S3. MOs mainly involved in the electronic transitions of G+• computed at the TD-CAM-B3LYP/6-311++G**//CAM-B3LYP/6-311++G** level.

    fig. S4. Oxidation of G in ssDNA.

    table S1. Vertical optical transitions of G+•⋯Cl and G+• computed at the TD-CAM-B3LYP/6-311++G**//CAM-B3LYP/6-311++G** level.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Oxidation of G by SO4−•.
    • fig. S2. MOs mainly involved in the electronic transitions of G+•⋯Cl computed at the TD-CAM-B3LYP/6-311++G**//CAM-B3LYP/6-311++G** level.
    • fig. S3. MOs mainly involved in the electronic transitions of G+• computed at the TD-CAM-B3LYP/6-311++G**//CAM-B3LYP/6-311++G** level.
    • fig. S4. Oxidation of G in ssDNA.
    • table S1. Vertical optical transitions of G+•⋯Cl and G+• computed at the TD-CAM-B3LYP/6-311++G**//CAM-B3LYP/6-311++G** level.

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