Early events of DNA photodamage

Recent advances in multidimensional ultrafast spectroscopy

Multidimensional ultrafast spectroscopies are one of the premier tools to investigate condensed phase dynamics of biological, chemical and functional nanomaterial systems. As they reach maturity, the variety of frequency domains that can be explored has vastly increased, with experimental techniques capable of correlating excitation and emission frequencies from the terahertz through to the ultraviolet. Some of the most recent innovations also include extreme cross-peak spectroscopies that directly correlate the dynamics of electronic and vibrational states. This review article summarizes the key technological advances that have permitted these recent advances, and the insights gained from new multidimensional spectroscopic probes.

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Photoactivated proton coupled electron transfer in DNA: insights from quantum mechanical calculations

The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect.

Photorelaxation and Photorepair Processes in Nucleic and Amino Acid Derivatives

Understanding the fundamental interaction between electromagnetic radiation and matter is essential for a large number of phenomena, with significance to civilization.[...].

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

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 T³ and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints.

Excited-State Dynamics in O6-Methylguanosine: Impact of O6-Methylation on the Relaxation Mechanism of Guanine Monomers

Absorption of ultraviolet radiation by DNA bases results in ultrafast internal conversion to the ground state, which minimizes photodamage. However, exogenous and endogenous alkylating agents present in the cellular environment can methylate the nucleobases in DNA. In particular, methylation of guanosine at the O⁶ position in DNA leads to the formation of the O⁶-methylguanosine adduct, which may alter the photostability of DNA. This contribution demonstrates that O⁶-methylation of guanosine red shifts its ground-state absorption spectrum and slows down the rate of internal conversion to the ground state by ∼40-fold in aqueous solution. The 40-fold decrease in the rate of excited-state decay increases the probability of photodamage within cellular DNA. It is proposed that the longer decay lifetime corresponds to relaxation of the excited-state population in O⁶-methylguanosine along a C6-puckered reaction coordinate in the ¹ππ*(L_a) potential energy surface that runs parallel to an ultrafast internal conversion pathway along a C2-puckered coordinate.

UV-induced damage to DNA: effect of cytosine methylation on pyrimidine dimerization

Methylation/demethylation of cytosine plays an important role in epigenetic signaling, the reversibility of epigenetic modifications offering important opportunities for targeted therapies. Actually, methylated sites have been correlated with mutational hotspots detected in skin cancers. The present brief review discusses the physicochemical parameters underlying the specific ultraviolet-induced reactivity of methylated cytosine. It focuses on dimerization reactions giving rise to cyclobutane pyrimidine dimers and pyrimidine (6–4) pyrimidone adducts. According to recent studies, four conformational and electronic factors that are affected by cytosine methylation may control these reactions: the red-shift of the absorption spectrum, the lengthening of the excited state lifetime, changes in the sugar puckering modifying the stacking between reactive pyrimidines and an increase in the rigidity of duplexes favoring excitation energy transfer toward methylated pyrimidines.

A theoretical study of the light-induced cross-linking reaction of 5-fluoro-4-thiouridine with thymine

In contrast to photophysics of thio-substituted nucleobases, their photoinduced cross-linking reactions with canonical nucleobases remain scarcely investigated computationally. In this work, we have adopted combined CASPT2/PCM//CASSCF and B3LYP-D3/PCM electronic structure methods to study this kind of photochemical reaction of 5-fluoro-4-thiouridine (truncated 5-fluoro-1-methyl-4-thiouracil used in calculations) and 1-methylthymine (referred to as thymine for clarity hereinafter). On the basis of CASPT2/PCM computed results, we have proposed two efficient excited-state relaxation pathways to populate the lowest T₁ state of the complex of 5-fluoro-1-methyl-4-thiouracil and thymine from its initially populated S₂(¹ππ*) state. In the first one, the S₂ system first hops to the S₁ state via an S₂/S₁ conical intersection, followed by a direct S₁ → T₁ intersystem crossing process enhanced by large S₁/T₁ spin-orbit coupling. In the second path, the resultant S₁ system first jumps to the T₂ state, from which an efficient T₂ → T₁ internal conversion occurs. The T₁ cross-linking reaction is overall divided into two phases. The first phase is a stepwise and nonadiabatic photocyclization reaction, which starts from the T₁ complex and ends up with an S₀ thietane intermediate. The second phase is a thermal reaction. The system first rearranges its four- and six-membered rings to form three new rings; then, an S₀ fluorine atom transfer occurs, followed by the formation of photoproducts. Finally, the present work paves the way for studying light-induced cross-linking reactions of thionucleobases with canonical bases in DNA and RNA.

Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog

Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.

Is UV-Induced Electron-Driven Proton Transfer Active in a Chemically Modified A·T DNA Base Pair?

Transient electronic and vibrational absorption spectroscopies have been used to investigate whether UV-induced electron-driven proton transfer (EDPT) mechanisms are active in a chemically modified adenine-thymine (A·T) DNA base pair. To enhance the fraction of biologically relevant Watson-Crick (WC) hydrogen-bonding motifs and eliminate undesired Hoogsteen structures, a chemically modified derivative of A was synthesized, 8-(tert-butyl)-9-ethyladenine (8tBA). Equimolar solutions of 8tBA and silyl-protected T nucleosides in chloroform yield a mixture of WC pairs, reverse WC pairs, and residual monomers. Unlike previous transient absorption studies of WC guanine-cytosine (G·C) pairs, no clear spectroscopic or kinetic evidence was identified for the participation of EDPT in the excited-state relaxation dynamics of 8tBA·T pairs, although ultrafast (sub-100 fs) EDPT cannot be discounted. Monomer-like dynamics are proposed to dominate in 8tBA·T.

Small RNA-mediated repair of UV-induced DNA lesions by the DNA DAMAGE-BINDING PROTEIN 2 and ARGONAUTE 1

As photosynthetic organisms, plants need to prevent irreversible UV-induced DNA lesions. Through an unbiased, genome-wide approach, we have uncovered a previously unrecognized interplay between Global Genome Repair and small interfering RNAs (siRNAs) in the recognition of DNA photoproducts, prevalently in intergenic regions. Genetic and biochemical approaches indicate that, upon UV irradiation, the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) of Arabidopsis thaliana form a chromatin-bound complex together with 21-nt siRNAs, which likely facilitates recognition of DNA damages in an RNA/DNA complementary strand-specific manner. The biogenesis of photoproduct-associated siRNAs involves the noncanonical, concerted action of RNA POLYMERASE IV, RNA-DEPENDENT RNA POLYMERASE-2, and DICER-LIKE-4. Furthermore, the chromatin association/dissociation of the DDB2-AGO1 complex is under the control of siRNA abundance and DNA damage signaling. These findings reveal unexpected nuclear functions for DCL4 and AGO1, and shed light on the interplay between small RNAs and DNA repair recognition factors at damaged sites.

The Cartography of UV-induced DNA Damage Formation and DNA Repair

DNA damage presents a barrier to DNA-templated biochemical processes, including gene expression and faithful DNA replication. Compromised DNA repair leads to mutations, enhancing the risk for genetic diseases and cancer development. Conventional experimental approaches to study DNA damage required a researcher to choose between measuring bulk damage over the entire genome, with little or no resolution regarding a specific location, and obtaining data specific to a locus of interest, without a global perspective. Recent advances in high-throughput genomic tools overcame these limitations and provide high-resolution measurements simultaneously across the genome. In this review, we discuss the available methods for measuring DNA damage and their repair, focusing on genomewide assays for pyrimidine photodimers, the major types of damage induced by ultraviolet irradiation. These new genomic assays will be a powerful tool in identifying key components of genome stability and carcinogenesis.

Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs

It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G^- with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G^- nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G^--A and 8-oxo-G^--C base pairs are likely too short-lived to be efficient electron-transfer repair agents.

Solvent effects on the excited state characteristics of adenine–thymine base pairs

A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.

The excited-state decay mechanism of 2,4-dithiothymine in the gas phase, microsolvated surroundings, and aqueous solution

We have employed computational methods to systematically explore the excited-state decay mechanism of 2,4-dithiothymine.

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

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.

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer

The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

DNA Repair by DNA: The UV1C DNAzyme Catalyzes Photoreactivation of Cyclobutane Thymine Dimers in DNA More Effectively than Their de Novo Formation

UV1C, a 42-nt DNA oligonucleotide, is a deoxyribozyme (DNAzyme) that optimally uses 305 nm wavelength light to catalyze photoreactivation of a cyclobutane thymine dimer placed within a gapped, unnatural DNA substrate, TDP. Herein we show that UV1C is also capable of photoreactivating thymine dimers within an authentic single-stranded DNA substrate, LDP. This bona fide UV1C substrate enables, for the first time, investigation of whether UV1C catalyzes only photoreactivation or also the de novo formation of thymine dimers. Single-turnover experiments carried out with LDP and UV1C, relative to control experiments with LDP alone in single-stranded and double-stranded contexts, show that while UV1C does modestly promote thymine dimer formation, its major activity is indeed photoreactivation. Distinct photostationary states are reached for LDP in its three contexts: as a single strand, as a constituent of a double-helix, and as a 1:1 complex with UV1C. The above results on the cofactor-independent photoreactivation capabilities of a catalytic DNA reinforce a series of recent, unexpected reports that purely nucleotide-based photoreactivation is also operational within conventional double-helical DNA.

