Hydrogen-Abstracted Adenine−Thymine Radicals with Interesting Transferable Properties

Traceless Tandem Lesion Formation in DNA from a Nitrogen-Centered Purine Radical

Nitrogen-centered nucleoside radicals are commonly produced reactive intermediates in DNA exposed to γ-radiolysis and oxidants, but their reactivity is not well understood. Examination of the reactivity of independently generated 2'-deoxyadenosin- N6-yl radical (dA•) reveals that it is an initiator of tandem lesions, an important form of DNA damage that is a hallmark of γ-radiolysis. dA• yields O₂-dependent tandem lesions by abstracting a hydrogen atom from the C5-methyl group of a 5'-adjacent thymidine to form 5-(2'-deoxyuridinyl)methyl radical (T•). The subsequently formed thymidine peroxyl radical adds to the 5'-adjacent dG, ultimately producing a 5'-OxodGuo-fdU tandem lesion. Importantly, the initial hydrogen abstraction repairs dA• to form dA. Thus, the involvement of dA• in tandem lesion formation is traceless by product analysis. The tandem lesion structure, as well as the proposed mechanism, are supported by LC-MS/MS, isotopic labeling, chemical reactivity experiments, and independent generation of T•. Tandem lesion formation efficiency is dependent on the ease of ionization of the 5'-flanking sequence, and the yields are >27% in the 5'-d(GGGT) flanking sequence. The traceless involvement of dA• in tandem lesion formation may be general for nitrogen-centered radicals in nucleic acids, and presents a new pathway for forming a deleterious form of DNA damage.

Aminyl Radical Generation via Tandem Norrish Type I Photocleavage, β-Fragmentation: Independent Generation and Reactivity of the 2'-Deoxyadenosin- N6-yl Radical

Formal hydrogen atom abstraction from the nitrogen-hydrogen bonds in purine nucleosides produces reactive intermediates that are important in nucleic acid oxidation. Herein we describe an approach for the independent generation of the purine radical resulting from hydrogen atom abstraction from the N6-amine of 2'-deoxyadenosine (dA•). The method involves sequential Norrish Type I photocleavage of a ketone (7b) and β-fragmentation of the initially formed alkyl radical (8b) to form dA• and acetone. The formation of dA• was followed by laser flash photolysis, which yields a transient with λ_max ≈ 340 nm and a broader weaker absorption centered at ∼560 nm. This transient grows in at ≥2 × 10⁵ s^-1; however, computations and reactivity data suggest that β-fragmentation occurs much faster, implying the consumption of dA• as it is formed. Continuous photolysis of 7b in the presence of ferrous ion or thiophenol produces good yields of dA, whereas less reactive thiols afford lower yields presumably due to a polarity mismatch. This tandem photochemical, β-fragmentation method promises to be useful for site-specific production of dA• in nucleic acid oligomers and/or polymers and also for the production of aminyl radicals, in general.

DFT study on the radical anions formed by primaquine and its derivatives

The electron affinities (EA) of the 8-aminoquinoline antimalarial drug primaquine and several of its metabolites were studied using the density functional theory method. We first considered six substituents at the 5-position, -CH(3), -OH, -OCH(3), -Ph, -OPh, and -CHO. We found that in the gas phase the adiabatic EAs are similar to that of the parent primaquine for the -CH(3), -OH, and -OCH(3) substituents. In contrast, the -Ph, -OPh, and -CHO substituents all markedly increase the adiabatic EA. However, only the -CHO substituted compound is predicted to form a stable covalently bound radical anion in the gas phase due to its significant positive vertical EA relative to that of the parent primaquine. In addition, when the 8-position is substituted by the N-hydroxyl group or a quinone-imine structure is formed, the electron capture ability is significantly increased. In aqueous solution, all these molecules have significantly larger adiabatic EAs than in the gas phase. In addition, all of the vertical EAs are positive in aqueous solution. The implications of these findings for contributing to our mechanistic understanding of the red cell toxicity of 8-aminoquinoline compounds are further discussed.

Elementary lesions in DNA subunits: electron, hydrogen atom, proton, and hydride transfers

When DNA is damaged by ionizing radiation, the genes in a cell may acquire mutations or the cell could die. The smallest known DNA-damaging unit is an electron, often low-energy secondary electrons. Additional electrons and transfers involving hydrogen atoms, protons, and hydride anions can damage DNA subunits, including individual nucleobases and nucleoside pairs. Researchers would like to better understand the molecular mechanisms involved in DNA damage from ionizing radiation. In this Account, we highlight our theoretical investigations of the molecular mechanisms of DNA damage using quantum mechanical models. Our investigations use robust theoretical methods with computations conducted in the gas phase and with solution models. We calculate adiabatic electron affinities (AEAs), which describe the energetics of electronic attachment to closed-shell DNA subunits, for the free bases, nucleosides, nucleotides, base pairs, and single and double DNA strand units. Electron affinities for free nucleobases yield the order uracil > thymine > cytosine > guanine > adenine and the same order for the DNA nucleosides, mononucleotides, and nucleoside 3',5'-diphosphates. AEA values increase steadily with the size and complexity of the system because of greater hydration, glycosylation, nucleotide formation, and base pairing. We predict and experimental results partially confirm that most of the more complex and hydrated species are observable as radical anions. Our modeling studies indicate that depyrimidination reactions of radical anion nucleosides release cytosine more often than thymine. Recent experimental results support those findings. Our theoretical studies of DNA base-pair radical anions predict increases in electron affinity accompanying H bonding and solvation. Electron addition facilitates some proton transfers in these pairs, which results in strongly perturbed pairing configurations. Of all nucleobase moieties within the more complex radical anion systems, thymine is best able to retain a negative charge. Charge and spin are well-separated in some of these systems. Radical species derived via hydrogen abstraction from DNA subunits yield large AEA values because they form closed-shell anions. Our studies predict single-strand breaks following H abstraction from nucleotides. Some H-abstraction processes in the DNA base pairs lead to severe distortions in pairing configuration based on our calculations. This body of systematic theoretical studies provides realistic descriptions of some events that lead to elementary DNA lesions, while providing rationalizations for many observed phenomena. Such approaches can lead to the design of new experiments, which would contribute to our understanding of the chemical physics of nucleic acids.

Electron attachment to the hydrogenated Watson-Crick guanine cytosine base pair (GC+H): conventional and proton-transferred structures

The anionic species resulting from hydride addition to the Watson-Crick guanine-cytosine (GC) DNA base pair are investigated theoretically. Proton-transferred structures of GC hydride, in which proton H1 of guanine or proton H4 of cytosine migrates to the complementary base-pair side, have been studied also. All optimized geometrical structures are confirmed to be minima via vibrational frequency analyses. The lowest energy structure places the additional hydride on the C6 position of cytosine coupled with proton transfer, resulting in the closed-shell anion designated 1T (G(-)C(C6)). Energetically, the major groove side of the GC pair has a greater propensity toward hydride/hydrogen addition than does the minor grove side. The pairing (dissociation) energy and electron-attracting ability of each anionic structure are predicted and compared with those of the neutral GC and the hydrogenated GC base pairs. Anion 8T (G(O6)C(-)) is a water-extracting complex and has the largest dissociation energy. Anion 2 (GC(C4)(-)) and the corresponding open-shell radical GC(C4) have the largest vertical electron detachment energy and adiabatic electron affinity, respectively. From the difference between the dissociation energy and electron-removal ability of the normal GC anion and the most favorable structure of GC hydride, it is clear that one may dissociate the GC anion and maintain the integrity of the GC hydride.