Stabilization of Mixed Frenkel-Charge Transfer Excitons Extended Across Both Strands of Guanine-Cytosine DNA Duplexes

Comparison of the mechanisms of DNA damage following photoexcitation and chemiexcitation

In this review, we compare the mechanisms and consequences of electronic excitation of DNA via photon absorption or photosensitization, as well as by chemically induced generation of excited states. The absorption of UV radiation by DNA is known to produce cyclobutane pyrimidine dimers (CPDs) and thymine pyrimidone photoproducts. Photosensitizers are known to enable such transformations using UV-A and visible light by generating triplet species able to transfer energy to DNA. Conversely, chemiexcitation of DNA is a process related to the formation of high energy peroxides whose decomposition leads to triplet excited species. In practice, both photoexcitation and chemiexcitation produce reactive excited species able to promote some DNA nucleobases to their excited state. We discuss the effect of epigenetic methylation modifications of DNA and the role of endogenous and exogenous photosensitizers on the formation of DNA photoproducts via triplet-triplet energy transfer as well as oxidative DNA damages. The mechanisms of pathogenic pathway involving the generation of CPDs via chemiexcitation (namely dark CPDs, dCPDs) are discussed and compared with photoexcitation considering their spatiotemporal characteristics. Recognition of the multifaceted noxious effects of UV radiation opens new horizons for the development of effective electronically excited quenchers, thereby providing a crucial step toward mitigating DNA photodamage.

On the Use of the Intrinsic DNA Fluorescence for Monitoring Its Damage: A Contribution from Fundamental Studies

The assessment of DNA damage by means of appropriate fluorescent probes is widely spread. In the specific case of UV-induced damage, it has been suggested to use the emission of dimeric photoproducts as an internal indicator for the efficacy of spermicidal lamps. However, in the light of fundamental studies on the UV-induced processes, outlined in this review, this is not straightforward. It is by now well established that, in addition to photodimers formed via an electronic excited state, photoionization also takes place with comparable or higher quantum yields, depending on the irradiation wavelength. Among the multitude of final lesions, some have been fully characterized, but others remain unknown; some of them may emit, while others go undetected upon monitoring fluorescence, the result being strongly dependent on both the irradiation and the excitation wavelength. In contrast, the fluorescence of undamaged nucleobases associated with emission from ππ* states, localized or excitonic, appearing at wavelengths shorter than 330 nm is worthy of being explored to this end. Despite its low quantum yield, it is readily detected nowadays. Its intensity decreases due to the disappearance of the reacting nucleobases and the loss of exciton coherence provoked by the presence of lesions, independently of their type. Thus, it could potentially provide valuable information about the DNA damage induced, not only by UV radiation but also by other sanitizing or therapeutic agents.

The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes

During the past few years, several studies reported that a significant part of the intrinsic fluorescence of DNA duplexes decays with surprisingly long lifetimes (1-3 ns) at wavelengths shorter than the ππ* emission of their monomeric constituents. This high-energy nanosecond emission (HENE), hardly discernible in the steady-state fluorescence spectra of most duplexes, was investigated by time-correlated single-photon counting. The ubiquity of HENE contrasts with the paradigm that the longest-lived excited states correspond to low-energy excimers/exciplexes. Interestingly, the latter were found to decay faster than the HENE. So far, the excited states responsible for HENE remain elusive. In order to foster future studies for their characterization, this Perspective presents a critical summary of the experimental observations and the first theoretical approaches. Moreover, some new directions for further work are outlined. Finally, the obvious need for computations of the fluorescence anisotropy considering the dynamic conformational landscape of duplexes is stressed.

Fluorescence of Bimolecular Guanine Quadruplexes: From Femtoseconds to Nanoseconds

The paper deals with the fluorescence of guanine quadruplexes (G4) formed by association of two DNA strands d(GGGGTTTTGGGG) in the presence of K⁺ cations, noted as OXY/K⁺ in reference to the protozoon Oxytricha nova, whose telomere contains TTTTGGGG repeats. They were studied by steady-state and time-resolved techniques, time-correlated single photon counting, and fluorescence upconversion. The maximum of the OXY/K⁺ fluorescence spectrum is located at 334 nm, and the quantum yield is 5.8 × 10^-4. About 75% of the photons are emitted before 100 ps and stem from ππ* states, possibly with a small contribution of charge transfer. Time-resolved fluorescence anisotropy measurements indicate that ultrafast (<330 fs) excitation transfer, due to internal conversion among exciton states, is more efficient in OXY/K⁺ compared to previously studied G4 structures. This is attributed to the arrangement of the peripheral thymines in two diagonal loops with restricted mobility, facilitating the interaction among them and with guanines. Thymines should also be responsible for a weak intensity excimer/exciplex emission band, peaking at 445 nm. Finally, the longest living fluorescence component (∼2.1 ns) is observed at the blue side of the spectrum. So far, high-energy long-lived emitting states had been reported only for double-stranded structures but not for G4.