Can a Six-Letter Alphabet Increase the Likelihood of Photochemical Assault to the Genetic Code?

In 2014, two unnatural nucleosides, d5SICS and dNaM, were shown to selectively base pair and replicate with high fidelity in a modified strain of E. coli, thus effectively expanding its genetic alphabet from four to six letters. More recently, a significant reduction in cell proliferation was reported in cells cultured with d5SICS, and putatively with dNaM, upon exposure to brief periods of near-visible radiation. The photosensitizing properties of the lowest-energy excited triplet state of both d5SICS and dNaM were implicated in their cytotoxicity. Importantly, however, the excited-state mechanisms by which near-visible excitation populates the triplet states of d5SICS and dNaM are currently unknown. In this study, steady-state and time-resolved spectroscopies are combined with quantum-chemical calculations in order to reveal the excited-state relaxation mechanisms leading to efficient population of the triplet states in these unnatural nucleosides in solution. It is shown that excitation of d5SICS or dNaM with near-visible light leads overwhelmingly to ultrafast population of their triplet states on the femtosecond time scale. The results presented in this work lend strong support to the proposal that photoexcitation of these unnatural nucleosides can accelerate oxidatively generated damage to DNA and other biomolecules within the cellular environment.

Life in the light: nucleic acid photoproperties as a legacy of chemical evolution

Photophysical investigations of the canonical nucleobases that make up DNA and RNA during the past 15 years have revealed that excited states formed by the absorption of UV radiation decay with subpicosecond lifetimes (i.e., <10(-12) s). Ultrashort lifetimes are a general property of absorbing sunscreen molecules, suggesting that the nucleobases are molecular survivors of a harsh UV environment. Encoding the genome using photostable building blocks is an elegant solution to the threat of photochemical damage. Ultrafast excited-state deactivation strongly supports the hypothesis that UV radiation played a major role in shaping molecular inventories on the early Earth before the emergence of life and the subsequent development of a protective ozone shield. Here, we review the general physical and chemical principles that underlie the photostability, or "UV hardiness", of modern nucleic acids and discuss the possible implications of these findings for prebiotic chemical evolution. In RNA and DNA strands, much longer-lived excited states are observed, which at first glance appear to increase the risk of photochemistry. It is proposed that the dramatically different photoproperties that emerge from assemblies of photostable building blocks may explain the transition from a world of molecular survival to a world in which energy-rich excited electronic states were eventually tamed for biological purposes such as energy transduction, signaling, and repair of the genetic machinery.

Chemical excitation of electrons: A dark path to melanoma

Sunlight's ultraviolet wavelengths induce cyclobutane pyrimidine dimers (CPDs), which then cause mutations that lead to melanoma or to cancers of skin keratinocytes. In pigmented melanocytes, we found that CPDs arise both instantaneously and for hours after UV exposure ends. Remarkably, the CPDs arising in the dark originate by a novel pathway that resembles bioluminescence but does not end in light: First, UV activates the enzymes nitric oxide synthase (NOS) and NADPH oxidase (NOX), which generate the radicals nitric oxide (NO) and superoxide (O2(-)); these combine to form the powerful oxidant peroxynitrite (ONOO(-)). A fragment of the skin pigment melanin is then oxidized, exciting an electron to an energy level so high that it is rarely seen in biology. This process of chemically exciting electrons, termed "chemiexcitation", is used by fireflies to generate light but it had never been seen in mammalian cells. In melanocytes, the energy transfers radiationlessly to DNA, inducing CPDs. Chemiexcitation is a new source of genome instability, and it calls attention to endogenous mechanisms of genome maintenance that prevent electronic excitation or dissipate the energy of excited states. Chemiexcitation may also trigger pathogenesis in internal tissues because the same chemistry should arise wherever superoxide and nitric oxide arise near cells that contain melanin.

