A new photoreactivating enzyme that specifically repairs ultraviolet light-induced (6-4)photoproducts

Prospecting bioactivity in Antarctic algae: A review of extracts, isolated compounds and their effects

Algae and its metabolites have been a popular subject of research in numerous fields over the years. Various reviews have been written on algal bioactive components, but a specific focus on Antarctic-derived algae is seldom reviewed. Due to the extreme climate conditions of Antarctica, it is hypothesized that the acclimatized algae may have given rise to a new set of bioactive compounds as a result of adaptation. Although most studies done on Antarctic algae are based on ecological and physiological studies, as well as in the field of nanomaterial synthesis, some studies point out the potential therapeutic properties of these compounds. As an effort to shed light on a different application of Antarctic algae, this review focuses on evaluating its different medicinal properties, including antimicrobial, anticancer, antioxidative, anti-inflammatory, and skin protective effects.

Full Dynamical and Ab Initio Investigation of the Electron Transfer-Mediated Decay Mechanism of He+ in the Presence of Heavier Alkali Dimers

We have studied the electron transfer-mediated decay (ETMD) process for the 1s ionized state of the He atom in the presence of a heavier alkali homonuclear dimer (Na2, K2, and Rb2) as well as heteronuclear dimer (LiNa, NaK, and KRb). In our computation, we have considered all the alkali dimers being in the singlet electronic ground state. The electron transfer from the alkali dimer to He (1s-1) leads to the emission of another electron from the alkali dimer into the continuum. We have investigated the impact of the distance of the He atom from the center of mass of the alkali dimer on the ETMD decay width. We also performed the Born-Oppenheimer molecular dynamics simulation to understand the impact of nuclear dynamics on the ETMD process.

Phylogenetic distribution, structural analysis and interaction of nucleotide excision repair proteins in cyanobacteria

Cyanobacteria are photosynthetic Gram-negative, oxygen evolving prokaryotes with cosmopolitan distribution. Ultraviolet radiation (UVR) and other abiotic stresses result in DNA lesions in cyanobacteria. Nucleotide excision repair (NER) pathway removes the DNA lesions produced by UVR to normal DNA sequence. In cyanobacteria, detailed knowledge about NER proteins is poorly studied. Therefore, we have studied the NER proteins in cyanobacteria. Analyses of 289 amino acids sequence from 77 cyanobacterial species have revealed the presence of a minimum of one copy of NER protein in their genome. Phylogenetic analysis of NER protein shows that UvrD has maximal rate of amino acid substitutions which resulted in increased branch length. The motif analysis shows that UvrABC proteins is more conserved than UvrD, Further, UvrA with UvrB protein interacts with each other and form stable complex which have DNA binding domain on the surface of the complex. UvrB also have DNA binding domain. Positive electrostatic potential was found in the DNA binding region, which is followed by negative and neutral electrostatic potential. Additionally, the surface accessibility values at the DNA strands of T5-T6 dimer binding site were maximal. Protein nucleotide interaction shows the strong binding of T5-T6 dimer with NER proteins of Synechocystis sp. PCC 6803. This process repairs the UV-induced DNA lesions in dark when photoreactivation is inactive. Regulation of NER proteins protect cyanobacterial genome and maintain the fitness of organism under different abiotic stresses.

Preparation of CPD Photolyase Nanoliposomes Derived from Antarctic Microalgae and Their Effect on UVB-Induced Skin Damage in Mice

UVB radiation is known to trigger the block of DNA replication and transcription by forming cyclobutane pyrimidine dimer (CPD), which results in severe skin damage. CPD photolyase, a kind of DNA repair enzyme, can efficiently repair CPDs that are absent in humans and mice. Although exogenous CPD photolyases have beneficial effects on skin diseases, the mechanisms of CPD photolyases on the skin remain unknown. Here, this study prepared CPD photolyase nanoliposomes (CPDNL) from Antarctic Chlamydomonas sp. ICE-L, which thrives in harsh, high-UVB conditions, and evaluated their protective mechanisms against UVB-induced damage in mice. CPDNL were optimized using response surface methodology, characterized by a mean particle size of 105.5 nm, with an encapsulation efficiency of 63.3%. Topical application of CPDNL prevented UVB-induced erythema, epidermal thickness, and wrinkles in mice. CPDNL mitigated UVB-induced DNA damage by significantly decreasing the CPD concentration. CPDNL exhibited antioxidant properties as they reduced the production of reactive oxygen species (ROS) and malondialdehyde. Through activation of the NF-κB pathway, CPDNL reduced the expression of pro-inflammatory cytokines including IL-6, TNF-α, and COX-2. Furthermore, CPDNL suppressed the MAPK signaling activation by downregulating the mRNA and protein expression of ERK, JNK, and p38 as well as AP-1. The MMP-1 and MMP-2 expressions were also remarkably decreased, which inhibited the collagen degradation. Therefore, we concluded that CPDNL exerted DNA repair, antioxidant, anti-inflammation, and anti-wrinkle properties as well as collagen protection via regulation of the NF-κB/MAPK/MMP signaling pathways in UVB-induced mice, demonstrating that Antarctic CPD photolyases have the potential for skincare products against UVB and photoaging.

The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution

The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.

Structural Changes during the Photorepair and Binding Processes of Xenopus (6-4) Photolyase with (6-4) Photoproducts in Single- and Double-Stranded DNA

Photolyases (PHRs) repair ultraviolet (UV)-induced DNA photoproducts into normal bases. In this study, we measured the conformational changes upon photoactivation and photorepair processes of a PHR and its specific substrates, (6-4)PHR and a pyrimidine(6-4)pyrimidone photoproduct ((6-4)PP), by light-induced difference Fourier transform infrared (FT-IR) spectroscopy. The single-stranded DNA with (6-4)PP (ss(6-4)PP) was used as a substrate and the resultant FT-IR spectra were compared with the previous results on double-stranded DNA with (6-4)PP (ds(6-4)PP). In the excess amount of substrate to the enzyme, different ss(6-4)PP photorepair FT-IR signals were obtained in an illumination time-dependent manner. As reported for ds(6-4)PP, the early stages of the photoreaction involve the changes in the ss(6-4)PP only, while the late stages of the reaction involve the ss(6-4)PP repair-associated changes and dissociation from (6-4)PHR. From these spectra, difference spectra originating from the binding/dissociation spectrum were extracted. The signals of the C═O stretches of (6-4)PP and repaired thymines in the single- and double-stranded DNA were tentatively assigned. The C═O stretches of (6-4)PP were observed at frequencies that reflect single- and double-stranded DNA environments in aqueous solution, reflecting the different hydrogen-bonding environments. The conformational changes of PHR upon binding of ss(6-4)PP and ds(6-4)PP were similar, suggesting that the conformational change is limited to the (6-4)PP binding pocket region. We interpreted that ds(6-4)PP may be bound together without any special mechanism for flipping out.

Computational Studies on Photolyase (Phr) Proteins of Cyanobacteria

Photolyases (Phrs) are enzymes that utilize blue/ultraviolet (UV-A) region of light for repairing UV-induced cyclopyramidine dimer. We have studied Phr groups by bioinformatic analyses as well as active-site and structural modeling. The analysis of 238 amino acid sequences from 85 completely sequenced cyanobacterial genomes revealed five classes of Phrs, i.e., CPD Gr I, 6-4 Phrs/cryptochrome, Cry-DASH, Fe-S bacteria Phrs, and a group having fewer number of amino acids (276-385) in length. Distribution of Phr groups in cyanobacteria belonging to the order Synechococcales was found to be influenced by the habitats of the organisms. Class V Phrs were exclusively present in cyanobacteria. Unique motif and binding sites were reported in Group II and III. Fe-S protein binding site was only present in Group V. Active site residues and putative CPD/6-4pp binding residues are charged amino acids which were present on the surface of the proteins. Majority of hydrophilic amino acid residues were present on surface of Phrs. Sequence analysis confirmed the diverse nature of Phrs, though, sequence diversity does not affect their overall 3D structure. Protein-ligand interaction analysis identified novel CPD/6-4PP binding sites on Phrs. This structural information of Phrs can be used for the preparation of efficient Phr based formulations.

A partial photoreactivation defect phenotype is not due to unrepaired ultraviolet-induced pyrimidine dimers in ultraviolet-sensitive mutants of Neurospora crassa

Photoreactivation is a mechanism in which photolyase directly repairs either cyclobutane pyrimidine dimers (CPDs) or (6-4) photoproducts [(6-4) PPs] caused by ultraviolet (UV) light. In the filamentous fungus Neurospora crassa, some UV-sensitive mutants such as mus-44 have been reported to exhibit a partial photoreactivation defect (PPD) phenotype, but its mechanism has not been elucidated for a long time. In this study, the N. crassa CPD photolyase PHR was overexpressed in the Δmus-44 strain, but photoreactivation ability was not increased. Furthermore, Escherichia coli CPD photolyase or Arabidopsis thaliana (6-4) PP photolyase was also introduced into Δmus-44; however, the PPD phenotype was not complemented. These results suggested that the PPD phenotype in N. crassa is not caused by residual unrepaired pyrimidine dimers, which are the main type of DNA damage caused by UV irradiation. Finally, we revealed that Δmus-44, but not the Δmus-43 strain, which does not show the PPD phenotype, displayed higher sensitivity with increasing dose rate of UV. Moreover, Δmus-44 was also sensitive to an interstrand crosslinking agent. This indicates that the high dose of UV in our experimental condition induces DNA damage other than pyrimidine dimers, and that such damage is a likely cause of the PPD phenotype.

Involvement of glycogen metabolism in circadian control of UV resistance in cyanobacteria

Most organisms harbor circadian clocks as endogenous timing systems in order to adapt to daily environmental changes, such as exposure to ultraviolet (UV) light. It has been hypothesized that the circadian clock evolved to prevent UV-sensitive activities, such as DNA replication and cell division, during the daytime. Indeed, circadian control of UV resistance has been reported in several eukaryotic organisms, from algae to higher organisms, although the underlying mechanisms remain unknown. Here, we demonstrate that the unicellular cyanobacterium Synechococcus elongatus PCC 7942 exhibits a circadian rhythm in resistance to UV-C and UV-B light, which is higher during subjective dawn and lower during subjective dusk. Nullification of the clock gene cluster kaiABC or the DNA-photolyase phr abolished rhythmicity with constitutively lower resistance to UV-C light, and amino acid substitutions of KaiC altered the period lengths of the UV-C resistance rhythm. In order to elucidate the molecular mechanism underlying the circadian regulation of UV-C resistance, transposon insertion mutants that alter UV-C resistance were isolated. Mutations to the master circadian output mediator genes sasA and rpaA and the glycogen degradation enzyme gene glgP abolished circadian rhythms of UV-C resistance with constitutively high UV-C resistance. Combining these results with further experiments using ATP synthesis inhibitor and strains with modified metabolic pathways, we showed that UV-C resistance is weakened by directing more metabolic flux from the glycogen degradation to catabolic pathway such as oxidative pentose phosphate pathway and glycolysis. We suggest glycogen-related metabolism in the dark affects circadian control in UV sensitivity, while the light masks this effect through the photolyase function.

Most organisms harbor circadian clocks to adapt to daily environmental changes. It has been hypothesized that adaptation to UV radiation during the day was a driving force of the evolution of the circadian clock (known as “the flight from light” hypothesis). Thus, understanding the relationship with UV resistance is important to consider the physiological relevance and an evolutionary origin of the circadian clock. We here demonstrate that the unicellular cyanobacterium, Synechococcus elongatus exhibits a circadian rhythm in resistance to UV-C light, which is higher and lower during subjective dawn and dusk, respectively. This rhythm was abolished by nullification of the clock gene cluster kaiABC, and the period length was changed consistently by period mutations on kaiC. Genetic screening revealed that nullification of clock-associating genes sasA, cikA and rpaA, and of a glycogen degradation enzyme gene glgP abolished or attenuated the UV-resistance rhythm. Combining these results with further experiments using an ATP synthesis inhibitor and strains with modified metabolic pathways, we suggest a that the circadian clock confers adaptive fitness by balancing a trade-off between glycogen-related energy metabolism and the UV-resistance property.

The tail of cryptochromes: an intrinsically disordered cog within the mammalian circadian clock

Cryptochrome (CRY) proteins play an essential role in regulating mammalian circadian rhythms. CRY is composed of a structured N-terminal domain known as the photolyase homology region (PHR), which is tethered to an intrinsically disordered C-terminal tail. The PHR domain is a critical hub for binding other circadian clock components such as CLOCK, BMAL1, PERIOD, or the ubiquitin ligases FBXL3 and FBXL21. While the isolated PHR domain is necessary and sufficient to generate circadian rhythms, removing or modifying the cryptochrome tails modulates the amplitude and/or periodicity of circadian rhythms, suggesting that they play important regulatory roles in the molecular circadian clock. In this commentary, we will discuss how recent studies of these intrinsically disordered tails are helping to establish a general and evolutionarily conserved model for CRY function, where the function of PHR domains is modulated by reversible interactions with their intrinsically disordered tails.

Influence of the Linking Bridge on the Photoreactivity of Benzophenone-Thymine Conjugates

Benzophenone (BP) is present in a variety of bioactive molecules. This chromophore is able to photosensitize DNA damage, where one of the most relevant BP/DNA interactions occurs with thymine (Thy). In view of the complex photoreactivity previously observed for dyads containing BP covalently linked to thymidine, the aim of this work is to investigate whether appropriate changes in the nature of the spacer could modulate the intramolecular BP/Thy photoreactivity, resulting in an enhanced selectivity. Accordingly, the photobehavior of a series of dyads derived from BP and Thy, separated by linear linkers of different length, has been investigated by steady-state photolysis, as well as femtosecond and nanosecond transient absorption spectroscopy. Irradiation of the dyads led to photoproducts arising from formal hydrogen abstraction or Paterno-Büchi (PB) photoreaction, with a chemoselectivity that was clearly dependent on the nature of the linking bridge; moreover, the PB process occurred with complete regio- and stereoselectivity. The overall photoreactivity increased with the length of the spacer and correlated well with the rate constants estimated from the BP triplet lifetimes. A reaction mechanism explaining these results is proposed, where the key features are the strain associated with the reactive conformations and the participation of triplet exciplexes.

Interatomic and Intermolecular Coulombic Decay

Interatomic or intermolecular Coulombic decay (ICD) is a nonlocal electronic decay mechanism occurring in weakly bound matter. In an ICD process, energy released by electronic relaxation of an excited atom or molecule leads to ionization of a neighboring one via Coulombic electron interactions. ICD has been predicted theoretically in the mid nineties of the last century, and its existence has been confirmed experimentally approximately ten years later. Since then, a number of fundamental and applied aspects have been studied in this quickly growing field of research. This review provides an introduction to ICD and draws the connection to related energy transfer and ionization processes. The theoretical approaches for the description of ICD as well as the experimental techniques developed and employed for its investigation are described. The existing body of literature on experimental and theoretical studies of ICD processes in different atomic and molecular systems is reviewed.

Regiochemical memory in the adiabatic photolysis of thymine-derived oxetanes. A combined ultrafast spectroscopic and CASSCF/CASPT2 computational study

The photoinduced cycloreversion of oxetanes has been thoroughly investigated in connection with the photorepair of the well-known DNA (6-4) photoproducts. In the present work, the direct photolysis of the two regioisomers arising from the irradiation of benzophenone (BP) and 1,3-dimethylthymine (DMT), namely the head-to-head (HH-1) and head-to-tail (HT-1) oxetane adducts, has been investigated by combining ultrafast spectroscopy and theoretical multiconfigurational quantum chemistry analysis. Both the experimental and computational results agree with the involvement of an excited triplet exciplex 3[BPDMT]* for the photoinduced oxetane cleavage to generate 3BP* and DMT through an adiabatic photochemical reaction. The experimental signature of 3[BPDMT]* is the appearance of an absorption band at ca. 400 nm, detected by femtosecond transient absorption spectroscopy. Its formation is markedly regioselective, as it is more efficient and proceeds faster for HH-1 (∼2.8 ps) than for HT-1 (∼6.3 ps). This is in line with the theoretical analysis, which predicts an energy barrier to reach the triplet exciplex for HT-1, in contrast with a less hindered profile for HH-1. Finally, the more favorable adiabatic cycloreversion of HH-1 compared to that of HT-1 is explained by its lower probability to reach the intersystem crossing with the ground state, which would induce a radiationless deactivation process leading either to a starting adduct or to a dissociated BP and DMT.

Regioselectivity in the adiabatic photocleavage of DNA-based oxetanes

The photocleavage of oxetanes composed of benzophenone and uracil or thymine derivatives takes place through an adiabatic process, which is markedly affected by the oxetane regiochemistry and by the nucleobase substitutions at positions 1 and 5.

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

Cryptochromes are ubiquitous flavin-binding light sensors closely related to DNA-repairing photolyases. The animal-like cryptochrome CraCRY from the green alga Chlamydomonas reinhardtii challenges the paradigm of cryptochromes as pure blue-light receptors by acting as a (6-4) photolyase, using 8-hydroxy-5-deazaflavin (8-HDF) as a light-harvesting antenna with a 17.4 Å distance to flavin and showing spectral sensitivity up to 680 nm. The expanded action spectrum is attributed to the presence of the flavin neutral radical (FADH^•) in the dark, despite a rapid FADH^• decay observed in vitro in samples exclusively carrying flavin. Herein, the red-light response of CraCRY carrying flavin and 8-HDF was studied, revealing a 3-fold prolongation of the FADH^• lifetime in the presence of 8-HDF. Millisecond time-resolved ultraviolet-visible spectroscopy showed the red-light-induced formation and decay of an absorbance band at 458 nm concomitant with flavin reduction. Time-resolved Fourier transform infrared (FTIR) spectroscopy and density functional theory attributed these changes to the deprotonation of 8-HDF, challenging the paradigm of 8-HDF being permanently deprotonated in photolyases. FTIR spectra showed changes in the hydrogen bonding network of asparagine 395, a residue suggested to indirectly control flavin protonation, indicating the involvement of N395 in the stabilization of FADH^•. Fluorescence spectroscopy revealed a decrease in the energy transfer efficiency of 8-HDF upon flavin reduction, possibly linked to 8-HDF deprotonation. The discovery of the interdependence of flavin and 8-HDF beyond energy transfer processes highlights the essential role of the antenna, introducing a new concept enabling CraCRY and possibly other bifunctional cryptochromes to fulfill their dual function.

New Vision in Photoprotection and Photorepair

Chronic exposure to solar radiation is associated with an increased incidence of skin cancer worldwide and more specifically with non-melanoma skin cancers and actinic keratosis. At the cellular level DNA damage is the main event following ultraviolet (UV) exposure. The kind of lesions produced depends on the wavelength and the energy profile of the radiation, with different photoproducts being formed as a result. Although endogenous DNA repair mechanisms are somewhat effective in repairing DNA, some DNA damage persists and can accumulate with chronic exposure. UV protection strategies, such as sunscreen use, are important in limiting further DNA damage. Several published studies have demonstrated the protective effect that regular use of sunscreen can have against the development of skin cancers. Newer options that aim to help repair damaged DNA may have an important role in reducing the incidence of chronic sun exposure-related photoaging and non-melanoma skin cancers. Photolyase, which is capable of repairing cyclobutane dimers formed as a result of DNA irradiation, is one such novel ingredient. In the first part of this paper we review the rationale for a combined treatment approach of photoprotection and photorepair with photolyase. In the second part we evaluate several published clinical studies, which suggest a beneficial effect in preventing new skin lesions in photodamaged skin. A strategy of photoprotection plus photorepair appears to be relevant for all persons with a high level of solar exposure and those at a higher risk for developing skin cancers.

An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase

Reduced anionic flavin adenine dinucleotide (FADH^- ) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA. The initial step involves photoinduced electron transfer from *FADH^- to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD-dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (k_ET ) through superexchange. No study has succeeded in removing or modifying this Ade to test these hypotheses. Here, FAD analogs containing either an ethano- or etheno-bridged Ade between the AN1 and AN6 atoms (e-FAD and ε-FAD, respectively) were used to reconstitute apo-PL, giving e-PL and ε-PL respectively. The reconstitution yield of e-PL was very poor, suggesting that the hydrophobicity of the ethano group prevented its uptake, while ε-PL showed 50% reconstitution yield. The substrate binding constants for ε-PL and rPL were identical. ε-PL showed a 15% higher steady-state repair yield compared to FAD-reconstituted photolyase (rPL). The acceleration of repair in ε-PL is discussed in terms of an ε-Ade radical intermediate vs superexchange mechanism.

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.

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.

Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD

Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV-induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state upon illumination, which might induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed. We identified a site facing FAD (Ala377 in Escherichia coli CPD photolyase and Val415 in dCRY), hereafter referred to as "site 377", that was distinctly conserved across these sequences: CPD photolyases often had Ala, Ser, or Asn at this site, whereas animal CRYs had Ile, Leu, or Val. The binding affinity for reduced FAD, but not the photorepair activity of E. coli photolyase, was dramatically impaired when replacing Ala377 with any of the three CRY residues. Conversely, in V415S and V415N mutants of dCRY, FAD was photoreduced to its fully reduced state after prolonged illumination, and light-dependent conformational changes of these mutants were severely inhibited. We speculate that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases.

Repair of (6-4) Lesions in DNA by (6-4) Photolyase: 20 Years of Quest for the Photoreaction Mechanism

Exposure of DNA to ultraviolet (UV) light from the Sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Nature has developed unique flavoenzymes, called DNA photolyases, that utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. In this review, we focus on the chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and describe the major events along the quest for the reaction mechanisms, over the 20 years since the discovery of (6-4) photolyase.

Animal Cryptochromes: Divergent Roles in Light Perception, Circadian Timekeeping and Beyond

Cryptochromes are evolutionarily related to the light-dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: Drosophila-like CRYs that act as nonvisual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate-like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors. Some animals have both types of CRYs, while others possess only one. Cryptochromes have two domains, the photolyase homology region (PHR) and an extended, intrinsically disordered C-terminus. While all animal CRYs share a high degree of sequence and structural homology in their PHR domains, the C-termini are divergent in both length and sequence identity. Recently, cryptochrome function has been shown to extend beyond its pivotal role in circadian clocks, participating in regulation of the DNA damage response, cancer progression and glucocorticoid signaling, as well as being implicated as possible magnetoreceptors. In this review, we provide a historical perspective on the discovery of animal cryptochromes, examine similarities and differences of the two types of animal cryptochromes and explore some of the divergent roles for this class of proteins.

Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory

Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) Photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH^- ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.

Targeted Inactivation of DNA Photolyase Genes in Medaka Fish (Oryzias latipes)

Proteins of the cryptochrome/photolyase family (CPF) exhibit sequence and structural conservation, but their functions are divergent. Photolyase is a DNA repair enzyme that catalyzes the light-dependent repair of ultraviolet (UV)-induced photoproducts, whereas cryptochrome acts as a photoreceptor or circadian clock protein. Two types of DNA photolyase exist: CPD photolyase, which repairs cyclobutane pyrimidine dimers (CPDs), and 6-4 photolyase, which repairs 6-4 pyrimidine-pyrimidone photoproducts (6-4PPs). Although the Cry-DASH protein is classified as a cryptochrome, it also has light-dependent DNA repair activity. To determine the significance of the three light-dependent repair enzymes in recovering from solar UV-induced DNA damage at the organismal level, we generated mutants in each gene in medaka using the CRISPR genome editing technique. The light-dependent repair activity of the mutants was examined in vitro in cultured cells and in vivo in skin tissue. Light-dependent repair of CPD was lost in the CPD photolyase-deficient mutant, whereas weak repair activity against 6-4PPs persisted in the 6-4 photolyase-deficient mutant. These results suggest the existence of a heretofore unknown 6-4PP repair pathway and thus improve our understanding of the mechanisms of defense against solar UV in vertebrates.

Latitudinal clines in gene expression and cis-regulatory element variation in Drosophila melanogaster

BACKGROUND

Organisms can rapidly adapt to their environment when colonizing a new habitat, and this could occur by changing protein sequences or by altering patterns of gene expression. The importance of gene expression in driving local adaptation is increasingly being appreciated, and cis-regulatory elements (CREs), which control and modify the expression of the nearby genes, are predicted to play an important role. Here we investigate genetic variation in gene expression in immune-challenged Drosophila melanogaster from temperate and tropical or sub-tropical populations in Australia and United States.

RESULTS

We find parallel latitudinal changes in gene expression, with genes involved in immunity, insecticide resistance, reproduction, and the response to the environment being especially likely to differ between latitudes. By measuring allele-specific gene expression (ASE), we show that cis-regulatory variation also shows parallel latitudinal differences between the two continents and contributes to the latitudinal differences in gene expression.

CONCLUSIONS

Both Australia and United States were relatively recently colonized by D. melanogaster, and it was recently shown that introductions of both African and European flies occurred, with African genotypes contributing disproportionately to tropical populations. Therefore, both the demographic history of the populations and local adaptation may be causing the patterns that we see.

Identification of medaka magnetoreceptor and cryptochromes

Magnetoreception is a hallmark ability of animals for orientation and migration via sensing and utilizing geomagnetic fields. Magnetoreceptor (MagR) and cryptochromes (Cry) have recently been identified as the basis for magnetoreception in Drosophila. However, it has remained unknown whether MagR and Cry have conserved roles in diverse animals. Here we report the identification and expression of magr and cry genes in the fish medaka (Oryzias latipes). Cloning and sequencing identified a single magr gene, four cry genes and one cry-like gene in medaka. By sequence alignment, chromosomal synteny and gene structure analysis, medaka cry2 and magr were found to be the orthologs of human Cry2 and Magr, with cry1aa and cry1ab being coorthologs of human Cry1. Therefore, magr and cry2 have remained as single copy genes, whereas cry1 has undergone two rounds of gene duplication in medaka. Interestingly, magr and cry genes were detected in various stages throughout embryogenesis and displayed ubiquitous expression in adult organs rather than specific or preferential expression in neural organs such as brain and eye. Importantly, magr knockdown by morpholino did not produce visible abnormality in developing embryos, pointing to the possibility of producing viable magr knockouts in medaka as a vertebrate model for magnet biology.

Rhodobacter sphaeroides CryB is a bacterial cryptochrome with (6-4) photolyase activity

Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions; instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Here we present evidence for a repair activity of (6-4) photoproducts by CryB and suggest a dual character combining the functions of cryptochromes and photolyases. We investigated the effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation). Remarkably, impairment of one of the two light absorbing cofactors, FAD or 6,7-dimethyl-8-ribityllumazine, only marginally affected the final survival rate but strongly decelerated photoreactivation kinetics. The impairment of both of them together through mutagenesis decreased CryB-dependent photoreactivation to the level of the ∆cryB knockout strain. The third cofactor, a [4Fe4S] iron-sulfur cluster, is indispensable for the structural integrity of the protein. The reduction of FAD via the conserved tryptophan W338, which is crucial for in vitro reduction and consequently DNA repair, is not required for in vivo photoreactivation, suggesting that this reduction pathway to FAD is dispensable in the cellular environment. This demonstrates that in vitro experiments give only limited information on in vivo photolyase activity.

Functional Conversion of CPD and (6-4) Photolyases by Mutation

Ultraviolet (UV) light from the sun damages DNA by forming a cyclobutane pyrimidine dimer (CPD) and pyrimidine(6-4)pyrimidone photoproducts [(6-4) PP]. Photolyase (PHR) enzymes utilize near-UV/blue light for DNA repair, which is initiated by light-induced electron transfer from the fully reduced flavin adenine dinucleotide chromophore. Despite similar structures and repair mechanisms, the functions of PHR are highly selective; CPD PHR repairs CPD, but not (6-4) PP, and vice versa. In this study, we attempted functional conversion between CPD and (6-4) PHRs. We found that a triple mutant of (6-4) PHR is able to repair the CPD photoproduct, though the repair efficiency is 1 order of magnitude lower than that of wild-type CPD PHR. Difference Fourier transform infrared spectra for repair demonstrate the lack of secondary structural alteration in the mutant, suggesting that the triple mutant gains substrate binding ability while it does not gain the optimized conformational changes from light-induced electron transfer to the release of the repaired DNA. Interestingly, the (6-4) photoproduct is not repaired by the reverse mutation of CPD PHR, and eight additional mutations (total of 11 mutations) introduced into CPD PHR are not sufficient. The observed asymmetric functional conversion is interpreted in terms of a more complex repair mechanism for (6-4) repair, which was supported by quantum chemical/molecular mechanical calculation. These results suggest that CPD PHR may represent an evolutionary origin for photolyase family proteins.

Essential Role of an Unusually Long-lived Tyrosyl Radical in the Response to Red Light of the Animal-like Cryptochrome aCRY

Cryptochromes constitute a group of flavin-binding blue light receptors in bacteria, fungi, plants, and insects. Recently, the response of cryptochromes to light was extended to nearly the entire visible spectral region on the basis of the activity of the animal-like cryptochrome aCRY in the green alga Chlamydomonas reinhardtii This finding was explained by the absorption of red light by the flavin neutral radical as the dark state of the receptor, which then forms the anionic fully reduced state. In this study, time-resolved UV-visible spectroscopy on the full-length aCRY revealed an unusually long-lived tyrosyl radical with a lifetime of 2.6 s, which is present already 1 μs after red light illumination of the flavin radical. Mutational studies disclosed the tyrosine 373 close to the surface to form the long-lived radical and to be essential for photoreduction. This residue is conserved exclusively in the sequences of other putative aCRY proteins distinguishing them from conventional (6-4) photolyases. Size exclusion chromatography showed the full-length aCRY to be a dimer in the dark at 0.5 mm injected concentration with the C-terminal extension as the dimerization site. Upon illumination, partial oligomerization was observed via disulfide bridge formation at cysteine 482 in close proximity to tyrosine 373. The lack of any light response in the C-terminal extension as evidenced by FTIR spectroscopy differentiates aCRY from plant and Drosophila cryptochromes. These findings imply that aCRY might have evolved a different signaling mechanism via a light-triggered redox cascade culminating in photooxidation of a yet unknown substrate or binding partner.

Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases

Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo-induced repair of (6-4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3' nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state.

Photochemistry of Wild-Type and N378D Mutant E. coli DNA Photolyase with Oxidized FAD Cofactor Studied by Transient Absorption Spectroscopy

DNA photolyases (PLs) and evolutionarily related cryptochrome (CRY) blue-light receptors form a widespread superfamily of flavoproteins involved in DNA photorepair and signaling functions. They share a flavin adenine dinucleotide (FAD) cofactor and an electron-transfer (ET) chain composed typically of three tryptophan residues that connect the flavin to the protein surface. Four redox states of FAD are relevant for the various functions of PLs and CRYs: fully reduced FADH(-) (required for DNA photorepair), fully oxidized FADox (blue-light-absorbing dark state of CRYs), and the two semireduced radical states FAD(.-) and FADH(.) formed in ET reactions. The PL of Escherichia coli (EcPL) has been studied for a long time and is often used as a reference system; however, EcPL containing FADox has so far not been investigated on all relevant timescales. Herein, a detailed transient absorption study of EcPL on timescales from nanoseconds to seconds after excitation of FADox is presented. Wild-type EcPL and its N378D mutant, in which the asparagine facing the N5 of the FAD isoalloxazine is replaced by aspartic acid, known to protonate FAD(.-) (formed by ET from the tryptophan chain) in plant CRYs in about 1.5 μs, are characterized. Surprisingly, the mutant protein does not show this protonation. Instead, FAD(.-) is converted in 3.3 μs into a state with spectral features that are different from both FADH(.) and FAD(.-) . Such a conversion does not occur in wild-type EcPL. The chemical nature and formation mechanism of the atypical FAD radical in N378D mutant EcPL are discussed.

Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase

Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleotide (FAD) is the chromophore of both PHRs, and the resting oxidized form (FAD(ox)), at least under in vitro purified conditions, is first photoconverted to the neutral semiquinoid radical (FADH(•)) form, followed by photoconversion into the enzymatically active fully reduced (FADH(-)) form. Previously, we reported light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR. Spectral differences between the absence and presence of (6-4) PP were observed in the photoactivation process. To identify the FTIR signals where these differences appeared, we compared the FTIR spectra of photoactivation (i) in the presence and absence of (6-4) PP, (ii) of (13)C labeling, (15)N labeling, and [(14)N]His/(15)N labeling, and (iii) of H354A and H358A mutants. We successfully assigned the vibrational bands for (6-4) PP, the α-helix and neutral His residue(s). In particular, we assigned three bands to the C ═ O groups of (6-4) PP in the three different redox states of FAD. Furthermore, the changed hydrogen bonding environments of C ═ O groups of (6-4) PP suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation.

Electron transfer mechanisms of DNA repair by photolyase

Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.

Dynamics and mechanisms of DNA repair by photolyase

Photolyases, a class of flavoproteins, use blue light to repair two types of ultraviolet-induced DNA damage, a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct (6-4PP). In this perspective, we review the recent progress in the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike the aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.

Photoreactivation of Escherichia coli is impaired at high growth temperatures

Photolyase repairs UV-induced lesions in DNA using light energy, which is the principle of photoreactivation. Active photolyase contains the two-electron-reduced flavin cofactor. We observed that photoreactivation of Escherichia coli was impaired at growth temperatures ⩾37°C, and growth in this temperature range also resulted in decreased photolyase protein levels in the cells. However, the levels of phr transcripts (encoding photolyase) were almost unchanged at the various growth temperatures. A lacZ-reporter under transcriptional control of the phr promoter showed no temperature-dependent expression. However, a translational reporter consisting of the photolyase N-terminal α/β domain-LacZ fusion protein exhibited lower β-galactosidase activity at high growth temperatures (37-42°C). These results indicated that the change in photolyase levels at different growth temperatures is post-transcriptional in nature. Limited proteolysis identified several susceptible cleavage sites in E. coli photolyase. In vitro differential scanning calorimetry and activity assays revealed that denaturation of active photolyase occurs at temperatures ⩾37°C, while apo-photolyase unfolds at temperatures ⩾25°C. Evidence from temperature-shift experiments also implies that active photolyase is protected from thermal unfolding and proteolysis in vivo, even at 42°C. These results suggest that thermal unfolding and proteolysis of newly synthesized apo-photolyase, but not active photolyase, is responsible for the impaired photoreactivation at high growth temperatures (37-42°C).

Eumetazoan cryptochrome phylogeny and evolution

Cryptochromes (Crys) are light sensing receptors that are present in all eukaryotes. They mainly absorb light in the UV/blue spectrum. The extant Crys consist of two subfamilies, which are descendants of photolyases but are now involved in the regulation of circadian rhythms. So far, knowledge about the evolution, phylogeny, and expression of cry genes is still scarce. The inclusion of cry sequences from a wide range of bilaterian species allowed us to analyze their phylogeny in detail, identifying six major Cry subgroups. Selective gene inactivations and stabilizations in multiple chordate as well as arthropod lineages suggest several sub- and/or neofunctionalization events. An expression study performed in zebrafish, the model organism harboring the largest amount of crys, showed indeed only partially overlapping expression of paralogous mRNA, supporting gene sub- and/or neofunctionalization. Moreover, the daily cry expression in the adult zebrafish retina indicated varying oscillation patterns in different cell types. Our extensive phylogenetic analysis provides for the first time an overview of cry evolutionary history. Although several, especially parasitic or blind species, have lost all cry genes, crustaceans have retained up to three crys, teleosts possess up to seven, and tetrapods up to four crys. The broad and cyclic expression pattern of all cry transcripts in zebrafish retinal layers implies an involvement in retinal circadian processes and supports the hypothesis of several autonomous circadian clocks present in the vertebrate retina.

Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins

Exposure to the ultraviolet component of sunlight causes DNA damage, which subsequently leads to mutations, cellular transformation, and cell death. DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts are more mutagenic than cyclobutane pyrimidine dimers. These lesions must be repaired because of the high mutagenic potential of (6-4) photoproducts. We here reviewed the structures of (6-4) photoproducts, particularly the detailed structures of the (6-4) lesion and (6-4) lesion-containing double-stranded DNA. We also focused on interactions with their binding proteins such as antibody Fabs, (6-4) photolyase, and nucleotide excision repair protein. The (6-4) photoproducts that bound to these proteins had common structural features: The 5'-side thymine and 3'-side pyrimidone bases of the T(6-4)T segment were in half-chair and planar conformations, respectively, and both bases were positioned nearly perpendicularly to each other. Interactions with binding proteins showed that the DNA helices flanking the T(6-4)T segment were largely kinked, and the flipped-out T(6-4)T segment was recognized by these proteins. These proteins had distinctive binding-site structures that were appropriate for their functions.

A quantum chemical perspective on (6-4) photolesion repair by photolyases

(6-4)-Photolyases are fascinating enzymes which repair (6-4)-DNA photolesions utilizing light themselves. It is well known that upon initial photo-excitation of an antenna pigment an electron is transferred from an adjacent FADH(-) cofactor to the photolesion initiating repair, i.e. restoration of the original undamaged DNA bases. Concerning the molecular details of this amazing repair mechanism, the early steps of energy transfer and catalytic electron generation are well understood, the terminal repair mechanism, however, is still a matter of ongoing debate. In this perspective article, recent results of quantum chemical investigations are presented, and their meaning for the repair mechanism under natural conditions is outlined. Consequences of natural light conditions, temperature and thermal equilibration are highlighted when issues like the initial protonation state of the relevant histidines and the lesion, or the direction of electron transfer are discussed.

Physiological aspects of UV-excitation of DNA

Solar ultraviolet (UV) radiation, mainly UV-B (280-315 nm), is one of the most potent genotoxic agents that adversely affects living organisms by altering their genomic stability. DNA through its nucleobases has absorption maxima in the UV region and is therefore the main target of the deleterious radiation. The main biological relevance of UV radiation lies in the formation of several cytotoxic and mutagenic DNA lesions such as cyclobutane pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers (DEWs), as well as DNA strand breaks. However, to counteract these DNA lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, excision repair, and mismatch repair (MMR). Photoreactivation involving the enzyme photolyase is the most frequently used repair mechanism in a number of organisms. Excision repair can be classified as base excision repair (BER) and nucleotide excision repair (NER) involving a number of glycosylases and polymerases, respectively. In addition to this, double-strand break repair, SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms to ensure genomic stability. This review concentrates on the UV-induced DNA damage and the associated repair mechanisms as well as various damage detection methods.