Determination of Redox Potentials for the Watson−Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues

Abstract

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.

Inorganic Polyphosphate Modulates TRPM8 Channels

“…potentials of less than -2.0 V [296,297]. On the other hand, as indicated by the energy diagram of Fig.…”

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

“…This neglects solvation and Coulombic stabilization, but these effects, although substantial, are similar in magnitude for all base dimers. The use of gas-phase quantities provides a consistent dataset for all nucleobases and avoids issues with follow-on reactions and solvent effects on redox data (23). Importantly, the use of solution-phase redox potentials does not change the quality of the correlation in Fig.…”

Base-Specific Ionization of Deprotonated Nucleotides by Resonance Enhanced Two-Photon Detachment

“…[20][21][22][23][24][25] In the solution phase, ionization potentials have been determined using PE spectroscopy on liquid microjets 26 and with ab initio [27][28][29][30] or semiempirical calculations. 31,32 Building on the gas phase work, the PE spectroscopy of isolated nucleotides and oligonucleotides has recently been studied by the Wang group with the aim of understanding how the ionization energy changes with the introduction of the sugar and phosphate backbone. 33 Deprotonation of the nucleotide, which occurs on the phosphate, 34,35 conveniently enables mass-selection prior to PE spectroscopy, and provides a protonation state analogous to that found in the natural environment.…”