Experimental and Theoretical Study of Deprotonation of DNA Adenine Cation Radical

Abstract

Among all the DNA components, extremely redox-active guanine (G) and adenine (A) bases are subject to facile loss of an electron and form cation radicals (G +• and A +•) when exposed to irradiation or radical oxidants. The subsequent deprotonation of G +• and A +• can invoke DNA damage or interrupt hole transfer in DNA. However, compared with intensive reports for G +• , studies on the deprotonation of A +• are still limited at present. Herein, we investigate the deprotonation behavior of A +• by time-resolved laser flash photolysis. The deprotonation product of A(N 6-H) • is observed and the deprotonation rate constant, (2.0±0.1)×10 7 s −1 , is obtained at room temperature. Further, the deprotonation rate constants of A +• are measured at temperatures varying from 280 K to 300 K, from which the activation energy for the N 6-H deprotonation is determined to be (17.1±1.0) kJ/mol by Arrhenius equation. In addition, by incorporating the aqueous solvent effect, we perform density functional theory calculations for A +• deprotonation in free base and in duplex DNA. Together with experimental results, the deprotonation mechanisms of A +• in free base and in duplex DNA are revealed, which are of fundamental importance for understanding the oxidative DNA damage and designing DNA-based electrochemical devices.

Rate Constants and Mechanisms for Reactions of Bromine Radicals with Trace Organic Contaminants

“…Adenine’s cation radical (ADN •+ ) was evidenced by the shoulder absorption around 400–460 nm at 3 μs . Later, the peak at 330 nm and the increase in the absorption at 500–600 nm are evidence of the formation of the adenine’s unprotonated radical (ADN­(−H) • ). , This suggests SET followed by deprotonation between ADN and Br 2 •– according to eqs and . The SET mechanism for the reaction between ADN and Br 2 •– was also supported by quantum chemical calculations (Δ G SET = −21.9 kcal mol –1 , Table S5). SET was reported to be the main reaction fashion of Br 2 •– in the literature .…”

“…Br 2 •– is often a one-electron oxidant in water. , Adenine (ADN) was selected as a model compound to explore the reaction mechanisms involved since its transient species have been well studied. , The time-resolved transient spectra of adenine reacting with Br 2 •– are shown in Figure f. The remarkable changes in the spectra over time exhibit both old species decay and new species formation.…”

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

“…In this work, laser flash photolysis experiments were first performed to obtain the activation energy of G •+ deprotonation. It is well-known that the SO 4 •– oxidizes G to G •+ and G •+ deprotonates to G­(N1–H) • by rapid loss of the imino proton at pH 7.0 (reactions and ). ,, In our experiments, the oxidizing radicals SO 4 •– are generated within the ∼14 ns laser pulse duration through the rapid photodissociation of S 2 O 8 2– by 355 nm laser irradiation (reaction ), ,,,, which ensures no interference with the detection of the oxidation reaction with G and subsequent deprotonation. According to previous pulse radiolysis studies, when the concentration of G is above 3 mM, the deprotonation of G •+ to G­(N1–H) • , rather than the bimolecular reaction of SO 4 •– oxidizing G, is the rate-determining step of the G­(N1–H) • formation (reactions and ).…”

“…•− are generated within the ∼14 ns laser pulse duration through the rapid photodissociation of S 2 O 8 2− by 355 nm laser irradiation (reaction 1), 23,24,31,39,41 which ensures no interference with the detection of the oxidation reaction with G and subsequent deprotonation. According to previous pulse radiolysis studies, 17 when the concentration of G is above 3 mM, the deprotonation of G •+ to G(N1−H) • , rather than the bimolecular reaction of SO 4…”

“…Nanosecond time-resolved transient absorption spectra were measured using a flash photolysis setup Edinburgh LP920 spectrometer (Edinburgh Instruments Ltd.) combined with a Nd:YAG laser (Spectra-Physics Lab 170, Newport Corp.). , Each measurement was performed in a 1 cm path length quartz cuvette that was put in the Oxford Instruments OptistatDN Cryostat and cooled to a certain temperature. The sample was excited by using a 355 nm laser pulse (1 Hz; 20 mJ/pulse; full width at half-maximum, ≈ 7 ns).…”