High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes

The publication deals with polymeric pA●pT and oligomeric A₂₀●T₂₀ DNA duplexes whose fluorescence is studied by time-correlated single photon counting. It is shown that their emission on the nanosecond timescale is largely dominated by high-energy components peaking at a wavelength shorter than 305 nm. Because of their anisotropy (0.02) and their sensitivity to base stacking, modulated by the duplex size and the ionic strength of the solution, these components are attributed to mixed ππ*/charge transfer excitons. As high-energy long-lived excited states may be responsible for photochemical reactions, their identification via theoretical studies is an important challenge.

Dual Time-Scale Proton Transfer and High-Energy, Long-Lived Excitons Unveiled by Broadband Ultrafast Time-Resolved Fluorescence in Adenine-Uracil RNA Duplexes

In contrast to the immense amount of research on electronically excited DNA, surprisingly little has been done about the excited states of RNA. Herein, we demonstrate an ultrafast broadband time-resolved fluorescence and fluorescence anisotropy study to probe directly the intrinsic fluorescence and overall dynamics of the fluorescence from a homopolymeric adenine·uracil RNA duplex adopting the A-form structure. The results unveiled complex deactivation through distinctive multichannels mediated by states of varied energy, a character of charge transfer, and a lifetime from sub-picosecond to nanoseconds. In particular, we observed an unprecedented kinetic isotopic effect and participation of unusual proton transfer from states in two discrete energies and time domains. We also identified a high-energy nanosecond emission that we attributed to its fluorescence anisotropy to long-lived weakly emissive excitons not reported in DNA. These distinguishing features originate from the stacking, pairing, and local hydration environment specific to the A-form conformation of the adenine·uracil double helix.

Assessing challenging intra- and inter-molecular charge-transfer excitations energies with double-hybrid density functionals

We investigate the performance of a set of recently introduced range-separated double-hybrid functionals, namely ωB2-PLYP, ωB2GP-PLYP, RSX-0DH, and RSX-QIDH models for hard-to-calculate excitation energies. We compare with the parent (B2-PLYP, B2GP-PLYP, PBE0-DH, and PBE-QIDH) and other (DSD-PBEP86) double-hybrid models as well as with some of the most widely employed hybrid functionals (B3LYP, PBE0, M06-2X, and ωB97X). For this purpose, we select a number of medium-sized intra- and inter-molecular charge-transfer excitations, which are known to be challenging to calculate using time-dependent density-functional theory (TD-DFT) and for which accurate reference values are available. We assess whether the high accuracy shown by the newest double-hybrid models is also confirmed for those cases too. We find that asymptotically corrected double-hybrid models yield a superior performance, especially for the inter-molecular charge-transfer excitation energies, as compared to standard double-hybrid models. Overall, the PBE-QIDH and its corresponding range-separated RSX-QIDH functional are recommended for general-purpose TD-DFT applications, depending on whether long-range effects are expected to play a significant role.

Fundamentals of the Intrinsic DNA Fluorescence

The intrinsic fluorescence of nucleic acids is extremely weak compared to that of the fluorescent labels used to probe their structural and functional behavior. Thus, for technical reasons, the investigation of the intrinsic DNA fluorescence was limited for a long time. But with the improvement in spectroscopic techniques, the situation started to change around the turn of the century. During the past two decades, various factors modulating the static and dynamic properties of the DNA fluorescence have been determined; it was shown that, under certain conditions, quantum yields may be up 100 times higher than what was known so far. The ensemble of these studies opened up new paths for the development of label-free DNA fluorescence for biochemical applications. In parallel, these studies have shed new light on the primary processes leading to photoreactions that damage DNA when it absorbs UV radiation.We have been studying a variety of DNA systems, ranging from the monomeric nucleobases to double-stranded and four-stranded structures using fluorescence spectroscopy. The specificity of our work resides in the quantitative association of the steady-state fluorescence spectra with time-resolved data recorded from the femtosecond to the nanosecond timescales, made possible by the development of specific methodologies.Among others, our fluorescence studies provide information on the energy and the polarization of electronic transitions. These are valuable indicators for the evolution of electronic excitations in complex systems, where the electronic coupling between chromophores plays a key role. Highlighting collective effects that originate from electronic interactions in DNA multimers is the objective of the present Account.In contrast to the monomeric chromophores, whose fluorescence decays within a few picoseconds, that of DNA multimers persists on the nanosecond timescale. Even if long-lived states represent only a small fraction of electronic excitations, they may be crucial to the DNA photoreactivity because the probability to reach reactive conformations increases over time, owing to the incessant structural dynamics of nucleic acids.Our femtosecond studies have revealed that an ultrafast excitation energy transfer takes place among the nucleobases within duplexes and G-quadruplexes. Such an ultrafast process is possible when collective states are populated directly upon photon absorption. At much longer times, we discovered an unexpected long-lived high-energy emission stemming from what was coined "HELM excitons". These collective states, whose emission increases with the duplex size, could be responsible for the delayed fluorescence of ππ* states observed for genomic DNA.Most studies dealing with excited-state relaxation in DNA were carried out with excitation in the absorption band peaking at around 260 nm. We went beyond this and also performed the first time-resolved study with excitation in the UVA spectral range, where a very weak absorption tail is present. The resulting fluorescence decays are much slower and the fluorescence quantum yields are much higher than for UVC excitation. We showed that the base pairing of DNA strands enhances the UVA fluorescence and, in parallel, increases the photoreactivity because it modifies the nature of the involved collective excited states.

The epigenetic DNA modification 5-carboxylcytosine promotes high levels of cyclobutane pyrimidine dimer formation upon UVB irradiation

In mammals, DNA methyltransferases create 5-methylcytosines (5mC) predominantly at CpG dinucleotides. 5mC oxidases convert 5mC in three consecutive oxidation steps to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and then 5-carboxylcytosine (5caC). Upon irradiation with UV light, dipyrimidines containing C, 5mC and 5hmC are known to form cyclobutane pyrimidine dimers (CPDs) as major DNA photolesions. However, the photobiology of 5fC and 5caC has remained largely unexplored. Here, we tested a series of oligonucleotides with single or multiple positions carrying cytosine (C), 5mC, 5hmC, 5fC or 5caC and irradiated them with different sources of UV irradiation. While UVC radiation produced CPDs near dipyrimidines containing all types of modified cytosine bases, UVB radiation produced by far the highest levels of CPDs near 5caC-containing sequences. Dipyrimidines one or two nucleotide positions adjacent to 5caC but not always those involving this modified base directly were the major sites for these prominent UVB photoproducts. This selectivity did not depend on whether 5caC was present on one or both DNA strands at CpG sequences. We also observed a tendency of the 5caC-containing DNA strands to undergo apparent covalent crosslinking. This reaction occurred with UVB or UVC but not with UVA irradiation. Our data show that 5-carboxylcytosine, although generally a rare base in the genome, can nonetheless make a strong contribution to sequence-specific DNA damage perhaps by acting as a DNA-intrinsic photosensitizer.

Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States

The design of more efficient photosensitizers is a matter of great importance in the field of cancer treatment by means of photodynamic therapy. One of the main processes involved in the activation of apoptosis in cancer cells is the oxidative stress on DNA once a photosensitizer is excited by light. As a consequence, it is very relevant to investigate in detail the binding modes of the chromophore with DNA, and the nature of the electronically excited states that participate in the induction of DNA damage, for example, charge-transfer states. In this work, we investigate the electronic structure of the anthraquinone photosensitizer intercalated into a double-stranded poly(dG-dC) decamer model of DNA. First, the different geometric configurations are analyzed by means of classical molecular dynamics simulations. Then, the excited states for the most relevant poses of anthraquinone inside the binding pocket are computed by an electrostatic-embedding quantum mechanics/molecular mechanics approach, where anthraquinone and one of the nearby guanine residues are described quantum mechanically to take into account intermolecular charge-transfer states. The excited states are characterized as monomer, exciton, excimer, and charge-transfer states based on the analysis of the transition density matrix, and each of these contributions to the total density of states and absorption spectrum is discussed in terms of the stacking interactions. These results are relevant as they represent the footing for future studies on the reactivity of anthraquinone derivatives with DNA and give insights on possible geometrical configurations that potentially favor the oxidative stress of DNA.

DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets

The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.

Electronic spectroscopy of isolated DNA polyanions

We address whether action spectroscopy could be used to investigate structural changes in gas-phase biomolecule (e.g. nucleic acid) ions, owing to changes in the environments of their chromophores, while taking advantage of the additional spectrometric separation of complex mixtures.

Formation of UV-induced DNA damage contributing to skin cancer development

UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto-oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280-320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (64PPs). Less energetic but 20-times more intense UVA (320-400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8-oxo-7,8-dihydroguanine (8-oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8-oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV-induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.

Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation

Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.

Evolution of the Excitonic State of DNA Stacked Thymines: Intrabase ππ* → S0 Decay Paths Account for Ultrafast (Subpicosecond) and Longer (>100 ps) Deactivations

Monomer-like ring puckering decay paths for two stacked quantum mechanical thymines inside a solvated DNA duplex described at the molecular mechanics level are mapped using a hybrid CASPT2//CASSCF/MM protocol that accounts for steric, electronic and electrostatic interactions within the nucleobases native environment. Asymmetric stacking between nucleobases open ups different intrabase ππ* decay paths accounting for distinctive excited state lifetimes, spanning the subps to subns time window.

DNA as UV light-harvesting antenna

The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.

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.

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.

Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.

The spectral properties of DNA and RNA macromolecules at low temperatures: fundamental and applied aspects

This paper summarizes the results of studies of the spectral properties-optical absorption, fluorescence and phosphorescence-of DNA and RNA macromolecules and synthetic poly-, oligo- and mono-nucleotides, which have been carried out in our laboratory. The system of first excited singlet and triplet energy levels for DNA and RNA is evaluated using low-temperature (4.2 K-77 K) luminescent measurements. The traps of the singlet and triplet electronic excitations in these compounds are identified. An important self-protection mechanism against photo-damage of DNA and RNA by UV photons or penetrative radiation based on the capture of triplet electronic-energy excitations by the most photostable centers-in DNA, the complex formed by neighboring adenosine (A) and thymidine (T) links; in RNA, the adenosine links-is described. It is confirmed that despite similarities in the chemical and partly energy structures DNA is more stable than RNA. The spectral manifestation of the telomeres (the important functional system) in DNA macromolecules is examined. The results obtained on telomere fragments provide the possibility of finding the configuration peculiarities of the triplet excitations traps in DNA macromolecules. The resulting spreading length of the migrating singlet (l _s) and triplet (l _t) excitations for DNA and RNA macromolecules are evaluated.

Onset of the Electronic Absorption Spectra of Isolated and π-Stacked Oligomers of 5,6-Dihydroxyindole: An Ab Initio Study of the Building Blocks of Eumelanin

Eumelanin is a naturally occurring skin pigment which is responsible for developing a suntan. The complex structure of eumelanin consists of π-stacked oligomers of various indole derivatives, such as the monomeric building block 5,6-dihydroxyindole (DHI). In this work, we present an ab initio wave-function study of the absorption behavior of DHI oligomers and of doubly and triply π-stacked species of these oligomers. We have simulated the onset of the electronic absorption spectra by employing the MP2 and the linear-response CC2 methods. Our results demonstrate the effect of an increasing degree of oligomerization of DHI and of an increasing degree of π-stacking of DHI oligomers on the onset of the absorption spectra and on the degree of red-shift toward the visible region of the spectrum. We find that π-stacking of DHI and its oligomers substantially red-shifts the onset of the absorption spectra. Our results also suggest that the optical properties of biological eumelanin cannot be simulated by considering the DHI building blocks alone, but instead the building blocks indole-semiquinone and indole-quinone have to be considered as well. This study contributes to advancing the understanding of the complex photophysics of the eumelanin biopolymer.

Excited-State Dynamics of DNA Duplexes with Different H-Bonding Motifs

The excited-state dynamics of three distinct forms of the d(GC)9·d(GC)9 DNA duplex were studied by combined time-resolved infrared experiments and quantum mechanical calculations. In the B- and Z-forms, bases on opposite strands form Watson-Crick (WC) base pairs but stack differently because of salt-induced changes in backbone conformation. At low pH, the two strands associate by Hoogsteen (HG) base pairing. Ultraviolet-induced intrastrand electron transfer (ET) triggers interstrand proton transfer (PT) in the B- and Z-forms, but the PT pathway is blocked in the HG duplex. Despite the different decay mechanisms, a common excited-state lifetime of ∼ 30 ps is observed in all three duplex forms. The ET-PT pathway in the WC duplexes and the solely intrastrand ET pathway in the HG duplex yield the same pair of π-stacked radicals on one strand. Back ET between these radicals is proposed to be the rate-limiting step behind excited-state deactivation in all three duplexes.

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-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.