Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation

Abstract

There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.

Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA

“…Nevertheless, the SB cross sections per nucleotide ( Table 2) vary strongly for each sequence and irradiation energy from 0.43 to 11.98 • 10 −16 cm 2 , which indicates that they are not additive under the assumption that each nucleotide is equivalent. Comparing the DNA sequences d(A 16 ) and d(A 20 ), the cross sections for SBs do not continue the increasing trend, but decrease significantly for d(A 20 ) at all electron energies. Tentatively, we assume that this can be ascribed to a conformational change occurring in the longer oligonucleotides.…”

“…In the following, we will first discuss the energy dependence of SB cross sections, and then the dependence on the oligonucleotide length. 12 1.34 ± 0.17 6.95 ± 1.12 6.32 ± 0.59 3.10 ± 0.54 33.12 5 -dA 16 1 Figure 3 shows the SB cross sections as a function of electron energy between 5.0 and 10.0 eV. All determined DNA strand break cross sections σSB are in the regime of 10 −15 cm 2 with the highest cross sections for d(A16) at all electron energies.…”

“…All determined DNA strand break cross sections σ SB are in the regime of 10 −15 cm 2 with the highest cross sections for d(A 16 ) at all electron energies. Below the ionization threshold, DNA bases can either be damaged by pulsed lasers (~4.6 eV) [15,16], Klicken oder tippen Sie hier, um Text einzugeben. which results in oxidative damage to the DNA, or at specific electron energies through anion resonances, i.e., TNI states, which can either decay by autodetachment (AD) of the extra electron or dissociation (DEA).…”

“…Figure 5b illustrates the conformational change if the DNA reaches a certain length. Additionally, for the folded d(A 20 ) hairpin, one can assume in the first approximation that the geometrical cross section increases compared to d(A 16 ). The drop of the SB cross section must then be explained by an increase of the stability of the DNA hairpin due to the additional hydrogen bonds.…”

“…In the present work, we extend these studies to systematically investigate the effect of the oligonucleotide length on the SB cross section upon LEE irradiation. We quantify and compare DNA strand breaks for various lengths of polyadenine ssDNA (4,8,12,16, and 20 nucleotides). The DNA target sequences are irradiated with electron energies of 5.0, 7.0, 8.4, and 10 eV, which covers the energy range of secondary electrons produced in water radiolysis and which are close to typical energies at which SSBs have been observed before [13].…”