Excited State Pathways Leading to Formation of Adenine Dimers

Bányász, Ákos; Martínez‐Fernández, Lara; Ketola, Tiia-Maaria; Muñoz-Losa, Aurora; Esposito, Luciana; Markovitsi, Dimitra; Improta, Roberto

doi:10.1021/acs.jpclett.6b00660

Cited by 28 publications

(39 citation statements)

References 22 publications

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“…This computational approach has been already applied to study the optical properties of dA and A-tracts. 19, 23, 32–34 The calculated spectra, red-shifted by 0.55 eV (see SI, Sections 4 and 5 for a more detailed discussion), are in very good agreement with the experimental spectra. In particular, the computed spectrum of (A-H6)• (Figure 4a) is extremely close to that shown in Figure 2b, providing a broad peak around 620 nm and another peak at ca .…”

supporting

confidence: 68%

“…(b) Triangles: difference of the (dA) 20 spectra recorded at 0.1 and 20 ms, associated with adenine dimerization; 19 solid line: spectrum obtained upon 193 nm excitation of 5′-dAMP at 300 ns. 6 Inset in (a): Correlation of transient absorbance detected at 600 nm and 0.1 ms with the concentration of ejected hydrated electrons.…”

Section: Figurementioning

confidence: 99%

“…18 However, the spectral and dynamical features of the resulting radicals have not been properly studied. An important difficulty arises from the fact that, in addition to the radical species resulting from ionization of A-tracts, we also have the formation of adenine 19 or thymine dimers 20 which may affect both the spectrum profile and its dynamics. A key point in our time-resolved experiments was the quantification of the various UV-induced species.…”

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confidence: 99%

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UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization

Bányász

Ketola

Muñoz-Losa

et al. 2016

J. Phys. Chem. Lett.

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Adenyl radicals generated in DNA single and double strands, (dA)20 and (dA)20•(dT)20, by one- and two-photon ionization by 266 nm laser pulses decay at 600 nm with half-times of 1.0 ± 0.1 and 4 ± 1 ms, respectively. While ionization initially forms the cation radical, the radicals detected for (dA)20 are quantitatively identified as N6-deprotonated adenyl radicals by their absorption spectrum, which is computed quantum mechanically employing TD-DFT. Theoretical calculations show that deprotonation of the cation radical induces only weak spectral changes, in line with the spectra of the adenyl radical cation and the deprotonated radical trapped in low temperature glasses.

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confidence: 68%

Section: Figurementioning

confidence: 99%

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confidence: 99%

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UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization

Bányász

Ketola

Muñoz-Losa

et al. 2016

J. Phys. Chem. Lett.

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“…DFT and its time‐dependent version (TD‐DFT) have been used to optimize the ground (S 0 ) and excited state (S 1 ) of the (dA) 2 (dT) 2 system. The M052X functional was selected since it has been successfully applied in previous analogous studies regarding pyrimidine and/or purine photodimerization . M052X incorporates specific corrections to correctly describe dispersion interactions and charge‐transfer transitions, improving the performance of the “standard” functionals when treating a strongly coupled multichromophore system.…”

Section: Computational Detailsmentioning

confidence: 99%

Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6–4 Thymine–Thymine Photodimerization in a DNA Duplex

Conti

Martínez‐Fernández

Esposito

et al. 2017

Chemistry A European J

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The T-T photodimerization paths leading to the formation of cyclobutane pyrimidine dimer (CPD) and 6-4 pyrimidine pyrimidone (64-PP), the two main DNA photolesions, have been resolved for a T-T step in a DNA duplex by two complementary state-of-the-art quantum mechanical approaches: QM(CASPT2//CASSCF)/MM and TD-DFT/PCM. Based on the analysis of several different representative structures, we define a new-ensemble of cooperating geometrical and electronic factors (besides the distance between the reacting bonds) ruling T-T photodimerization in DNA. CPD is formed by a barrierless path on an exciton state delocalized over the two bases. Large interbase stacking and shift values, together with a small pseudorotation phase angle for T at the 3'-end, favor this reaction. The oxetane intermediate, leading to a 64-PP adduct, is formed on a singlet T→T charge-transfer state and is favored by a large interbase angle and slide values. A small energy barrier (<0.3 eV) is associated to this path, likely contributing to the smaller quantum yield observed for this process. Eventually, a clear directionality is always shown by the electronic excitation characterizing the singlet photoactive state driving the photodimerization process: an exciton that is more localized on T and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints.

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“…10,12,13 (iii) The transient absorption spectra associated with photoionization should be disentangled from those arising from UV-induced base dimerization reactions. 14,15 Fig. 1 (a) Absorption spectra of (AT) 10 (black) and dAMP (grey); (b) typical melting curve obtained for (AT) 10 .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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Excited State Pathways Leading to Formation of Adenine Dimers

Cited by 28 publications

References 22 publications

UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization

UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization

Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6–4 Thymine–Thymine Photodimerization in a DNA Duplex

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

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