Do photolyases need to provide considerable activation energy for the splitting of cyclobutane pyrimidine dimer radical anions?

Time-resolved crystallography captures light-driven DNA repair

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.

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.

Dynamics and mechanism of UV-damaged DNA repair in indole-thymine dimer adduct: molecular origin of low repair quantum efficiency

Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.

Excited-state proton coupled electron transfer between photolyase and the damaged DNA through water wire: a photo-repair mechanism

The photolyase enzyme absorbs blue light to repair damaged DNA through a cyclic electron transfer reaction. A description of the underlying mechanism has proven to be a challenging issue for both experimental and theoretical studies. In the present work, combined CASPT2//CASSCF/AMBER (QM/MM) calculations have been performed for damaged DNA in photolyase. A proton-coupled electron transfer (PCET) mechanism has been determined for restoring cyclobutane pyrimidine dimer (CPD) to two normal thymine bases by irradiation of photolyase. A well-defined water wire between FADH(-) and CPD was determined as a bridge to assist the PCET process within FADH(-) and thereby trigger the forward electron transfer to CPD. The subsequent CPD splitting and the alternation of the H-bond pattern proceed in a concerted way, which makes the productive backward electron transfer occur on an ultrafast timescale. A local minimum of SCT((1)ππ*)-LMin was identified on the pathway of the futile backward electron transfer (BET), which is stabilized by the strong H-bond interaction between the water wire and CPD. As a result, the futile BET process is endothermic by ∼18.0 kcal mol(-1), which is responsible for a 2.4 ns timescale inferred experimentally for the futile BET process. Besides the unbiased interpretation for the majority of the experimental findings, the present study provides a new excited-state PCET mechanism, which leads to a significant step toward a deeper understanding of the photo-repair process of damaged-DNA by the photolyase enzyme.

Substituent effects on photosensitized splitting of thymine cyclobutane dimer by an attached indole

In chromophore-containing cyclobutane pyrimidine dimer (CPD) model systems, solvent effects on the splitting efficiency may depend on the length of the linker, the molecular conformation, and the oxidation potential of the donor. To further explore the relationship between chromophore structure and splitting efficiency, we prepared a series of substituted indole-T< >T model compounds 2 a-2 g and measured their splitting quantum yields in various solvents. Two reverse solvent effects were observed: an increase in splitting efficiency in solvents of lower polarity for models 2 a-2 d with an electron-donating group (EDG), and vice versa for models 2 e-2 g with an electron-withdrawing group (EWG). According to the Hammett equation, the negative value of the slope of the Hammett plot indicates that the indole moiety during the T< >T-splitting reaction loses negative charge, and the larger negative value implies that the repair reaction is more sensitive to substituent effects in low-polarity solvents. The EDGs of the models 2 a-2 d can delocalize the charge-separated state, and low-polarity solvents make it more stable, which leads to higher splitting efficiency in low-polarity solvents. Conversely, the EWGs of models 2 e-2 g favor destabilization of the charge-separated state, and high-polarity solvents decrease the destabilization and hence lead to more efficient splitting in high-polarity solvents.

The radical cationic repair pathway of cyclobutane pyrimidine dimer: the effect of sugar-phosphate backbone

Radical cationic repair process of cis-syn thymine dimer has been investigated when (1) sugar-phosphate backbones were substituted by hydrogen atoms, (2) phosphate group was substituted by two hydrogen atoms each on a sugar ring and (3) sugar-phosphate backbone was taken into account. The effect of the interactions between N1 and N1' lone pairs and the C6-C6' antibonding orbital are the most important evidences for the cleavage of the C6-C6' bond in the first step of radical cationic repair mechanism in the absence of the sugar-phosphate backbone. The impact of the N1 and N1' lone pairs on the C6-C6' bond cleavage decreases and the energy barrier of the cleavage of that bond significantly increases in the presence of the deoxynucleoside sugars and the sugar-phosphate backbone.

Dynamics and mechanism of DNA repair in a biomimetic system: flavin-thymine dimer adduct

To mimic photolyase for efficient repair of UV-damaged DNA, numerous biomimetic systems have been synthesized, but all show low repair efficiency. The molecular mechanism of this low-efficiency process is still poorly understood. Here we report our direct mapping of the repair processes of a flavin-thymine dimer adduct with femtosecond resolution. We followed the entire dynamic evolution and observed direct electron transfer (ET) from the excited flavin to the thymine dimer in 79 ps. We further observed two competitive pathways, productive dimer ring splitting within 435 ps and futile back-ET in 95 ps. Our observations reveal that the underlying mechanism for the low repair quantum yield of flavin-thymine dimer adducts is the short-lived excited flavin moiety and the fast dynamics of futile back-ET without repair.

An AIMD study of the CPD repair mechanism in water: reaction free energy surface and mechanistic implications

In a series of two papers, we report the detailed mechanism of cyclobutane pyrimidine dimer repair in aqueous solvent using ab initio molecular dynamics simulations (AIMD). Umbrella sampling is used to determine the free energy surface for dimer splitting. The two-dimensional free energy surface for splitting of the C5-C5' and C6-C6' bonds on the anion surface is reported. The splitting of the C5-C5' and C6-C6' bonds occurs on a picosecond time scale. The transition state along the splitting coordinate in the anion state coincides with a maximum in the free energy along the same coordinate on the neutral surface. The implication is that back electron transfer occurring before the anion reaches the transition state leads to reformation of the cyclobutane dimer, while back electron transfer after transit through the transition state, leads to successful repair. On the basis of our calculations for CPD splitting in water, we propose a framework for understanding how various factors, such as solvent polarity, can control repair efficiency. This framework explains why back electron transfer leads predominantly to unsuccessful repair in some situations, and successful repair in others. A key observation is that the same free energy surfaces that control dimer splitting also govern how the back electron transfer rate changes during the splitting process. Configurational changes of the dimer along the splitting coordinate are also documented.

An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting

In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5' and C6-C6' bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Nonequilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects. Throughout the splitting of C5-C5' and C6-C6' bonds, a significant amount of excess charge is delocalized onto the solvent. We have verified that this is not an artifact of the electronic density functional theory (DFT) method used for this anionic system with Schrödinger equation-based quantum chemical cluster calculations. The amount and variability of charge delocalization changes with the course of the reaction. The splitting of the C6-C6' bond is accompanied by both an increase in electron density on the C6 and C6' carbon atoms and an increase in the water density near those atoms. These features are observed both in our equilibrium umbrella sampling simulations and nonequilibrium trajectories.

Photosensitized splitting of thymine dimer or oxetane unit by a covalently N-linked carbazole via electron transfer in different marcus regions

Although many similarities exist between the two classes of enzymes, cyclobutane photolyases and (6-4) photolyases have certain important differences. The most significant difference is in their repair quantum yields, cyclobutane photolyases with a uniformly high efficiency (0.7-0.98) and very low repair efficiency for (6-4) photolyases (0.05-0.1). To understand the significant difference, we prepared two classes of model compounds, covalently N-linked dimer- (1) or oxetane-carbazole (2) compounds with a dimethylene or trimethylene group as a linker. Under light irradiation, the dimer or oxetane unit of model compounds can be sensitized to split by the excited carbazole via an intramolecular electron transfer. The splitting reaction of dimer or oxetane unit in model compounds is strongly solvent dependent. In nonpolar solvents, such as cyclohexane or THF, no fluorescence quenching of the carbazole moiety of model compounds relative to a free carbazole, N-methylcarbazole, was observed and thus no splitting occurred. In polar solvents, two classes of model compounds reveal two reverse solvent effects on the splitting quantum yield. One is an inverse relation between the quantum yield and the polarity of the solvent for dimer-model systems, and another is a normal relation for oxetane-model systems. This phenomenon was also observed with another two classes of model compounds, covalently linked dimer- or oxetane-indole. Based on Marcus theory and thermodynamic data, it has been rationalized that the two reverse solvent effects derive from back electron transfer in the splitting process lying in the different Marcus regions. Back electron transfer lies in the Marcus inverted region for dimer-model systems and the normal region for oxetane-model systems. From repair solvent behavior of the two classes of model compounds, we gained some insights into the major difference in the repair efficiency for the two classes of photolyases.

Reaction mechanisms of DNA photolyase

DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH° occur in overall 1ns. Whereas the kinetics of FADH° was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH° to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.

What is adenine doing in photolyase?

The short answer to the title question is that it acts as an electrostatic bouncer that shoves the charge flow from flavin toward the DNA lesion that photolyase repairs. This explanation is provided by an explicit time-dependent quantum mechanical approach, which is used to investigate the electron transfer process that triggers the repair mechanism. The transfer occurs from the flavin photolyase cofactor to the cyclobutane ring of DNA, previously formed by light-induced cycloaddition of adjacent pyrimidine bases. The electron wave function dynamics accurately accounts for the previously proposed mechanism of transfer via the terminal methyl group of the flavin moiety present in the catalytic electron-donor cofactor, FADH(-), which also contains adenine. This latter moiety, which has often been assumed to be present mainly for structural reasons, instantaneously modifies the interaction between acceptor and donor by a variation of the electrostatic interactions so that the presence of its local atomic charges is necessary to trigger the transfer. In principle, knowledge of the details of the electron transfer dynamics and of the important role of polarization effects can be exploited to improve the efficiency of the repair mechanism in artificial systems.

Origin of solvent dependence of photosensitized splitting of a cyclobutane pyrimidine dimer by a covalently linked chromophore

In model studies involving the mechanisms of DNA photolyases, two reverse solvent effects on the quantum yield of photosensitized splitting of a cyclobutane pyrimidine dimer (CPD) by a covalently linked chromophore have been reported. One is an increase in the splitting efficiency in lower polarity solvents for model compounds with a short linker between the dimer and the chromophore. Another is more efficient splitting in higher polarity solvents for model compounds with a flexible and long linker. To unravel mechanisms of two opposite solvent effects, five covalently linked indole-dimer compounds with different-length linkers were prepared. Two solvent effects as described above were observed through measuring quantum yields of dimer splitting of these model compounds in four solvents. According to Marcus theory, back electron transfer in the splitting reaction was analyzed quantitatively in light of relative data of a model compound in four solvents. It was demonstrated that the dependence of the quantum yield on solvent polarity for the flexible long-linker system would derive from the change in the distance between a dimer unit (acceptor) and an indole moiety (electron donor) in different solvents. With increasing solvent polarity, a U-shaped conformation of the model compound would become a preferred conformation because of the hydrophobic interaction between indole and dimer moiety, and their distances would become closer. On the basis of Marcus theory, calculated results reveal that the rate of back electron transfer would be slowed down with increasing solvent polarity and the distance reduced, giving a more efficient splitting. Meanwhile, some new insights into mechanisms of DNA photoreactivation mediated by photolyases were gained.

Active site of Escherichia coli DNA photolyase: Asn378 is crucial both for stabilizing the neutral flavin radical cofactor and for DNA repair

Escherichia coli DNA photolyase repairs cyclobutane pyrimidine dimer (CPD) in UV-damaged DNA through a photoinduced electron transfer mechanism. The catalytic activity of the enzyme requires fully reduced FAD (FADH (-)). After purification in vitro, the cofactor FADH (-) in photolyase is oxidized into the neutral radical form FADH (*) under aerobic conditions and the enzyme loses its repair function. We have constructed a mutant photolyase in which asparagine 378 (N378) is replaced with serine (S). In comparison with wild-type photolyase, we found N378S mutant photolyase containing oxidized FAD (FAD ox) but not FADH (*) after routine purification procedures, but evidence shows that the mutant protein contains FADH (-) in vivo as the wild type. Although N378S mutant photolyase is photoreducable and capable of binding CPD in DNA, the activity assays indicate the mutant protein is catalytically inert. We conclude that the Asn378 residue of E. coli photolyase is crucial both for stabilizing the neutral flavin radical cofactor and for catalysis.