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.     

Axial‐Bonding Heterotrimers Based on Tetrapyrrolic Rings: Synthesis,Characterization, and Redox and Photophysical Properties

We prepared two heterooligomeric arrays based on free base/metalloporphyrins at axial positions and a metalloid phthalocyanine as a basal scaffolding unit by using the axial‐bonding capabilities as well as the known oxophilicity of dihydroxytin(IV) phthalocyanine. Both heterotrimers were completely characterized by elemental analysis, MALDI‐TOF MS, and ¹H NMR (one‐ and two‐dimensional), UV/Vis, and fluorescence spectroscopy as well as cyclic voltammetry. The ground‐state properties indicate that there is minimal π–π interaction between the macrocyclic units. The excited‐state properties show that there is electronic energy transfer competing with photoinduced electron transfer from the singlet state of the axial porphyrin to the central metalloid phthalocyanine and a photoinduced electron transfer from the ground state of the axial porphyrin to the singlet state of the central metalloid phthalocyanine.     

Coronenetetraimide‐Centered Cruciform Pentamers Containing Multiporphyrin Units: Synthesis and Sequential Photoinduced Energy‐ and Electron‐Transfer Dynamics

A series of coronenetetraimide (CorTIm)‐centered cruciform pentamers containing multiporphyrin units, in which four porphyrin units are covalently linked to a CorTIm core through benzyl linkages, were designed and synthesized to investigate their structural, spectroscopic, and electrochemical properties as well as photoinduced electron‐ and energy‐transfer dynamics. These systems afforded the first synthetic case of coroneneimide derivatives covalently linked with dye molecules. The steady‐state absorption and electrochemical results indicate that a CorTIm and four porphyrin units were successfully characterized by the corresponding reference monomers. In contrast, the steady‐state fluorescence measurements demonstrated that strong fluorescence quenching relative to the corresponding monomer units was observed in these pentamers. Nanosecond laser flash photolysis measurements revealed the occurrence of intermolecular electron transfer from triplet excited state of zinc porphyrins to CorTIm. Femtosecond laser‐induced transient absorption measurements for excitation of the CorTIm unit clearly demonstrate the sequential photoinduced energy and electron transfer between CorTIm and porphyrins, that is, occurrence of the initial energy transfer from CorTIm (energy donor) to porphyrins (energy acceptor) and subsequent electron transfer from porphyrins (electron donor) to CorTIm (electron acceptor) in these pentamers, whereas only the electron‐transfer process from porphyrins to CorTIm was observed when we mainly excite porphyrin units. Finally, construction of high‐order supramolecular patterning of these pentamers was performed by utilizing self‐assembly and physical dewetting during the evaporation of solvent.     

Elucidation of the Dexter‐Type Energy Transfer in DNA by Thymine–Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides

C‐nucleosides of 4‐methylbenzophenone, 4‐methoxybenzophenone, and 2′‐methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A‐T base pairs was observed that agrees with a Dexter‐type triplet–triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.     

Allyloxyporphyrin‐Functionalized Multiwalled Carbon Nanotubes: Synthesis by Radical Polymerization and Enhanced Optical‐Limiting Properties

Allyloxyporphyrin‐functionalized multiwalled carbon nanotubes (MWCNT‐TPP) were synthesized by radical polymerization and characterized by FTIR, UV/Vis absorption, and X‐ray photoelectron spectroscopy; elemental analysis; TEM; and thermogravimetric analysis. Z‐scan studies revealed that this nanohybrid exhibits enhanced nonlinear optical (NLO) properties compared to a control sample consisting of a covalently unattached physical blend of MWCNTs and porphyrin, as well as to the separate MWCNTs and porphyrin. At the wavelengths used, the mechanism of enhanced optical limiting likely involves reverse saturable absorption, nonlinear scattering, and photoinduced electron/energy transfer between the MWCNTs and the porphyrin. The role of electron/energy transfer in the NLO performance of MWCNT‐TPP was investigated by Raman and fluorescence spectroscopy.     

Molecular switches controlled by light

The photochemical processes of singlet-singlet energy transfer and photoinduced electron transfer are important not only in natural and artificial photosynthetic energy conversion, but also in a variety of other scientific and technological applications. Controlling these functions at the molecular level using outside stimuli is an interesting scientific challenge. Photochromes, organic molecules that are isomerized by light between two stable forms, can be covalently linked to other chromophores, and changes in their properties resulting from photoisomerization used to switch electron and energy transfer on or off. Simple single- and double-throw molecular switches have been constructed, as well as Boolean logic gates. Such molecules are potentially useful in light-controlled molecular data processing and storage applications.     

Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)(2)](2+)

The UV/Visible absorption properties of a polypyridyl ruthenium complex upon intercalation on DNA are studied at the mixed quantum mechanics molecular mechanics level of theory. Vertical excitation transitions are computed by time dependent density functional theory. Particular emphasis is put on the different levels at which the macromolecular environment is treated, and in particular on the analysis of the effect of mechanical, electrostatic and polarizable embedding. We show that with the highest level of theory the experimental absorption wavelengths are reproduced with a difference of only 2 or 3 nm for the low energy bands. The systematic analysis of the individual vertical transitions allows us to get much more insights into the role played by the environment, in particular, in metal to ligand and intra ligand charge transfer transitions that can lead to the production of DNA oxidative lesions exploitable in phototherapy.     

Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.     

DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5‐Methyl‐2‐pyrimidone Deoxyribonucleoside

The main chromophore of (6‐4) photoproducts, namely, 5‐methyl‐2‐pyrimidone (Pyo), is an artificial noncanonical nucleobase. This chromophore has recently been reported as a potential photosensitizer that induces triplet damage in thymine DNA. In this study, we investigate the spectroscopic properties of the Pyo unit embedded in DNA by means of explicit solvent molecular‐dynamics simulations coupled to time‐dependent DFT and quantum‐mechanics/molecular‐mechanics techniques. Triplet‐state transfer from the Pyo to the thymine unit was monitored in B‐DNA by probing the propensity of this photoactive pyrimidine analogue to induce a Dexter‐type triplet photosensitization and subsequent DNA damage.     

Synthesis,Electrochemistry, and Photophysics of Aza‐BODIPY Porphyrin Dyes

The synthesis of dyad and triad aza‐BODIPY‐porphyrin systems in two steps starting from an aryl‐substituted aza‐BODIPY chromophore is described. The properties of the resulting aza‐BODIPY‐porphyrin conjugates have been extensively investigated by means of electrochemistry, spectroelectrochemistry, and absorption/emission spectroscopy. Fluorescence measurements have revealed a dramatic loss of luminescence intensity, mainly due to competitive energy transfer and photoinduced electron transfer involving charge separation followed by recombination.     

Cyanobuta‐1,3‐dienes as Novel Electron Acceptors for Photoactive Multicomponent Systems

The synthesis, electrochemical, and photophysical properties of five multicomponent systems featuring a Zn^II porphyrin (ZnP) linked to one or two anilino donor‐substituted pentacyano‐ (PCBD) or tetracyanobuta‐1,3‐dienes (TCBD), with and without an interchromophoric bridging spacer (S), are reported: ZnP‐S‐PCBD ( 1 ), ZnP‐S‐TCBD ( 2 ), ZnP‐TCBD ( 3 ), ZnP‐(S‐PCBD)₂ ( 4 ), and ZnP‐(S‐TCBD)₂ ( 5 ). By means of steady‐state and time‐resolved absorption and luminescence spectroscopy (RT and 77 K), photoinduced intramolecular energy and electron transfer processes are evidenced, upon excitation of the porphyrin unit. In systems equipped with the strongest acceptor PCBD and the spacer ( 1 , 4 ), no evidence of electron transfer is found in toluene, suggesting ZnP→PCBD energy transfer, followed by ultrafast (<10 ps) intrinsic deactivation of the PCBD moiety. In the analogous systems with the weaker acceptor TCBD ( 2 , 5 ), photoinduced electron transfer occurs in benzonitrile, generating a charge‐separated (CS) state lasting 2.3 μs. Such a long lifetime, in light of the high Gibbs free energy for charge recombination (ΔG_CR=?1.39 eV), suggests a back‐electron transfer process occurring in the so‐called Marcus inverted region. Notably, in system 3 lacking the interchromophoric spacer, photoinduced charge separation followed by charge recombination occur within 20 ps. This is a consequence of the close vicinity of the donor–acceptor partners and of a virtually activationless electron transfer process. These results indicate that the strongly electron‐accepting cyanobuta‐1,3‐dienes might become promising alternatives to quinone‐, perylenediimide‐, and fullerene‐derived acceptors in multicomponent modules featuring photoinduced electron transfer.     

Theoretical Study on the Photo-Oxidation and Photoreduction of an Azetidine Derivative as a Model of DNA Repair

Photocycloreversion plays a central role in the study of the repair of DNA lesions, reverting them into the original pyrimidine nucleobases. Particularly, among the proposed mechanisms for the repair of DNA (6-4) photoproducts by photolyases, it has been suggested that it takes place through an intermediate characterized by a four-membered heterocyclic oxetane or azetidine ring, whose opening requires the reduction of the fused nucleobases. The specific role of this electron transfer step and its impact on the ring opening energetics remain to be understood. These processes are studied herein by means of quantum-chemical calculations on the two azetidine stereoisomers obtained from photocycloaddition between 6-azauracil and cyclohexene. First, we analyze the efficiency of the electron-transfer processes by computing the redox properties of the azetidine isomers as well as those of a series of aromatic photosensitizers acting as photoreductants and photo-oxidants. We find certain stereodifferentiation favoring oxidation of the cis-isomer, in agreement with previous experimental data. Second, we determine the reaction profiles of the ring-opening mechanism of the cationic, neutral, and anionic systems and assess their feasibility based on their energy barrier heights and the stability of the reactants and products. Results show that oxidation largely decreases the ring-opening energy barrier for both stereoisomers, even though the process is forecast as too slow to be competitive. Conversely, one-electron reduction dramatically facilitates the ring opening of the azetidine heterocycle. Considering the overall quantum-chemistry findings, N,N-dimethylaniline is proposed as an efficient photosensitizer to trigger the photoinduced cycloreversion of the DNA lesion model.     

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5‐ethyl‐6‐phenylphenanthridinium and uncharged 3,8‐diamino‐6‐phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge‐transfer terms are also important. The ΔG of ethidium intercalation to DNA was estimated at ?4.5 kcal mol^?1 and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non‐covalent stacking (including charge‐transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.     

Elucidation of the Key Role of [Ru(bpy)3]2+ in Photocatalyzed RAFT Polymerization

Photocatalysis reactions using [Ru^II(bpy)₃]²⁺ were studied on the example of visible‐light‐sensitized reversible addition–fragmentation chain transfer (RAFT) polymerization. Although both photoinduced electron‐ and energy‐transfer mechanisms are able to describe this interaction, no definitive experimental proof has been presented so far. This paper investigates the actual mechanism governing this reaction. A set of RAFT agents was selected, their redox potentials measured by cyclic voltammetry, and relaxed triplet energies calculated by quantum mechanics. Gibbs free‐energy values were calculated for both electron‐ and energy‐transfer mechanisms. Quenching rate constants were determined by laser flash photolysis. The results undoubtedly evidence the involvement of a photoinduced energy‐transfer reaction. Controlled photopolymerization experiments are discussed in the light of the primary photochemical process and photodissociation ability of RAFT agent triplet states.     

Improving the Photoinduced Charge Separation Parameters in Corrole–Perylene Carboximide Dyads by Tuning the Redox and Spectroscopic Properties of the Components

A couple of corrole–perylene carboximide dyads ( C2‐PIa and C2‐PIx ) have been synthesized and their photoreactivity has been evaluated. We aimed at obtaining better performances for photoinduced charge separation, both in terms of efficiency and in terms of lifetime, with respect to formerly studied systems. The energy level of the charge‐separated state was tuned by selecting perylene and corrole components with diverse redox and spectroscopic properties. High spectroscopic energy levels of the perylene carboximide derivatives (PIs) allow a fast charge separation to be maintained in competition with an energy‐transfer process from the PI to the corrole unit. Yields and lifetimes of charge separation in toluene are, respectively, 75 % and 2.5 μs for C2‐PIa and 65 % and 24 ns for C2‐PIx . The results and the effect of solvent polarity are discussed in the framework of current energy‐ and electron‐transfer theories.     

Photoinduced processes in interlocked structures containing porphyrins

The recent literature on photoactive interlocked structures containing porphyrins is reviewed. Catenanes and rotaxanes studied both in the author's laboratory and by other groups, displaying either photoinduced energy or electron transfer processes are reported. In addition to porphyrins, the examined structures contain photo or electroactive components as C₆₀, paraquat, ferrocene, aromatic amines. Both metal catenanes/rotaxanes and free catenanes/rotaxanes are discussed and the differences in their behavior is outlined with respect to structural rigidity and electronic coupling properties. The role of different conformations and their effect on photophysical properties is examined. In spite of their uncommon topology, these arrays behave similarly to covalently or self-assembled photoactive multi-component architectures and display fast energy/electron transfer rates and high charge separation efficiency. A rationale for this behavior is provided.     

Ultrafast Energy Transfer in Triptycene‐Grafted Bodipy Scaffoldings

A series of new compounds in which various Bodipy dyes are grafted logically on triptycene rigid structures are synthesized and characterized, and their absorption spectra and photophysical properties are studied, also by pump‐probe transient absorption spectroscopy. The studied compounds are: the mono‐Bodipy species TA, TB, and TC (where A, B, and C identify different Bodipy subunits absorbing and emitting at different wavelengths), the multichromophore species TA₃, which bears three identical A subunits, and the three multichromophoric species TAB, TBC, and TABC, all of them containing at least two different types of Bodipy subunits. The triptycene moiety plays the role of a rigid scaffold, keeping the various dyes at predetermined distances and allowing for a three‐dimensional structural arrangement of the multichromophoric species. The absorption spectra of the multichromophoric Bodipy species are essentially additive, indicating that negligible inter‐chromophoric interaction takes place at the ground state. Luminescence properties and transient absorption spectroscopy indicate that a very fast (on the picosecond time scale) and efficient photoinduced energy transfer occurs in all the multi‐Bodipy species, with the lower‐energy Bodipy subunits of each multi‐Bodipy compounds playing the role of an electronic energy collector. In TAB, an energy transfer from the A‐type Bodipy subunit to the B‐type one takes place with a rate constant of 1.6×10¹⁰ s^?1, whereas in TBC an energy transfer from the B‐type Bodipy subunit to the C‐type subunit is bi‐exponential, exhibiting rate constants of 1.7×10¹¹ and 1.9×10¹⁰ s^?1; the possible presence of different conformers with different donor–acceptor distances in this bichromophoric species is proposed to cause the bi‐exponential energy‐transfer process. Interpretation of the intricate energy‐transfer pathways occurring in TABC is made with the help of the processes identified in the bichromophoric compounds. In all cases, the measured energy‐transfer rate constants agree with a Förster mechanism for the energy‐transfer processes.     

HOMO Stabilisation in π‐Extended Dibenzotetrathiafulvalene Derivatives for Their Application in Organic Field‐Effect Transistors

Three new organic semiconductors, in which either two methoxy units are directly linked to a dibenzotetrathiafulvalene (DB‐TTF) central core and a 2,1,3‐chalcogendiazole is fused on the one side, or four methoxy groups are linked to the DB‐TTF, have been synthesised as active materials for organic field‐effect transistors (OFETs). Their electrochemical behaviour, electronic absorption and fluorescence emission as well as photoinduced intramolecular charge transfer were studied. The electron‐withdrawing 2,1,3‐chalcogendiazole unit significantly affects the electronic properties of these semiconductors, lowering both the HOMO and LUMO energy levels and hence increasing the stability of the semiconducting material. The solution‐processed single‐crystal transistors exhibit high performance with a hole mobility up to 0.04 cm² V^?1 s^?1 as well as good ambient stability.     

Modelling Photosynthesis with ZnII‐Protoporphyrin All‐DNA G‐Quadruplex/Aptamer Scaffolds

All‐DNA scaffolds act as templates for the organization of photosystem I model systems. A series of DNA templates composed of Zn^II‐protoporphyrin IX (Zn^IIPPIX)‐functionalized G‐quadruplex conjugated to the 3′‐ or 5′‐end of the tyrosinamide (TA) aptamer and Zn^IIPPIX/G‐quadruplex linked to the 3′‐ and 5′‐ends of the TA aptamer through a four‐thymidine bridge. Effective photoinduced electron transfer (ET) from Zn^IIPPIX/G‐quadruplex to bipyridinium‐functionalized tyrosinamide, TA‐MV²⁺, bound to the TA aptamer units is demonstrated. The effectiveness of the primary ET quenching of Zn^IIPPIX/G‐quadruplex by TA‐MV²⁺ controls the efficiency of the generation of TA‐MV^+.. The photosystem‐controlled formation of TA‐MV^+. by the different photosystems dictates the secondary activation of the ET cascade corresponding to the ferredoxin‐NADP⁺ reductase (FNR)‐catalysed reduction of NADP⁺ to NADPH by TA‐MV^+., and the sequestered alcohol dehydrogenase catalysed reduction of acetophenone to 1‐phenylethanol by NADPH.     

Electron-transfer oxidation properties of DNA bases and DNA oligomers

Kinetics for the thermal and photoinduced electron-transfer oxidation of a series of DNA bases with various oxidants having the known one-electron reduction potentials (E(red)) in an aqueous solution at 298 K were examined, and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of DNA bases and the intrinsic barrier of the electron transfer. Although the E(ox) value of GMP at pH 7 is the lowest (1.07 V vs SCE) among the four DNA bases, the highest E(ox) value (CMP) is only 0.19 V higher than that of GMP. The selective oxidation of GMP in the thermal electron-transfer oxidation of GMP results from a significant decrease in the pH dependent oxidation potential due to the deprotonation of GMP*+. The one-electron reduced species of the photosensitizer produced by photoinduced electron transfer are observed as the transient absorption spectra when the free energy change of electron transfer is negative. The rate constants of electron-transfer oxidation of the guanine moieties in DNA oligomers with Fe(bpy)3(3+) and Ru(bpy)3(3+) were also determined using DNA oligomers containing different guanine (G) sequences from 1 to 10 G. The rate constants of electron-transfer oxidation of the guanine moieties in single- and double-stranded DNA oligomers with Fe(bpy)3(2+) and Ru(bpy)3(3+) are dependent on the number of sequential guanine molecules as well as on pH.