A Quantum Chemical Study of Photoinduced DNA Repair: On the Splitting of Pyrimidine Model Dimers Initiated by Electron Transfer

DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283

DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.

Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically

The cyclobutane pyrimidine dimer (CPD) is a major photoproduct of deoxyribonucleic acid (DNA) that is damaged by ultraviolet light. This DNA lesion can be repaired by DNA photolyase with the aid of UV light and two cofactors. To understand the repair mechanism of CPD and whether protonation of CPD participates in the DNA repair process, the cycloreversion reactions of four CPD models and proton transfers between the adjacent residue Glu283 and CPD models were explored through the quantum mechanical method. Two-dimensional maps of potential energy surface in a vacuum and in implicit water solution were calculated at the ωB97XD/6-311++G(2df,2pd) level. One-dimensional potential energy profiles were computed for proton transfer reactions. Among the models that have been considered, both in a vacuum and in water solution, the results indicate that the most likely repair mechanism involves CPD^•2- radical anion splitting in a stepwise manner. C5-C5' splits first, and C6-C6' splits later. The computed free energies of activation of the two splitting steps are 0.9 and 3.1 kcal/mol, respectively. The adjacent Glu283 may stabilize the CPD^•2- radical anion through hydrogen bond and increase the quantum yield; however, protonating the CPD radical anion by Glu283 cannot accelerate the rate of ring opening.

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.

Stabilization of radical anion states of nucleobases in DNA

Trapping of an electron by DNA leads to the formation of radical anion states of pyrimidine bases. Because these states play an important role in biological and chemical processes, their computational treatment is of particular interest. We show that simple electrostatic and quantum chemical models can accurately reproduce the adiabatic electron affinities (EAs) of short DNA stacks recently derived from high-level ab initio calculations (M. Kobylecka, J. Leszczynski, and J. Rak, J. Am. Chem. Soc., 2008, 130, 15683). The electrostatic interaction of an excess electron localized on cytosine or thymine with intra- and inter-strand adjacent nucleobases is found to strongly affect the energy of the radical anions. This interaction is the main origin of the dependence of EA of nucleobases on the nature of neighboring base pairs. In particular, the states XT(-)Y and XC(-)Y, where X and Y = C, T, are, by ca. 0.7 eV, more stable than radical anions GT(-)G and GC(-)G. We find that second-neighbor effects can also significantly modulate EAs, although being smaller than the effects of adjacent bases. The strongest destabilizing effect is found for 5'-GC and 3'-GC, while the 5'-AT base pair stabilizes the radical anion states. Using a combined QM/MD approach, we consider how structural fluctuations of DNA influence the stability of the radical anion states. Despite large dispersions of the stabilization energies due to conformational dynamics of DNA, there are only few thermally accessible structures where GT(-)G and GC(-)G are energetically more favorable than the corresponding pyrimidine triplets. Although stabilization energies calculated for stacks of regular structure are in qualitative agreement with the QM/MD results, structural fluctuations of pi stacks should be taken into account for more accurate description of the excess electron trapped by DNA. The results obtained in this study suggest that simple electrostatic models, in combination with MD simulations, can be very helpful to explore the long time scale behavior of radical anions in DNA.

Photolysis of the sulfonamide bond of metal complexes of N-dansyl-1,4,7,10-tetraazacyclododecane in aqueous solution: a mechanistic study and application to the photorepair of cis,syn-cyclobutane thymine photodimer

Sulfonamide constitutes a ubiquitous functional group that is frequently used in organic chemistry, analytical chemistry, and medicinal chemistry. We report herein on the photolysis of a dansylamide moiety of 1-dansyl-1,4,7,10-tetraazzacyclododecane (N-dansylcyclen, L(2)) in the presence of a zinc(II) ion in aqueous solution. By potentiometric pH titrations, the complexation constant for the 1:1 complex of L(2) and Zn(2+), log K(s)(ZnL(2)), in aqueous solution at 25 degrees C with I = 0.1 (NaNO(3)) was determined to be 6.5+/-0.1. The structure of the ZnL(2) complex was confirmed by single-crystal X-ray diffraction analysis. During fluorescence titrations of L(2) with Zn(2+) (irradiation at 308 or 350 nm) in aqueous solution at pH 7.4 (10 mM HEPES with I = 0.1 (NaNO(3))) and 25 degrees C, considerable enhancement in fluorescence emission of the Zn(2+) complex of L(2) (ZnL(2)) was observed, while metal-free L(2) exhibited only a negligible emission change upon UV irradiation. It was revealed that this emission enhancement arose from the photoinduced cleavage of a sulfonylamide moiety in ZnL(2), yielding the Zn(2+)-cyclen complex and 5-dimethylaminonaphthalene-1-sulfinic acid, which has a greater quantum yield (Phi) for fluorescence emission than that of L(2) and ZnL(2). For comparison, the photolysis of N-(1-naphthalenesulfonyl)cyclen (L(3)) and its Zn(2+) complex (ZnL(3)) under the same conditions (irradiation at 313 nm) gave the corresponding sulfonate (1-naphthylsulfonate). We also describe the results of a photoreversion reaction of cis,syn-cyclobutane thymine photodimer (T[c,s]T) utilizing the photolysis of ZnL(2) and ZnL(3).

Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA

Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.

A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA

The reaction pathways for the photochemical formation of cyclobutane thymine dimers in DNA are explored using hybrid density functional theory techniques. It is concluded that the thymine-thymine [2 + 2] cycloaddition displays favorable energy barriers and reaction energies in both the triplet and the singlet excited states. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction. The triplet mechanism is thus completely different from the concerted singlet state cycloaddition processes. The key geometric features and electron spin densities are also discussed. Bulk solvation has a major effect by reducing the barriers and increasing the diradical stabilities. The present results provide a rationale for the faster cycloreaction observed in the singlet excited states than in the triplet excited states.

Computational studies of DNA photolyase

The electron transfer catalyzed (ETC) repair of the DNA photolesion cyclobutane pyrimidine dimer (CPD) is mediated by the enzyme DNA photolyase. Due to its importance as part of the cancer prevention mechanism in many organisms, but also due to its unique mechanism, this DNA photoreactivation is a topic of intense study. The progress in the application of computational methods to three aspects of the ETC repair of CPD is reviewed: (i) electronic structure calculations of the cycloreversion of the CPD radical cation and radical anion, (ii) MD simulations of the DNA photolyase and its complex to photodamaged DNA, and (iii) the structure and dynamics of photodamaged DNA. The contributions of this work to the overall understanding of the reaction and its relationship to the available experimental work are highlighted.

MS-CASPT2 calculation of excess electron transfer in stacked DNA nucleobases

Calculations using the complete active space self-consistent field (CASSCF) and complete active space second-order perturbation (CASPT2) methods, and the multistate formulation of CASPT2 (MS-CASPT2), are performed for the ground and excited states of radical anions consisting of two pi-stacked nucleobases. The electronic couplings for excess electron transfer (EET) in the pi-stacks are estimated by using the generalized Mulliken-Hush approach. We compare results obtained within the different methods with data derived using Koopmans' theorem approximation at the Hartree-Fock level. The results suggest that although the one-electron scheme cannot be applied to calculate electron affinities of nucleobases, it provides reasonable estimates for EET energies. The electronic couplings calculated with KTA lie between the CASPT2 and the MS-CASPT2 based values in almost all cases.

Electron-Transfer Induced Repair of 6-4 Photoproducts in DNA: A Computational Study

The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C-O bond followed by cleavage of the C-C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C-N and C-C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase

More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle. Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme alone is not sufficient to fully understand the enzyme's action on UV-damaged DNA. Much effort has therefore been invested to learn more about, for example, the geometry of the enzyme-substrate complex, and the mechanism and pathways of intra-enzyme and enzyme <-->DNA electron transfer. Many of the key results from biochemical and molecular biology characterizations of the enzyme or the enzyme-substrate complex have been summarized in a number of reviews. Complementary to these articles, this review focuses on recent biophysical studies of photoreactivation comprising work performed from the early 1990s until the present.

Dissociative electron transfer to and from pyrimidine cyclobutane dimers: an electrochemical study

Cyclic voltammetry was used to study the reduction and oxidation behaviour of several pyrimidine cyclobutane dimers mimicking UV induced lesion in DNA strands in polar solvents (N,N-dimethylformamide and acetonitrile). Both electron injection and removal to and from the dimers, respectively, lead to their cleavage and reformation of the monomeric base. The influence of stereochemistry and substitution pattern at the cyclobutane motif on the reactivity has been studied. It appears that the repair process always proceeds in a sequential fashion with initial formation of a dimer ion radical intermediate, which then undergoes ring opening by homolytic cleavage of the two C-C bonds. Standard redox potentials for the formation of both radical anion and radical cation state of the dimers were determined. Quantum calculations on simplified model compounds reveal the reason for the finding that the exergonic homolytic cleavages of the carbon-carbon bonds are endowed with sizeable activation barriers. The consequences of these mechanistic studies on the natural enzymatic repair by photolyase enzyme are discussed.

On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: why are thymines more reactive?

