Mechanism of UV-induced formation of Dewar lesions in DNA

Visible-Light-Mediated [2+2] Photocycloadditions of Alkynes

Visible-light-mediated [2+2] photocycloaddition reaction can be considered an ideal solution due to its green and sustainable properties, and is one of the most efficient methods to synthesize four-membered ring motifs. Although research on the [2+2] photocycloaddition of alkynes is challenging because of the diminished reactivity of alkynes, and the more significant ring strain of the products, remarkable achievements have been made in this field. In this article, we highlight the recent advances in visible-light-mediated [2+2] photocycloaddition reactions of alkynes, with focus on the reaction mechanism and the late-stage synthetic applications. Advances in obtaining cyclobutenes, azetines, and oxetene active intermediates continue to be breakthroughs in this fascinating field of research.

From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions

This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.

New strategies for the synthesis of 1- and 2-azetines and their applications as value-added building blocks

Four-membered nitrogen-containing heterocycles are highly desirable functional groups with synthetic and biological applications. Unsaturated four-membered N-heterocycles, 1- and 2-azetines, are historically underexplored, but have recently been gaining interest due to the development of new synthetic methods to access these compounds, and to their potential as reactive intermediates. This review covers both the synthesis and applications of azetines, with a focus on synthetic methods to access azetines developed since 2018, and a comprehensive review of the reactivity and applications of azetines as starting materials or intermediates to access both other heterocycles and complex products.

Tracking excited state decay mechanisms of pyrimidine nucleosides in real time

DNA owes its remarkable photostability to its building blocks-the nucleosides-that efficiently dissipate the energy acquired upon ultraviolet light absorption. The mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy experiments with broad spectral coverage and state-of-the-art mixed quantum-classical dynamics with spectral signal simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. We track the wave packet motion from the Franck-Condon region to the conical intersections (CIs) with the ground state and observe spectral signatures of excited-state vibrational modes. 5mUrd exhibits an order of magnitude longer lifetime with respect to Urd due to the solvent reorganization needed to facilitate bulky methyl group motions leading to the CI. This activates potentially lesion-inducing dynamics such as ring opening. Involvement of the 1nπ* state is found to be negligible.

Prebiotic photoredox synthesis from carbon dioxide and sulfite

Carbon dioxide (CO2) is the major carbonaceous component of many planetary atmospheres, which includes the Earth throughout its history. Carbon fixation chemistry-which reduces CO2 to organics, utilizing hydrogen as the stoichiometric reductant-usually requires high pressures and temperatures, and the yields of products of potential use to nascent biology are low. Here we demonstrate an efficient ultraviolet photoredox chemistry between CO2 and sulfite that generates organics and sulfate. The chemistry is initiated by electron photodetachment from sulfite to give sulfite radicals and hydrated electrons, which reduce CO2 to its radical anion. A network of reactions that generates citrate, malate, succinate and tartrate by irradiation of glycolate in the presence of sulfite was also revealed. The simplicity of this carboxysulfitic chemistry and the widespread occurrence and abundance of its feedstocks suggest that it could have readily taken place on the surfaces of rocky planets. The availability of the carboxylate products on early Earth could have driven the development of central carbon metabolism before the advent of biological CO2 fixation.

1- and 2-Azetines via Visible Light-Mediated [2 + 2]-Cycloadditions of Alkynes and Oximes

Azetines, four-membered unsaturated nitrogen-containing heterocycles, hold great potential for drug design and development but remain underexplored due to challenges associated with their synthesis. We report an efficient, visible light-mediated approach toward 1- and 2-azetines relying on alkynes and the unique triplet state reactivity of oximes, specifically 2-isoxazolines. While 2-azetine products are accessible upon intermolecular [2 + 2]-cycloaddition via triplet energy transfer from a commercially available iridium photocatalyst, the selective formation of 1-azetines proceeds upon a second, consecutive, energy transfer process. Mechanistic studies are consistent with a stepwise reaction mechanism via N-O bond homolysis following the second energy transfer event to result in the formation of 1-azetine products. Characteristic for this method is its operational simplicity, mild conditions, and modular approach that allow for the synthesis of functionalized azetines and tetrahydrofurans (via in situ hydrolysis) from readily available precursors.

Remote Photodamaging of DNA by Photoinduced Energy Transport

Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.

Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of Drosophila melanogaster

While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of Drosophila melanogaster (D. melanogaster). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH^- cofactor that facilitates reduction of the photoproduct. Microscopic details of the collective reaction coordinate of ET reactions are identified that involve the reorganization of the hydrogen bond network and structural relaxation of the active site. The simulations reveal complex active site relaxation dynamics involving distinguished amino acids (Lys246, His365, and His369), conformational reorganization of the hydroxyl group of the (6-4) photoproduct, and a strengthening of hydrogen bonds with immobilized water molecules. In particular, rotation of the Lys246 side chain is found to impose a double-well character along the reaction coordinate of the ET reaction. Our findings suggest that the primary ET reactions in the (6-4) photoproduct enzyme repair complex of D. melanogaster are governed by a complex multi-minima active site relaxation dynamics and potentially precede the equilibration of the protein. ET pathways mediated by the adenine moiety and the 5' side of the photoproduct are proposed to be relevant for triggering the catalytic (6-4) photoproduct reactivation.

Uncommon Four-Membered Building Blocks - Cyclobutenes, Azetines and Thietes

Strained ring systems have gained considerable importance over the last few years for their implication in natural product syntheses or in drug discovery programs. We present herein a recollection of our work on the construction and functionalization of unsaturated four-membered carbo- and heterocycles in the context of the literature, as well as their applications in further reactions.

All You Need Is Light. Photorepair of UV-Induced Pyrimidine Dimers

Although solar light is indispensable for the functioning of plants, this environmental factor may also cause damage to living cells. Apart from the visible range, including wavelengths used in photosynthesis, the ultraviolet (UV) light present in solar irradiation reaches the Earth's surface. The high energy of UV causes damage to many cellular components, with DNA as one of the targets. Putting together the puzzle-like elements responsible for the repair of UV-induced DNA damage is of special importance in understanding how plants ensure the stability of their genomes between generations. In this review, we have presented the information on DNA damage produced under UV with a special focus on the pyrimidine dimers formed between the neighboring pyrimidines in a DNA strand. These dimers are highly mutagenic and cytotoxic, thus their repair is essential for the maintenance of suitable genetic information. In prokaryotic and eukaryotic cells, with the exception of placental mammals, this is achieved by means of highly efficient photorepair, dependent on blue/UVA light, which is performed by specialized enzymes known as photolyases. Photolyase properties, as well as their structure, specificity and action mechanism, have been briefly discussed in this paper. Additionally, the main gaps in our knowledge on the functioning of light repair in plant organelles, its regulation and its interaction between different DNA repair systems in plants have been highlighted.

Formation and Recognition of UV-Induced DNA Damage within Genome Complexity

Ultraviolet (UV) light is a natural genotoxic agent leading to the formation of photolesions endangering the genomic integrity and thereby the survival of living organisms. To prevent the mutagenetic effect of UV, several specific DNA repair mechanisms are mobilized to accurately maintain genome integrity at photodamaged sites within the complexity of genome structures. However, a fundamental gap remains to be filled in the identification and characterization of factors at the nexus of UV-induced DNA damage, DNA repair, and epigenetics. This review brings together the impact of the epigenomic context on the susceptibility of genomic regions to form photodamage and focuses on the mechanisms of photolesions recognition through the different DNA repair pathways.

UV-Induced Charge-Transfer States in Short Guanosine-Containing DNA Oligonucleotides

Charge transfer has proven to be an important mechanism in DNA photochemistry. In particular, guanine (dG) plays a major role as an electron donor, but the photophysical dynamics of dG-containing charge-transfer states have not been extensively investigated so far. Here, we use UV pump (266 nm) and picosecond IR probe (∼5-7 μm) spectroscopy to study ultrafast dynamics in dG-containing short oligonucleotides as a function of sequence and length. For the pure purine oligomers, we observed lifetimes for the charge-transfer states of the order of several hundreds of picoseconds, regardless of the oligonucleotide length. In contrast, pyrimidine-containing dinucleotides d(GT) and d(GC) show much faster relaxation dynamics in the 10 to 30 ps range. In all studied nucleotides, the charge-transfer states are formed with an efficiency of the order of ∼50 %. These photophysical characteristics will lead to an improved understanding of DNA damage and repair processes.

