Populations and Dynamics of Guanine Radicals in DNA strands—Direct versus Indirect Generation

Abstract

Guanine radicals, known to be involved in the damage of the genetic code and aging, are studied by nanosecond transient absorption spectroscopy. They are generated in single, double and four-stranded structures (G-quadruplexes) by one and two-photon ionization at 266 nm, corresponding to a photon energy lower than the ionization potential of nucleobases. The quantum yield of the one-photon process determined for telomeric G-quadruplexes (TEL25/Na+) is (5.2 ± 0.3) × 10−3, significantly higher than that found for duplexes containing in their structure GGG and GG sequences, (2.1 ± 0.4) × 10−3. The radical population is quantified in respect of the ejected electrons. Deprotonation of radical cations gives rise to (G-H1)• and (G-H2)• radicals for duplexes and G-quadruplexes, respectively. The lifetimes of deprotonated radicals determined for a given secondary structure strongly depend on the base sequence. The multiscale non-exponential dynamics of these radicals are discussed in terms of inhomogeneity of the reaction space and continuous conformational motions. The deviation from classical kinetic models developed for homogeneous reaction conditions could also be one reason for discrepancies between the results obtained by photoionization and indirect oxidation, involving a bi-molecular reaction between an oxidant and the nucleic acid.

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

“…28 Coming to radicals, their spectra ( Figure 3) are determined after the decay of e hyd -. As in the case of previously studied G-quadruplexes, [4][5][6] the spectrum at 3 µs exhibits a broad band in the visible, explained by the coexistence of (G) + and (G-H2)  . When the transient absorbance A is divided by the [e hyd -] 0 determined for the same excitation intensity, the radical spectrum can be quantitatively described by a linear combination of the (G) + and (G-H2)  spectra in a ratio 0.4/0.6 (Figure 3a), considering the corresponding spectra reported for either monomeric guanosines [29][30] or (TG4T) 4 /Na + .…”

“…They were excited by 5 ns laser pulses at 266 nm ( Figure SI-1), with incident intensity lower than 2x10 6 Wcm -2 , thus avoiding two-photon ionization of the solvent. Two different scenarios were invoked to explain G-quadruplex ionization by low-energy photons: [5][6] (A) the specific arrangement of guanines lowers their VIP, or (B) electron detachment occurs after excited state relaxation towards charge transfer (CT) states.…”

Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions

“…Accordingly, the transient absorption signals at 512 nm shown in Figure 5 , where the intensity at 3 µs is normalized to 1, represents the survival probability P t of the total radical population at time t, i.e., the fraction of the initial radical concentration at time t: P t = [R] t /[R] 0 . For a quantitative description, the experimental traces recorded on the microsecond and millisecond time-scale were fitted with bi-exponential functions, although such fits have no physical meaning [ 10 ]. Thus, we found that the radical decay spans more than four orders of magnitude; at 50 µs, 80% of the radical population is present, while at 10 ms, this percentage dwindles down to 20%.…”

“…We showed that two different processes take place. First, deprotonation of radical cations occurs in the position 2, giving rise to (G-H2) • radicals instead of the (G-H1) • radicals (Figure 1a), which are observed for the dGMP mononucleotide [13] and various duplexes [10,14,15]. Such a different deprotonation route, which was initially detected by photosensitized oxidation of G-quadruplexes [16], is due to the fact The above-mentioned studies were performed by transient absorption spectroscopy using not only low-energy (266 nm) but also low-intensity excitation (5 ns laser pulses, incident intensity lower than 2 × 10 6 Wcm −2 ).…”

“…The term 'low-energy' is used in comparison to the ionization potential of the various components of nucleic acids, which preclude vertical electron photo-detachment upon irradiation around the absorption maximum (~260 nm). Yet, one-photon ionization quantum yields (φ 1 ) ranging from 3.5 × 10 −3 to 8.1 × 10 −3 were determined at 266 nm for four different G-quadruplex structures [8][9][10][11][12]. These structures were formed by folding of the telomeric sequences GGG(TTAGGG) 3 and TAGGG(TTAGGG) 3 TT in the presence of Na + ions (TEL21/Na + and A large number of articles reports oxidative damage and/or charge transport in G-quadruplexes, in which G radical generation is mediated by other molecules.…”