The reaction pathways for thermal and photochemical formation of cyclobutane pyrimidine dimers in DNA are explored using density functional theory techniques. Although it is found that the thermal [2 + 2] cycloadditions of thymine + thymine (T + T --> T x T), cytosine + cytosine (C + C --> C x C) and cytosine + thymine (C + T --> C x T) all are similarly unfavorable in terms of energy barriers and reaction energies, the excited-state energy curves associated with the corresponding photochemical cycloadditions display differences that--in line with experimental findings--unanimously point to the predominance of T x T in UV-irradiated DNA. It is shown that the photocycloaddition of thymines is facilitated by the fact that the S1 state of the corresponding reactant complex lies comparatively high in energy. Moreover, at a nuclear configuration coinciding with the ground-state transition structure, the excited-state energy curve displays an absolute minimum only for the T + T system. Finally, the T + T system is also associated with the most favorable excited-state energy barriers and has the smallest S2-S0 energy gap at the ground-state transition structure.

Thermodynamics, kinetics, and dynamics of the two alternative aniomesolytic fragmentations of C-O bonds: an electrochemical and theoretical study

Fragmentation reactions of radical anions (mesolytic cleavages) of cyanobenzyl alkyl ethers (intramolecular dissociative electron transfer, heterolytic cleavages) have been studied electrochemically. The intrinsic barriers for the processes have been established from the experimental thermodynamic and kinetic parameters. These values are more than 3 kcal/mol lower as an average than the related homolytic mesolytic fragmentations of radical anions of 4-cyanophenyl ethers. In the particular case of isomers 4-cyanobenzyl phenyl ether and 4-cyanophenyl benzyl ether, the difference in intrinsic barriers amounts to 5.5 kcal/mol, and this produces an energetic crossing where the thermodynamically more favorable process (homolytic) is the kinetically slower one. The fundamental reasons for this behavior have been established by means of theoretical calculations within the density functional theory framework, showing that, in this case, the factors that determine the kinetics are clearly different (mainly present in the transition state) from those that determine the thermodynamics and they are not related to the regioconservation of the spin density ("spin regioconservation principle"). Our theoretical results reproduce quite well the experimental energetic difference of barriers and demonstrate the main structural origin of the difference.

Evidence of powerful substrate electric fields in DNA photolyase: implications for thymidine dimer repair

DNA photolyase is a flavoprotein that repairs cyclobutylpyrimidine dimers by ultrafast photoinduced electron transfer. One unusual feature of this enzyme is the configuration of the FAD cofactor, where the isoalloxazine and adenine rings are nearly in vdW contact. We have measured the steady-state and transient absorption spectra and excited-state decay kinetics of oxidized (FAD-containing, folate-depleted) Escherichia coli DNA photolyase with and without dinucleotide and polynucleotide single-stranded thymidine dimer substrates. The steady-state absorption spectrum for the enzyme-polynucleotide substrate complex showed a blue shift, as seen previously by Jorns et al. (1). No shift was observed for the dinucleotide substrate, suggesting that there are significant differences in the binding geometry of dinucleotide versus polynucleotide dimer lesions. Evidence was obtained from transient absorption experiments for a long-lived charge-transfer complex involving the isoalloxazine of the FAD cofactor. No evidence of excited-state quenching was measurable upon binding either substrate. To explain these data, we hypothesize the existence of a large substrate electric field in the cavity containing the FAD cofactor. A calculation of the magnitude and direction of this dipolar electric field is consistent with electrochromic band shifts for both S(0) --> S(1) and S(0) --> S(2) transitions. These observations suggest that the substrate dipolar electric field may be a critical component in its electron-transfer-mediated repair by photolyase and that the unique relative orientation of the isoalloxazine and adenine rings may have resulted from the consequences of the dipolar substrate field.

Oxidative cleavage of a cyclobutane pyrimidine dimer by photochemically generated nitrate radicals (no(3)*)

[reaction: see text] Photochemically generated nitrate radicals (NO(3)(*)) cleave the stereoisomeric N,N-dimethyl-substituted uracil cyclobutane dimers 1a-d into the monomeric uracil derivative 2 as the major reaction pathway. A preferred splitting of the syn dimers 1a,b was observed. The reaction is expected to proceed through initial one-electron oxidation with formation of an intermediate cyclobutane radical cation 11. In addition to cycloreversion, competing reaction steps of 11, which lead to the observed byproducts, are suggested.

Electron Transfer Catalyzed [2 + 2] Cycloreversion of Benzene Dimers

The catalysis of the [2 + 2] cycloreversion of the anti-o,o'-benzene dimer 1 and the syn-o,o'-naphthalene-benzene dimer 2 through thermal and photoinduced electron transfer is studied using experimental and computational methods. The reaction of the radical cations formed by electron transfer is at least 10(5) times faster than the thermal background reaction. It is demonstrated that the photoinduced electron transfer catalyzed reaction proceeds via an electron transfer sensitized pathway and that the observed inverse secondary deuterium isotope effect of 0.91 +/- 0.02 on the reaction is due to the equilibrium isotope effect on the electron transfer step. The relevance of these findings on the mechanism of the electron transfer catalyzed [2 + 2] cycloreversion of the biologically important cis,syn-cyclobutane-thymine dimer is also discussed.