Detection of the thietane precursor in the UVA formation of the DNA 6-4 photoadduct

Notwithstanding the central biological role of the (6-4) photoadduct in the induction of skin cancer by sunlight, crucial mechanistic details about its formation have evaded characterization despite efforts spanning more than half a century. 4-Thiothymidine (4tT) has been widely used as an important model system to study its mechanism of formation, but the excited-state precursor, the intermediate species, and the time scale leading to the formation of the (6-4) photoadduct have remained elusive. Herein, steady-state and time-resolved spectroscopic techniques are combined with new and reported quantum-chemical calculations to demonstrate the excited state leading to the formation of the thietane intermediate, its rate, and the formation of the (6-4) photoadduct using the 5’-TT(4tT)T(4tT)TT-3’ DNA oligonucleotide. Efficient, sub-1 ps intersystem crossing leads to the population of a triplet minimum of the thietane intermediate in as short as 3 ps, which intersystem crosses to its ground state and rearranges to form the (6-4) photoadduct.

The mechanisms of formation of the (6-4) photoproducts in DNA damage by sunlight is still debated. Here the authors show, by optical spectroscopies and computations, the details of the formation of a (6-4) photoadduct via the thietane intermediate in a single-stranded DNA oligonucleotide.

Investigation of the Electrooxidation of Thymine on Screen-Printed Carbon Electrodes by Hyphenation of Electrochemistry and Mass Spectrometry

The electrooxidation of thymine on screen-printed carbon electrodes was investigated utilizing different complementary instrumental approaches. The potential-dependent product profile was obtained by recording real-time mass voltammograms. Electrochemical flow cells with integrated disposable electrodes were directly coupled with mass spectrometry to facilitate a very fast detection of electrogenerated species. Thymine dimers were found at a potential of about 1.1 V in ammonium acetate (pH 7.0) and 1.25 V in ammonium hydrogen carbonate electrolyte (pH 8.0). Electrochemistry-capillary electrophoresis-mass spectrometry measurements revealed that two isobaric isomers of a dimeric oxidation product were formed. Separations at different time intervals between end of oxidation and start of separation showed that these were hydrated over time. An investigation of the pK_a values by changing the separation conditions in electrochemistry-capillary electrophoresis-ultraviolet-visible spectroscopy measurements allowed for further characterization of the primary oxidation products. The results showed that both isomers exhibited two deprotonation steps. The oxidation products were further characterized by high-performance liquid chromatography-tandem mass spectrometry. Based on the obtained data, the main oxidation products of thymine in aqueous solution could most likely be identified as N(1)-C(5') and N(1)-C(6') linked dimer species evolving into the corresponding dimer hydrates over time. The presented methods for online characterization of electrochemically pretreated samples showed that not only mass spectrometric data can be obtained by electrochemistry-mass spectrometry but also further characterizations such as the investigation of product stability and the pH-dependent protonation or deprotonation behavior are possible. This is valid not only for stable oxidation products but also for intermediates, as analysis can be carried out within a short time scale. Thus, a vast amount of valuable experimental data can be acquired, which can help in understanding electrooxidation processes.

Wavelength- and Tissue-dependent Variations in the Mutagenicity of Cyclobutane Pyrimidine Dimers in Mouse Skin

The cyclobutane pyrimidine dimer (CPD) is a main mutagenic photolesion in DNA produced by UVR. We previously studied the wavelength-dependent kinetics of mutation induction efficiency using monochromatic UVR sources and transgenic mice developed for mutation assay and established the action spectra of UVR mutagenicity in the mouse epidermis and dermis. Here, we further established the action spectra of CPD and pyrimidine(6-4)pyrimidone photoproduct formation in the same tissues and in naked DNA using the same sources and mouse strain. Quantitative ELISA helped us estimate the photolesion formation efficiencies on a molecule-per-nucleotide basis. Using these action spectra, we confirmed that the UVR mutation mostly depends on CPD formation. Moreover, the mutagenicity of a CPD molecule (CPD mutagenicity) was found to vary by wavelength, peaking at approximately 313 nm in both the epidermis and dermis with similar wavelength-dependent patterns. Thus, the CPD formation efficiency is a main determinant of UVR mutagenicity in mouse skin, whereas a wavelength-dependent variation in the qualitative characteristics of CPD molecules also affects the mutagenic consequences of UVR insults. In addition, the CPD mutagenicity was always higher in the epidermis than in the dermis, suggesting different cellular responses to UVR between the two tissues irrespective of the wavelength.

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.

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.

Decay Pathways of Thymine Revisited

The decay of electronically excited states of thymine (Thy) and thymidine 5'-monophosphate (TMP) was studied by time-resolved UV/vis and IR spectroscopy. In addition to the well-established ultrafast internal conversion to the ground state, a so far unidentified UV-induced species is observed. In D₂O, this species decays with a time constant of 300 ps for thymine and of 1 ns for TMP. The species coexists with the lowest triplet state and is formed with a comparably high quantum yield of about 10% independent of the solvent. The experimentally determined spectral signatures are discussed in the light of quantum chemical calculations of the singlet and triplet excited states of thymine.

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions

Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors repairing CpDs, the intrinsic self-repairing capabilities of the GAT 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order [ADC(2)] method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the T 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T dimer. Consequently, the molecular mechanism of GAT 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S₁ potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S₁/S₀ state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.

Relative Contributions of UVB and UVA to the Photoconversion of (6-4) Photoproducts into their Dewar Valence Isomers

Dewar valence isomers are photoisomerization products of pyrimidine (6-4) pyrimidone photoproducts, a major class of UV-induced DNA lesions, which exhibits a maximal absorption around 320 nm. However, Dewar isomers are not produced in significant amounts in cells exposed to biologically relevant doses of UVB. In contrast, they are readily produced when cells are exposed to a combination of UVA and UVB. The present computational work demonstrates that, on the basis of known absorption properties and formation quantum yields, the difference in Dewar formation between the two types of radiation can be explained by the role of normal bases. In the UVB range, at the low level of (6-4) photoproducts present in cells exposed to realistic doses, normal bases are present in overwhelming amounts and absorb the vast majority of the incident photons. In contrast, the absorption of DNA bases is much weaker in the UVA range while that of (6-4) photoproducts is still significant, making photoisomerization possible. This two-photon process makes it difficult to define an action spectrum for the formation of Dewar isomers.

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.

Insight in DNA Repair of UV-induced Pyrimidine Dimers by Chromatographic Methods

UV-induced formation of pyrimidine dimers in DNA is a major deleterious event in both eukaryotic and prokaryotic cells. Accumulation of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts can lead to cell death or be at the origin of mutations. In skin, UV induction of DNA damage is a major initiating event in tumorigenesis. To counteract these deleterious effects, all cell types possess DNA repair machinery, such as nucleotide excision repair and, in some cell types, direct reversion. Different analytical approaches were used to assess the efficiency of repair and decipher the enzymatic mechanisms. We presently review the information provided by chromatographic methods, which are complementary to biochemical assays, such as immunological detection and electrophoresis-based techniques. Chromatographic assays are interesting in their ability to provide quantitative data on a wide range of damage and are also valuable tools for the identification of repair intermediates.

The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic Reagents - A Route to Thymidine (6-4) Photoproduct Analogues

This report describes an efficient procedure for the generation and isolation of various thymine and thymidine 5,6-epoxides from the corresponding trans-5,6-bromohydrins by reaction with triethylamine. The quantitative isolation of the epoxides, accomplished by solvent precipitation of triethylamine hydrobromide, enabled their regiospecific ring-opening at C6 position by organometallic nucleophiles. The reaction was amenable to a broad range of alkyl, aryl, alkenyl, and alkynyl organomagnesium, -zinc, -aluminum, or -boron reagents, although the reactivity was strongly affected by the electronic effects of N3 protecting group. Additionally, the reaction featured excellent cis-diastereoselectivity providing access to C6-carbon-functionalized dihydrothymidine cis-alcohols, which are synthetic derivatives of UV-induced DNA lesions, namely, thymidine (6-4) photoproducts.

Monitoring conical intersections in the ring opening of furan by attosecond stimulated X-ray Raman spectroscopy

Attosecond X-ray pulses are short enough to capture snapshots of molecules undergoing nonadiabatic electron and nuclear dynamics at conical intersections (CoIns). We show that a stimulated Raman probe induced by a combination of an attosecond and a femtosecond pulse has a unique temporal and spectral resolution for probing the nonadiabatic dynamics and detecting the ultrafast (∼4.5 fs) passage through a CoIn. This is demonstrated by a multiconfigurational self-consistent-field study of the dynamics and spectroscopy of the furan ring-opening reaction. Trajectories generated by surface hopping simulations were used to predict Attosecond Stimulated X-ray Raman Spectroscopy signals at reactant and product structures as well as representative snapshots along the conical intersection seam. The signals are highly sensitive to the changes in nonadiabatically coupled electronic structure and geometry.

Dewar valence isomers, the third type of environmentally relevant DNA photoproducts induced by solar radiation

UV-induced DNA damage is the main initiating event in solar carcinogenesis. UV radiation is known to induce pyrimidine dimers in DNA, including cyclobutane dimers and (6-4) photoproducts which have been extensively studied. In contrast, much less attention has been paid to Dewar valence isomers, the photoisomerisation product of (6-4) photoproducts. Yet, the available data show that Dewar isomers can be produced by exposure to sunlight and may lead to mutations. Dewars are thus environmentally and biologically relevant. The present review summarizes currently available information on the formation, mutagenic properties and repair of this class of UV-induced DNA damage.

Pyrimidinone: versatile Trojan horse in DNA photodamage?

(6-4) Photolesions between adjacent pyrimidine DNA bases are prone to secondary photochemistry. It has been shown that singlet excited (6-4) moieties form Dewar valence isomers as well as triplet excitations. We here report on the triplet state of a minimal model for the (6-4) photolesion, 1-methyl-2(1H)-pyrimidinone. Emphasis is laid on its ability to abstract hydrogen atoms from alcohols and carbohydrates. Steady-state and time-resolved experiments consistently yield bimolecular rate constants of ∼10(4) M(-1) s(-1) for the hydrogen abstraction. The process also occurs intramolecularly as experiments on zebularine (1-(β-d-ribofuranosyl)-2(1H)-pyrimidinone) show.

Solar UV radiation-induced DNA Bipyrimidine photoproducts: formation and mechanistic insights

This review chapter presents a critical survey of the main available information on the UVB and UVA bipyrimidine photoproducts which constitute the predominant recipient classes of photo-induced DNA damage. Evidence is provided that UVB irradiation of isolated DNA in aqueous solutions and in cells gives rise to the predominant generation of cis-syn cyclobutane pyrimidine dimers (CPDs) and, to a lesser extent, of pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), the importance of which is strongly primary sequence dependent. A notable change in the photoproduct distribution is observed when DNA either in the dry or in desiccated microorganisms is exposed to UVC or UVB photons with an overwhelming formation of 5-(α-thymidyl)-5,6-dihydrothymidine, also called spore photoproduct (dSP), at the expense of CPDs and 6-4PPs. UVA irradiation of isolated and cellular DNA gives rise predominantly to bipyrimidine photoproducts with the overwhelming formation of thymine-containing cyclobutane pyrimidine dimers at the exclusion of 6-4PPs. UVA photons have been shown to modulate the distribution of UVB dimeric pyrimidine photoproducts by triggering isomerization of the 6-4PPs into related Dewar valence isomers. Mechanistic aspects of the formation of bipyrimidine photoproducts are discussed in the light of recent photophysical and theoretical studies.

