Tracking DNA Excited States by Picosecond-Time-Resolved Infrared Spectroscopy: Signature Band for a Charge-Transfer Excited State in Stacked Adenine–Thymine Systems

Doorley, Gerard W.; Wojdyła, Michał; Watson, Graeme W.; Towrie, Michael; Parker, Anthony W.; Kelly, John M.; Quinn, Susan J.

doi:10.1021/jz401258n

Cited by 79 publications

(65 citation statements)

References 44 publications

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“…This observation is important for developing models to explain how CT states, which generally have low oscillator strengths, are reached from the initial excitons. These results and ones from recent studies (24)(25)(26) suggest that interbase ET is a primary event whenever nucleic acids absorb UV light.…”

Section: Discussionsupporting

confidence: 74%

“…The main finding of this study is that absorption of a UVB or UVC photon by the d(OA) dinucleotide transfers an electron from O to A, producing a radical ion pair; this supports the role of O as a flavin mimic, but this study also adds to evidence that photoinduced ET occurs generally and with relatively high quantum yield between any pair of stacked nucleobases (11,(24)(25)(26). The latter conclusion rests on strong thermodynamic and kinetic similarities between CT states in other dinucleotides and in d(OA).…”

Section: Discussionsupporting

confidence: 73%

“…The 60-ps lifetime of the radical ion pair state of d(OA) is in the range of lifetimes previously reported for the long-lived excited states detected in DNA/RNA dinucleotides (11,(24)(25)(26) and oligonucleotides (10,26,32). Earlier, Takaya et al (11) proposed that the long-lived excited states are exciplex states with substantial CT character that decay via CR on timescales of 10-100 ps, depending on the thermodynamic driving force.…”

Section: Discussionmentioning

confidence: 61%

See 2 more Smart Citations

Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide

Zhang

Dood

Beckstead

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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During the early evolution of life, 8-oxo-7,8-dihydro-2′-deoxyguanosine (O) may have functioned as a proto-flavin capable of repairing cyclobutane pyrimidine dimers in DNA or RNA by photoinduced electron transfer using longer wavelength UVB radiation. To investigate the ability of O to act as an excited-state electron donor, a dinucleotide mimic of the FADH 2 cofactor containing O at the 5′-end and 2′-deoxyadenosine at the 3′-end was studied by femtosecond transient absorption spectroscopy in aqueous solution. Following excitation with a UV pulse, a broadband mid-IR pulse probed vibrational modes of ground-state and electronically excited molecules in the double-bond stretching region. Global analysis of timeand frequency-resolved transient absorption data coupled with ab initio quantum mechanical calculations reveal vibrational marker bands of nucleobase radical ions formed by electron transfer from O to 2′-deoxyadenosine. The quantum yield of charge separation is 0.4 at 265 nm, but decreases to 0.1 at 295 nm. Charge recombination occurs in 60 ps before the O radical cation can lose a deuteron to water. Kinetic and thermodynamic considerations strongly suggest that all nucleobases can undergo ultrafast charge separation when π-stacked in DNA or RNA. Interbase charge transfer is proposed to be a major decay pathway for UV excited states of nucleic acids of great importance for photostability as well as photoredox activity.DNA photophysics | time-resolved vibrational spectroscopy | DNA charge transfer states | ab initio calculations | photoreactivation

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Section: Discussionsupporting

confidence: 74%

Section: Discussionsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 61%

See 1 more Smart Citation

Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide

Zhang

Dood

Beckstead

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…These not only provide the PEHs for mechanistic purposes, but can also yield excited state absorptions [49,50], cationic energies [41], and other related observables with direct experimental counterparts [51,52]. Experimentally, several techniques have been employed to study the photoinduced phenomena of DNA nucleobases, ranging from pump-probe [4,28,[53][54][55], time-resolved infrared [56][57][58][59], photoelectron [17,41,60,61] and recently even Auger spectroscopy [16]. This has allowed postulating different theoretical models to explain the photochemical decay paths of the canonical nucleobases and simulate a range of experimental spectroscopic observables, providing a molecular counterpart.…”

Section: Introductionmentioning

confidence: 99%

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

et al. 2016

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Abstract:The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1 (ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.

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“…Several explanations for these long-living states and the size of their spatial extent have been discussed in the literature (5)(6)(7)(8)(9). Delocalized excitons (9); excitons that decay to charge-separated states or neutral excimer states (10,11); exciplexes located on two neighboring bases (5,8,12,13); or even excited single bases, where steric interactions in the DNA strand impedes the ultrafast decay (14), have been proposed. Further computations suggest a decay of an initially populated delocalized exciton to localized neutral or charged excimer states (15)(16)(17).…”

mentioning

confidence: 99%

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Bucher

Pilles

Carell

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

115

139

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Base stacking in DNA is related to long-living excited states whose molecular nature is still under debate. To elucidate the molecular background we study well-defined oligonucleotides with natural bases, which allow selective UV excitation of one single base in the strand. IR probing in the picosecond regime enables us to dissect the contribution of different single bases to the excited state. All investigated oligonucleotides show long-living states on the 100-ps time scale, which are not observable in a mixture of single bases. The fraction of these states is well correlated with the stacking probabilities and reaches values up to 0.4. The longliving states show characteristic absorbance bands that can be assigned to charge-transfer states by comparing them to marker bands of radical cation and anion spectra. The charge separation is directed by the redox potential of the involved bases and thus controlled by the sequence. The spatial dimension of this charge separation was investigated in longer oligonucleotides, where bridging sequences separate the excited base from a sensor base with a characteristic marker band. After excitation we observe a bleach of all involved bases. The contribution of the sensor base is observable even if the bridge is composed of several bases. This result can be explained by a charge delocalization along a well-stacked domain in the strand. The presence of charged radicals in DNA strands after light absorption may cause reactions-oxidative or reductive damagecurrently not considered in DNA photochemistry.DNA photophysics | DNA damage | DNA electron transfer | ultrafast vibrational spectroscopy D NA photophysics is crucial for the understanding of lightinduced damage of the genetic code (1). The excited state of single DNA bases is known to decay extremely fast on the subpicosecond time scale, predominantly via internal conversion (2, 3). This ultrafast decay is assumed to suppress destructive decay channels, thereby protecting the DNA from photodamage and avoiding disintegration of the genetic information. In contrast to this ultrafast deactivation of single nucleobases, the biological relevant DNA strands show further long-living states (4, 5). Several explanations for these long-living states and the size of their spatial extent have been discussed in the literature (5-9). Delocalized excitons (9); excitons that decay to charge-separated states or neutral excimer states (10, 11); exciplexes located on two neighboring bases (5, 8, 12, 13); or even excited single bases, where steric interactions in the DNA strand impedes the ultrafast decay (14), have been proposed. Further computations suggest a decay of an initially populated delocalized exciton to localized neutral or charged excimer states (15-17). However, to our knowledge, a final understanding of the nature of these longliving states has not been reached. Related experiments were performed in the last decade to investigate charge transport processes in DNA, motivated by DNA electronics and oxidative damage (18,19). Charge ...

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Tracking DNA Excited States by Picosecond-Time-Resolved Infrared Spectroscopy: Signature Band for a Charge-Transfer Excited State in Stacked Adenine–Thymine Systems

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Cited by 79 publications

References 44 publications

Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide

Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

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