Formation of Sugar Radicals in RNA Model Systems and Oligomers via Excitation of Guanine Cation Radical

Abstract

In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.

Prototropic equilibria in DNA containing one-electron oxidized GC: intra-duplex vs. duplex to solvent deprotonation

“…As discussed in the introduction, it has been observed that sugar radical formation in dGuo 26 and in Guo 27 via photo-excitation of one-electron oxidized G depends on the protonation state of the one-electron oxidized guanine, and hence, on the pH of the solution. Substantial sugar radical formation (>80%) via photo-excitation of the cation radical (G• + ) but, at pH ≥9, only G(N1-H)• is present and only small amounts (ca.…”

“…≤10%) sugar radicals are been found on photoexcitation. 26, 27 Production of sugar radical in the ss DNA and RNA oligomers have also been reported via photo-excitation of G• + . 8, 26, 27, 29 –31 Thus, arguing from the pH dependence in the formation of sugar radicals via photo-excitation of nucleosides discussed above, it is expected that the extent of photo-conversion to sugar radicals via photo-excitation of G(N1-H)•:C(+H + ) might be significantly larger that that via photo-excitation of G(N1-H)•:C with the greatest extent of sugar radical formation on photo-excitation of the cation radical G• + :C. This hypothesis is tested in this work.…”

“…Sugar radical formation in dGuo and in Guo via photo-excitation of one-electron oxidized G has been observed to depend on the pH of the solution. 26, 27 Sugar radical formation on photo-excitation of the cation radical (G• + ) is most efficient with 80 to 100% conversion in dGuo 26 and in Guo 27 . However, at pH ≥9, where only G(N1-H)• is present, only small amounts (ca.…”

On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium

“…7 Moreover there is experimental evidence proving that oxidative events in the deoxyribose moiety are directly related to DNA strand scissions. [36][37][38][39] There are four mechanisms proposed so far explaining lesions in the sugar unit: direct H abstraction by OH, 22,23,37,39 direct ionization of the sugar-phosphate backbone followed by deprotonation, 37 hole transfer from G + to the sugar ring by photo-induced excitation, 38,[41][42][43][44][45][46] and direct deprotonation of the sugar unit in ground-state 2dG + . 23,47 However the effects of the presence of base-pairing and phosphate, solvent, and physiological pH have not been simultaneously included in these investigations.…”

Insight Into the Inhibition of Ribonucleotide Reductases by 2'-chloro-2'-deoxynucleotides and 2'-azido-2'-deoxynucleotides: Biomimetic Studies with Model Substrates

“…Following our works on DNA and RNA-radicals, 79,141,142,148,152,[158][159][160][161][162][163][164][165][166] the anisotropic simulations of the experimentally recorded ESR spectra were carried out by employing the Bruker programs (WIN-EPR and SimFonia). The ESR parameters (e.g., hyperfine coupling constant (HFCC) values, linwidth, etc.)…”