The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis

Ultrafast spectroscopy study of DNA photophysics after proflavine intercalation

Proflavine (PF), an acridine DNA intercalating agent, has been widespread applied as an anti-microbial and topical antiseptic agent due to its ability to suppress DNA replication. On the other hand, various studies show that PF intercalation to DNA can increase photogenotoxicity and has potential chances to induce carcinomas of skin appendages. However, the effects of PF intercalation on the photophysical and photochemical properties of DNA have not been sufficiently explored. In this study, the excited state dynamics of the PF intercalated d(GC)9 • d(GC)9 and d(AT)9 • d(AT)9 DNA duplex are investigated in an aqueous buffer solution. Under 267 nm excitation, we observed ultrafast charge transfer (CT) between PF and d(GC)9 • d(GC)9 duplex, generating a CT state with an order of magnitude longer lifetime compared to that of the intrinsic excited state reported for the d(GC)9 • d(GC)9 duplex. In contrast, no excited state interaction was detected between PF and d(AT)9 • d(AT)9. Nevertheless, a localized triplet state with a lifetime over 5 µs was identified in the PF-d(AT)9 • d(AT)9 duplex.

The Two Faces of the Guanyl Radical: Molecular Context and Behavior

The guanyl radical or neutral guanine radical G(-H)^• results from the loss of a hydrogen atom (H^•) or an electron/proton (e^–/H⁺) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC^•+ pair. The role of the two G(-H)^• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.

Multiscale Conformational Sampling Reveals Excited-State Locality in DNA Self-Repair Mechanism

Ultraviolet (UV) irradiation is known to be responsible for DNA damage. However, experimental studies in DNA oligonucleotides have shown that UV light can also induce sequence-specific self-repair. Following charge transfer from a guanine adenine sequence adjacent to a cyclobutane pyrimidine dimer (CPD), the covalent bond between the two thymines could be cleaved, recovering the intact base sequence. Mechanistic details promoting the self-repair remained unclear, however. In our theoretical study, we investigated whether optical excitation could directly lead to a charge-transfer state, thereby initiating the repair, or whether the initial excited state remains localized on a single nucleobase. We performed conformational sampling of 200 geometries of the damaged DNA double strand solvated in water and used a hybrid quantum and molecular mechanics approach to compute excited states at the complete active space perturbation level of theory. Analysis of the conformational data set clearly revealed that the excited-state properties are uniformly distributed across the fluctuations of the nucleotide in its natural environment. From the electronic wavefunction, we learned that the electronic transitions remained predominantly local on either adenine or guanine, and no direct charge transfer occurred in the experimentally accessed energy range. The investigated base sequence is not only specific to the CPD repair mechanism but ubiquitously occurs in nucleic acids. Our results therefore give a very general insight into the charge locality of UV-excited DNA, a property that is regarded to have determining relevance in the structural consequences following absorption of UV photons.

Independent Generation and Time-Resolved Detection of 2'-Deoxyguanosin-N2-yl Radicals

Guanine radicals are important reactive intermediates in DNA damage. Hydroxyl radical (HO. ) has long been believed to react with 2'-deoxyguanosine (dG) generating 2'-deoxyguanosin-N1-yl radical (dG(N1-H). ) via addition to the nucleobase π-system and subsequent dehydration. This basic tenet was challenged by an alternative mechanism, in which the major reaction of HO. with dG was proposed to involve hydrogen atom abstraction from the N2-amine. The 2'-deoxyguanosin-N2-yl radical (dG(N2-H). ) formed was proposed to rapidly tautomerize to dG(N1-H). . We report the first independent generation of dG(N2-H). in high yield via photolysis of 1. dG(N2-H). is directly observed upon nanosecond laser flash photolysis (LFP) of 1. The absorption spectrum of dG(N2-H). is corroborated by DFT studies, and anti- and syn-dG(N2-H). are resolved for the first time. The LFP experiments showed no evidence for tautomerization of dG(N2-H). to dG(N1-H). within hundreds of microseconds. This observation suggests that the generation of dG(N1-H). via dG(N2-H). following hydrogen atom abstraction from dG is unlikely to be a major pathway when HO. reacts with dG.

Deprotonation of Guanine Radical Cation G•+ Mediated by the Protonated Water Cluster

Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G^•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G^•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G^•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H₂O-PCM, 4H₂O-PCM, 5H₂O-PCM, and 7H₂O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G^•+.

Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by G-Quadruplexes and Modify Their Reactivity

G-Quadruplexes are formed by guanine rich DNA/RNA sequences in the presence of metal ions, which occupy the central cavity of these four-stranded structures. We show that these metal ions have a significant effect on the photogeneration and the reactivity of guanine radicals. Transient absorption experiments on G-quadruplexes formed by association of four TGGGGT strands in the presence of K⁺ reveal that the quantum yield of one-photon ionization at 266 nm (8.1 × 10^-3) is twice as high as that determined in the presence of Na⁺. Replacement of Na⁺ with K⁺ also suppresses one reaction path involving deprotonated radicals, (G-H2)^• → (G-H1)^• tautomerization. Such behavior shows that the underlying mechanisms are governed by dynamical processes, controlled by the mobility of metal ions, which is higher for Na⁺ than for K⁺. These findings may contribute to our understanding of the ultraviolet-induced DNA damage and optimize optoelectronic devices based on four-stranded structures, beyond DNA.

Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives

Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.