Intersystem crossing rates of S1 state keto-amino cytosine at low excess energy

The amino-keto tautomer of supersonic jet-cooled cytosine undergoes intersystem crossing (ISC) from the v = 0 and low-lying vibronic levels of its S1((1)ππ(∗)) state. We investigate these ISC rates experimentally and theoretically as a function of S1 state vibrational excess energy Eexc. The S1 vibronic levels are pumped with a ∼5 ns UV laser, the S1 and triplet state ion signals are separated by prompt or delayed ionization with a second UV laser pulse. After correcting the raw ISC yields for the relative S1 and T1 ionization cross sections, we obtain energy dependent ISC quantum yields QISC (corr)=1%-5%. These are combined with previously measured vibronic state-specific decay rates, giving ISC rates kISC = 0.4-1.5 ⋅ 10(9) s(-1), the corresponding S1⇝S0 internal conversion (IC) rates are 30-100 times larger. Theoretical ISC rates are computed using SCS-CC2 methods, which predict rapid ISC from the S1; v = 0 state with kISC = 3 ⋅ 10(9) s(-1) to the T1((3)ππ(∗)) triplet state. The surprisingly high rate of this El Sayed-forbidden transition is caused by a substantial admixture of (1)nOπ(∗) character into the S1((1)ππ(∗)) wave function at its non-planar minimum geometry. The combination of experiment and theory implies that (1) below Eexc = 550 cm(-1) in the S1 state, S1⇝S0 internal conversion dominates the nonradiative decay with kIC ≥ 2 ⋅ 10(10) s(-1), (2) the calculated S1⇝T1 ((1)ππ(∗)⇝(3)ππ(∗)) ISC rate is in good agreement with experiment, (3) being El-Sayed forbidden, the S1⇝T1 ISC is moderately fast (kISC = 3 ⋅ 10(9) s(-1)), and not ultrafast, as claimed by other calculations, and (4) at Eexc ∼ 550 cm(-1) the IC rate increases by ∼50 times, probably by accessing the lowest conical intersection (the C5-twist CI) and thereby effectively switching off the ISC decay channels.

Ultrafast dynamics of formation and autodetachment of a dipole-bound state in an open-shell π-stacked dimer anion

Isolated π-stacked dimer radical anions present the simplest model of an excess electron in a π-stacked environment. Here, frequency-, angle-, and time-resolved photoelectron imaging together with electronic structure calculations have been used to characterise the π-stacked coenzyme Q₀ dimer radical anion and its exited state dynamics. In the ground electronic state, the excess electron is localised on one monomer with a planar para-quinone ring, which is solvated by the second monomer in which carbonyl groups are bent out of the para-quinone ring plane. Through the π-stacking interaction, the dimer anion exhibits a number of charge-transfer (intermolecular) valence-localised resonances situated in the detachment continuum that undergo efficient internal conversion to a cluster dipole-bound state (DBS) on a ∼60 fs timescale. In turn, the DBS undergoes vibration-mediated autodetachment on a 2.0 ± 0.2 ps timescale. Experimental vibrational structure and supporting calculations assign the intermolecular dynamics to be facilitated by vibrational wagging modes of the carbonyl groups on the non-planar monomer. At photon energies ∼0.6-1.0 eV above the detachment threshold, a competition between photoexcitation of an intermolecular resonance leading to the DBS, and photoexcitation of an intramolecular resonance leading to monomer-like dynamics further illustrates the π-stacking specific dynamics. Overall, this study provides the first direct observation of both internal conversion of resonances into a DBS, and characterisation of a vibration-mediated autodetachment in real-time.

Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors

C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs.

Gas-Phase Cytosine and Cytosine-N1-Derivatives Have 0.1-1 ns Lifetimes Near the S1 State Minimum

Ultraviolet radiative damage to DNA is inefficient because of the ultrafast S1 ⇝ S0 internal conversion of its nucleobases. Using picosecond pump-ionization delay measurements, we find that the S1((1)ππ*) state vibrationless lifetime of gas-phase keto-amino cytosine (Cyt) is τ = 730 ps or ∼ 700 times longer than that measured by femtosecond pump-probe ionization at higher vibrational excess energy, Eexc. N1-Alkylation increases the S1 lifetime up to τ = 1030 ps for N1-ethyl-Cyt but decreases it to 100 ps for N1-isopropyl-Cyt. Increasing the vibrational energy to Eexc = 300-550 cm(-1) decreases the lifetimes to 20-30 ps. The nonradiative dynamics of S1 cytosine is not solely a property of the amino-pyrimidinone chromophore but is strongly influenced by the N1-substituent. Correlated excited-state calculations predict that the gap between the S2((1)nOπ*) and S1((1)ππ*) states decreases along the series of N1-derivatives, thereby influencing the S1 state lifetime.

High-Energy Long-Lived Mixed Frenkel-Charge-Transfer Excitons: From Double Stranded (AT)n to Natural DNA

The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV-induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine-thymine double-stranded structures (AT)n . Fluorescence measurements on (AT)n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time-dependent (TD)-DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine-to-thymine charge-transfer states. Emission from such high-energy long-lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π-π* states (≥0.1). An increase in the size of the system quenches π-π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π-π* and charge-transfer states. Subsequently, we identify the common features between the HELM states of (AT)n structures with those reported previously for alternating (GC)n : high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π-π* states, giving rise to delayed fluorescence.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

UV laser photoactivation of hexachloroplatinate bound to individual nucleobases in vacuo as molecular level probes of a model photopharmaceutical

UV excitation of mass-selected hexachloroplatinate–nucleobase clusters provides detailed insight into the photophysics and photochemistry of a model DNA photopharmaceutical.

Photoinduced long-lived charge transfer excited states in AT-DNA strands

The IR spectrum of a charge transfer (CT) excited electronic state in DNA has been computed for the first time, enabling assignment of the long-lived component of the transient IR spectrum of a d(AT)₉ single strand to an A → T CT state.

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

Absorption of UV-radiation in nucleotides initiates a number of photophysical and photochemical processes, which may finally cause DNA damage. One major decay channel of photoexcited DNA leads to reactive charge transfer states. This study shows that these states trigger self-repair of DNA photolesions. The experiments were performed by UV spectroscopy and HPLC on different single and double stranded oligonucleotides containing a cyclobutane pyrimidine dimer (CPD) lesion. In a first experiment we show that photoexcitation of adenine adjacent to a CPD has no influence on this lesion. However, excitation of a guanine (G) adenine (A) sequence leads to reformation of the intact thymine (T) bases. The involvement of two bases for the repair points to a long-living charge transfer state between G and A to be responsible for the repair. The negatively charged A radical anion donates an electron to the CPD, inducing ring splitting and repair. In contrast, a TA sequence, having an inverted charge distribution (T radical anion, A radical cation), is not able to repair the CPD lesion. The investigations show that the presence of an adjacent radical ion is not sufficient for repair. More likely it is the driving power represented by the oxidation potential of the radical ion, which controls the repair. Thus, repair capacities are strongly sequence-dependent, creating DNA regions with different tendencies of self-repair. This self-healing activity represents the simplest sequence-dependent DNA repair system.

UV-induced DNA Damage: The Role of Electronic Excited States

The knowledge of the fundamental processes induced by the direct absorption of UV radiation by DNA allows extrapolating conclusions drawn from in vitro studies to the in-vivo DNA photoreactivity. In this respect, the characterization of the DNA electronic excited states plays a key role. For a long time, the mechanisms of DNA lesion formation were discussed in terms of generic "singlet" and "triplet" excited state reactivity. However, since the beginning of the 21(st) century, both experimental and theoretical studies revealed the existence of "collective" excited states, i.e. excited states delocalized over at least two bases. Two limiting cases are distinguished: Frenkel excitons (delocalized ππ* states) and charge-transfer states in which positive and negative charges are located on different bases. The importance of collective excited states in photon absorption (in particular in the UVA spectral domain), the redistribution of the excitation energy within DNA, and the formation of dimeric pyrimidine photoproducts is discussed. The dependence of the behavior of the collective excited states on conformational motions of the nucleic acids is highlighted.

Mutations in Replicative Stress Response Pathways Are Associated with S Phase-specific Defects in Nucleotide Excision Repair

Nucleotide excision repair (NER) is a highly conserved pathway that removes helix-distorting DNA lesions induced by a plethora of mutagens, including UV light. Our laboratory previously demonstrated that human cells deficient in either ATM and Rad3-related (ATR) kinase or translesion DNA polymerase η (i.e. key proteins that promote the completion of DNA replication in response to UV-induced replicative stress) are characterized by profound inhibition of NER exclusively during S phase. Toward elucidating the mechanistic basis of this phenomenon, we developed a novel assay to quantify NER kinetics as a function of cell cycle in the model organism Saccharomyces cerevisiae. Using this assay, we demonstrate that in yeast, deficiency of the ATR homologue Mec1 or of any among several other proteins involved in the cellular response to replicative stress significantly abrogates NER uniquely during S phase. Moreover, initiation of DNA replication is required for manifestation of this defect, and S phase NER proficiency is correlated with the capacity of individual mutants to respond to replicative stress. Importantly, we demonstrate that partial depletion of Rfa1 recapitulates defective S phase-specific NER in wild type yeast; moreover, ectopic RPA1-3 overexpression rescues such deficiency in either ATR- or polymerase η-deficient human cells. Our results strongly suggest that reduction of NER capacity during periods of enhanced replicative stress, ostensibly caused by inordinate sequestration of RPA at stalled DNA replication forks, represents a conserved feature of the multifaceted eukaryotic DNA damage response.

Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil

Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations.