Molecular basis of DNA photodimerization: intrinsic production of cyclobutane cytosine dimers

Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs

The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.

Endogenous Photosensitizers in Human Skin

Endogenous photosensitizers play a critical role in both beneficial and harmful light-induced transformations in biological systems. Understanding their mode of action is essential for advancing fields such as photomedicine, photoredox catalysis, environmental science, and the development of sun care products. This review offers a comprehensive analysis of endogenous photosensitizers in human skin, investigating the connections between their electronic excitation and the subsequent activation or damage of organic biomolecules. We gather the physicochemical and photochemical properties of key endogenous photosensitizers and examine the relationships between their chemical reactivity, location within the skin, and the primary biochemical events following solar radiation exposure, along with their influence on skin physiology and pathology. An important take-home message of this review is that photosensitization allows visible light and UV-A radiation to have large effects on skin. The analysis presented here unveils potential causes for the continuous increase in global skin cancer cases and emphasizes the limitations of current sun protection approaches.

Chemiexcitation: Mammalian Photochemistry in the Dark†

Light is one way to excite an electron in biology. Another is chemiexcitation, birthing a reaction product in an electronically excited state rather than exciting from the ground state. Chemiexcited molecules, as in bioluminescence, can release more energy than ATP. Excited states also allow bond rearrangements forbidden in ground states. Molecules with low-lying unoccupied orbitals, abundant in biology, are particularly susceptible. In mammals, chemiexcitation was discovered to transfer energy from excited melanin, neurotransmitters, or hormones to DNA, creating the lethal and carcinogenic cyclobutane pyrimidine dimer. That process was initiated by nitric oxide and superoxide, radicals triggered by ultraviolet light or inflammation. Several poorly understood chronic diseases share two properties: inflammation generates those radicals across the tissue, and cells that die are those containing melanin or neuromelanin. Chemiexcitation may therefore be a pathogenic event in noise- and drug-induced deafness, Parkinson's disease, and Alzheimer's; it may prevent macular degeneration early in life but turn pathogenic later. Beneficial evolutionary selection for excitable biomolecules may thus have conferred an Achilles heel. This review of recent findings on chemiexcitation in mammalian cells also describes the underlying physics, biochemistry, and potential pathogenesis, with the goal of making this interdisciplinary phenomenon accessible to researchers within each field.

Photoreactive Cytosine-Functionalized Self-Assembled Micelles with Enhanced Cellular Uptake Capability for Efficient Cancer Chemotherapy

Design, fabrication, and control of photoreactive supramolecular macromers─which are composed of a thermoresponsive polymer backbone and photoreactive nucleobase end-groups─to achieve the desired physical-chemical performance and provide the high efficiency required for chemotherapy drug delivery purposes still present challenges. Herein, a difunctional cytosine-terminated supramolecular macromer was successfully obtained at high yield. UV-irradiation induces the formation of cytosine photodimers within the structure. The irradiated macromer can self-assemble into nanosized spherical micelles in water that possess a number of interesting and unique features, such as desired micellar size and morphology, tunable drug-loading capacity, and excellent structural stability in serum-containing medium, in addition to well-controlled drug-release behaviors in response to changes in environmental temperature and pH; these extremely desirable, rare features are required to augment the functions of polymeric nanocarriers for drug delivery. Importantly, a series of in vitro studies demonstrated that photodimerized cytosine moieties within the drug-loaded micelles substantially enhance their internalization and accumulation inside cells via endocytosis and subsequently lead to induction of massive apoptotic cell death compared with the corresponding nonirradiated micelles. Thus, this newly developed "photomodified" nanocarrier system could provide a potentially fruitful route to enhance the drug delivery performance of nanocages without the need to introduce targeting moieties or additional components.

Photoinduced phenomena in water solution of melamine explaining the photostability of the compound

Two tautomers of melamine (triamino and imino-diamino) were studied at the BLYP/aug-cc-pVDZ theoretical level. It was found that the two tautomers are bridged with the ¹πσ^* excited-state reaction path. The high photostability of melamine in water solution was explained with the mechanism of ring deformation which occurs along the ¹ππ^* excited-state reaction path. The two mechanisms are investigated at the TD BLYP level of theory using the linear interpolation in internal coordinates approach.

Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.

Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics*

Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.

On the Intrinsically Low Quantum Yields of Pyrimidine DNA Photodamages: Evaluating the Reactivity of the Corresponding Minimum Energy Crossing Points

The low quantum yield of photoformation of cyclobutane pyrimidine dimers and pyrimidine-pyrimidone (6-4) adducts in DNA bases is usually associated with the presence of more favorable nonreactive decay paths and with the unlikeliness of exciting the system in a favorable conformation. Here, we prove that the ability of the reactive conical intersection to bring the system either back to the absorbing conformation or to the photoproduct must be considered as a fundamental factor in the low quantum yields of the mentioned photodamage. In support of the proposed model, the one order of magnitude difference in the quantum yield of formation of the cyclobutane thymine dimer with respect to the thymine-thymine (6-4) adduct is rationalized here by comparing the reactive ability of the seam of intersections leading respectively to the cyclobutane thymine dimer and the oxetane precursor of the thymine-thymine (6-4) adduct at the CASPT2 level of theory.

Experimental and theoretical studies on thymine photodimerization mediated by oxidatively generated DNA lesions and epigenetic intermediates

Combined spectroscopic and computational studies reveal that, in spite of their structural similarities, 5-formyluracil and 5-formylcytosine photosensitize cyclobutane thymine dimers through two different types of mechanisms.

Ionic Liquid-Based Ultrasonic-Assisted Extraction to Analyze Seven Compounds in Psoralea Fructus Coupled with HPLC

Psoralea Fructus is widely used in traditional Chinese medicine (TCM), and the content of psoralen, isopsoralen, neobavaisoflavone, bavachin, psoralidin, isobavachalcone, and bavachinin A is the main quality control index of Psoralea Fructus because of its clinical effects. Thus, a fast and environmentally-benign extraction method of seven compounds in Psoralea Fructus is necessary. In this work, an ionic liquid-based ultrasonic-assisted method (ILUAE) for the extraction of seven compounds from Psoralea Fructus was proposed. Several ILs of different types and parameters, including the concentration of ILs, concentration of ethanol (EtOH), solid–liquid ratio, particle size, ultrasonic time, centrifugal speed, and ultrasonic power, were optimized by the Placket–Burman (PB) design and Box–Behnken response surface analysis. Under this optimal condition, the total extraction yield of the seven compounds in Psoralea Fructus was 18.90 mg/g, and significantly greater than the conventional 75% EtOH solvent extraction.

Triplet photosensitization mechanism of thymine by an oxidized nucleobase: from a dimeric model to DNA environment

Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA. In the present contribution, we use theoretical methodologies to study the triplet photosensitization mechanism of thymine exerted by ForU in a model dimer and in DNA environment. The photochemical pathways in the former system are described combining the CASPT2 and TD-DFT methods, whereas molecular dynamics simulations and QM/MM calculations are employed for the DNA duplex. It is unambiguously shown that the 1n,π* state localised in ForU mediates the population of the triplet manifold, most likely the 3π,π* state centred in ForU, whereas the 3π,π* state localized in thymine can be populated via triplet-triplet energy transfer given the small energy barrier of <0.23 eV determined for this pathway.

The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6-4) dimer formation

Density functional theory calculations were carried out to investigate the formation mechanism of the thymine-thymine (6-4) dimer ((6-4)TT), which is one of the main DNA lesions induced by ultraviolet radiation and is closely related to skin cancers. The DNA backbone was found to have nonnegligible effects on the triplet reaction pathway, particularly the reaction steps involving substantial base rotations. The mechanism for the isomerization from (6-4)TT to its Dewar valence isomer (DewarTT) was also explored, confirming the necessity of absorbing a second photon. In addition, the solvation effects were examined and showed considerable influence on the potential energy surface. Graphical Abstract DFT calculations on the influence of DNA backbone on the mechanism of UV-induced thymine-thymine (6-4) dimer formation.

Sequence dependence on DNA photochemistry: a computational study of photodimerization pathways in TpdC and dCpT dinucleotides

The excited states involved in the main photodimerization paths in TpdC and dCpT are mapped by PCM/TD-M052X calculations, considering different dinucleotide conformers. As for TT steps, a cyclobutane pyrimidine dimer (CPD) is formed on the PES of the lowest energy exciton, delocalized over two stacked pyrimidines; 6-4 pyrimidine-pyrimidone (64-PP) adduct's formation involves instead a 5'-ter → 3'-ter charge transfer state. For dCpT, 64-PP dimerization occurs via a two-step reaction, which proceeds through an oxetane intermediate. For TpdC, instead, the final 64-PP product is obtained in a single step and it is as stable as the CPD photoproduct, explaining the relatively large yield of 64-PP found experimentally for TC steps in DNA.

Photochemical Formation of Cyclobutane Pyrimidine Dimers in DNA through Electron Transfer from a Flanking Base

Electron transfer (ET) to a pyrimidine base from external moieties is a common step involved in the quenching or repair of the cyclobutane pyrimidine dimer (CPD). In contrast, we present a pathway that is initiated by an ET from a flanking guanine base to a pyrimidine base, leading to the formation of a CPD. We studied a T5mCG sequence with a methylated cytosine and our results demonstrate that the pathway involves the formation of an exciplex and intersystem crossings. This pathway also provides an explanation for why the mutational hot spots are correlated with the methylated CpG sequences, which has been a significant issue in cancer research.

Novel adenine/thymine photodimerization channels mapped by PCM/TD-DFT calculations on dApT and TpdA dinucleotides

Despite the biological relevance of AT-rich DNA sequences, the excited state paths associated with the photochemical reactions involving adenine and thymine stacked pairs have never been characterized, and the structure of the most abundant photoproduct in DNA is unknown. PCM/TD-M052X calculations on dApT and TpdA unveil the paths leading to the main photoproduct in TpdA, provide new insights into the reasons why it is not formed in dApT and show the existence of a new photochemical path, which could produce the precursor of the most abundant genomic AT/TA photoproduct. Our calculations confirm that anti/anti conformers are photochemically active and show that the dynamical solvation effects could significantly modulate the reaction yields.

Photoinduced formation mechanism of the thymine–thymine (6–4) adduct in DNA; a QM(CASPT2//CASSCF):MM(AMBER) study

Out-of-plane puckering of the C_4′ atom forming a new CC bond seems essential for oxetane formation.

Substitution of the laser borane anti-B18H22 with pyridine: a structural and photophysical study of some unusually structured macropolyhedral boron hydrides

One-step derivatization of the laser borane, anti-B₁₈H₂₂, with pyridine gives three uniquely structured macropolyhedral boranes with interesting photophysical properties.

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.

How Does Thymine DNA Survive Ultrafast Dimerization Damage?

The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright S_CT(¹ππ*) state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency.

Investigation of the mechanisms of photo-induced formation of cyclobutane dimers of cytosine and 2,4-diaminopyrimidine

The mechanisms of the formation of cyclobutane dimers (CBD) of cytosine and 2,4-diaminopyrimidine were studied at the CC2 theoretical level and cc-pVDZ basis functions. Four orientations of the two monomers are explored: cys-syn, cis-anti, trans-syn, and trans-anti. The research revealed that in all cases the cyclobutane structures are formed along the (1)ππ* excited-state reaction paths of the stacked aggregates. We localized the S1/S0 conical intersections mediating those transformations. The results obtained agree well with the previously reported investigations on the cis-syn cyclodimer formations of other pyrimidines.

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.

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.

Two-photon-absorption DNA sensitization via solvated electron production: unraveling photochemical pathways by molecular modeling and simulation

Infrared optical properties and photochemistry of a potential therapeutic dye interacting with DNA: a multiscale computational approach.

Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization

We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (³BP) on thymine nucleobase and backbone sugar.

Singlet-Triplet States Interaction Regions in DNA/RNA Nucleobase Hypersurfaces

The present study provides new insight into the intrinsic mechanisms for the population of the triplet manifold in DNA nucleobases by determining, at the multiconfigurational CASSCF/CASPT2 level, the singlet-triplet states crossing regions and the main decay paths for their lowest singlet and triplet states after near-UV irradiation. The studied singlet-triplet interacting regions are accessible along the minimum energy path of the initially populated singlet bright (1)ππ* state. In particular, all five natural DNA/RNA nucleobases have, at the end of the main minimum energy path and near a conical intersection of the ground and (1)ππ* states, a low-energy, easily accessible, singlet-triplet crossing region directly connecting the lowest singlet and triplet ππ* excited states. Adenine, thymine, and uracil display additional higher-energy crossing regions related to the presence of low-lying singlet and a triplet nπ* state. These funnels are absent in guanine and cytosine, which have the bright (1)ππ* state lower in energy and less accessible nπ* states. Knowledge of the location and accessibility of these regions, in which the singlet-triplet interaction is related to large spin-orbit coupling elements, may help to understand experimental evidence such as the wavelength dependence measured for the triplet formation quantum yield in nucleobases and the prevalence of adenine and thymine components in the phosphorescence spectra of DNA.

Excitonic splittings in molecular dimers: why static ab initio calculations cannot match them

After decades of research on molecular excitons, only few molecular dimers are available on which exciton and vibronic coupling theories can be rigorously tested. In centrosymmetric H-bonded dimers consisting of identical (hetero)aromatic chromophores, the monomer electronic transition dipole moment vectors subtract or add, yielding S₀ → S₁ and S₀ → S₂ transitions that are symmetry-forbidden or -allowed, respectively. Symmetry breaking by ¹²C/¹³C or H/D isotopic substitution renders the forbidden transition weakly allowed. The excitonic coupling (Davydov splitting) can then be measured between the S₀ → S₁ and S₀ → S₂ vibrationless bands. We discuss the mass-specific excitonic spectra of five H-bonded dimers that are supersonically cooled to a few K and investigated using two-color resonant two-photon ionization spectroscopy. The excitonic splittings Δ_calc predicted by ab initio methods are 5-25 times larger than the experimental excitonic splittings Δ_exp. The purely electronic ab initio splittings need to be reduced ("quenched"), reflecting the coupling of the electronic transition to the optically active vibrations of the monomers. The so-called quenching factors Γ < 1 can be determined from experiment (Γ_exp) and/or calculation (Γ_calc). The vibronically quenched splittings Γ·Δ_calc are found to nicely reproduce the experimental exciton splittings.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

DNA photochemistry: geometrically unconstrained pyrimidine (6-4) pyrimidone photoproducts do photoisomerize

Structural features are of major importance for the formation of mutagenic photoproducts in DNA. It was recently reported that lack of constraints between two adjacent nucleosidic units prevents the conversion of pyrimidine (6-4) pyrimidone photoproducts into their Dewar valence isomers. We here report that this is not the case for the thymidine photoproducts which, although unconstrained, are quantitatively converted into photolysis products identified as Dewar valence isomers by mass spectrometry and NMR and infrared spectroscopies.

Formation of cyclobutane thymine dimers by tiaprofenic acid and its photoproducts: approach to the photosensitizer triplet state energy limit value

Tiaprofenic acid family photosensitizes cyclobutane thymine dimer formation allowing to approach the lower limit threshold of a photosensitizer triplet state energy to excite the triplet state of thymine in DNA.

Photodynamic behavior of electronic coupling in a N-methylformamide dimer

The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.

A DFT Study of the Photochemical Dimerization of Methyl 3-(2-Furyl)acrylate and Allyl Urocanate

A DFT study of the photochemical dimerization of methyl 3-(2-furyl)acrylate is reported. The photochemical reaction gave a mixture of two dimers with high regioselectivity and good stereoselectivity. Calculations showed that benzophenone was able to act as a photosensitizer of the reaction. This compound populated the first excited triplet state of the substrate. The frontier orbitals interaction between LSOMO of the triplet state and HOMO of the ground state accounted for the observed high regioselectivity. Furthermore, the energy of all the possible triplet biradicals has been calculated, showing that the precursor of the main product was the triplet biradical with the lowest energy. The coupling of the atomic coefficients on the radical centres in the biradical intermediates allowed to justify the observed products. The same behavior was observed in the case of the photochemical dimerization of an urocanate ester and in the dimerization of liquid methyl cinnamate.

Computational reference data for the photochemistry of cyclobutane pyrimidine dimers

The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.

Contribution of cytosine-containing cyclobutane dimers to DNA damage produced by photosensitized triplet-triplet energy transfer

Mutagenic cyclobutane pyrimidine dimers (CPDs) can be induced in DNA through either direct excitation or photosensitized triplet-triplet energy transfer (TTET). In the latter pathway, thymines are expected to receive the excitation energy from the photosensitizer and react with adjacent pyrimidines. By using state-of-the art analytical tools, we provide herein additional information on the formation of cytosine-containing CPDs. We thus determined the yield of all possible CPDs upon TTET in a series of natural DNAs with various base compositions. We show that the distribution of CPDs cannot be explained only by excitation of individual thymines. We propose that the mechanism for TTET involves at least dinucleotides as the minimal targets. The observation of the formation of cytosine-cytosine CPDs also suggests that additional pathways are involved in this photosensitized reaction.

Photoinduced processes in nucleic acids

Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.