Early events of DNA photodamage

Ultraviolet (UV) radiation is a leading external hazard to the integrity of DNA. Exposure to UV radiation triggers a cascade of chemical reactions, and many molecular products (photolesions) have been isolated that are potentially dangerous for the cellular system. The early steps that take place after UV absorption by DNA have been studied by ultrafast spectroscopy. The review focuses on the evolution of excited electronic states, the formation of photolesions, and processes suppressing their formation. Emphasis is placed on lesions involving two thymine bases, such as the cyclobutane pyrimidine dimer, the (6-4) lesion, and its Dewar valence isomer.

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2'-deoxycytidine

Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebiotically plausible conditions. In this contribution, we present UV-irradiation experiments of β-2'-deoxycytidine in aqueous solution involving H-D exchange followed by NMR spectroscopic analysis of the photoproducts. We further elucidate the outcome of these experiments by means of high-level quantum chemical calculations. In particular, we show that prolonged UV-irradiation of cytidine may lead to H-C1' hydrogen atom abstraction by the carbonyl oxygen atom of cytosine. This process may enable photoanomerisation and nucleobase loss, two previously unexplained photoreactions observed in pyrimidine nucleotides.

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.

Identification of charge separated states in thymine single strands

UV excitation of the DNA single strand (dT)18 leads to electronically excited states that are potential gateways to DNA photolesions. Using time-resolved infrared spectroscopy we characterized a species with a lifetime of ∼100 ps and identified it as a charge separated excited state between two thymine bases.

The significance of the Dewar valence photoisomer as a UV radiation-induced DNA photoproduct in marine microbial communities

Induction of pyrimidine dimers in DNA by solar UV radiation has drastic effects on microorganisms. To better define the nature of these DNA photoproducts in marine bacterioplankton and eukaryotes, a study was performed during a cruise along a latitudinal transect in the Pacific Ocean. The frequency of all possible cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts (64PPs) and their related Dewar valence isomers (DEWs) was determined by high-performance liquid chromatography-mass spectrometry. Studied samples were bacterioplankton and eukaryotic fractions isolated from sea water either collected before sunrise or exposed to ambient sunlight from sunrise to sunset. Isolated DNA dosimeters were also exposed to daily sunlight for comparison purposes. A first major result was the observation in all samples of large amounts of DEWs, a class of photoproducts rarely considered outside photochemical studies. Evidence was obtained for a major role of UVA in the formation of these photoisomerization products of 64PPs. Considerations on the ratio between the different classes of photoproducts in basal and induced DNA damage suggests that photoenzymatic repair (PER) is an important DNA repair mechanism used by marine microorganisms occupying surface seawater in the open ocean. This result emphasizes the biological role of DEWs which are very poor substrate for PER.

Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions

Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.

Broadband infrared and Raman probes of excited-state vibrational molecular dynamics: simulation protocols based on loop diagrams

Vibrational motions in electronically excited states can be observed either by time and frequency resolved infrared absorption or by off resonant stimulated Raman techniques. Multipoint correlation function expressions are derived for both signals. Three representations which suggest different simulation protocols for the signals are developed. These are based on the forward and the backward propagation of the wavefunction, sum over state expansion using an effective vibrational Hamiltonian or a semiclassical treatment of a bath. We show that the effective temporal (Δt) and spectral (Δω) resolution of the techniques is not controlled solely by experimental knobs but also depends on the system dynamics being probed. The Fourier uncertainty ΔωΔt > 1 is never violated.

Unraveling the pathways to UVA-induced DNA photodamage: (6-4) photoproduct as a potential "Trojan Horse"

Double jeopardy: The Pyo chromophore in the (6-4) photoproduct is able to induce a secondary photoproduct in DNA by excitation with UVA light.

Repair of the (6-4) photoproduct by DNA photolyase requires two photons

It takes two (photons) to tango: Single-turnover flash experiments showed that the flavoenzyme (6-4) photolyase uses a successive two-photon mechanism to repair the UV-induced T(6-4)T lesion in DNA (see picture). The intermediate (X) formed by the first photoreaction is likely to be the oxetane-bridged dimer T(ox)T. The enzyme could stabilize the normally short-lived T(ox)T, allowing repair to be completed by the second photoreaction.

Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy

Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale.