Hole and excess electron transfer dynamics in DNA

Charge transfer in DNA attracts substantial attention from researchers in a wide group of fields such as bioscience, nanotechnology and physical chemistry. It is well known that both positive and negative charges, which are holes and excess electrons, respectively, contribute to the charge transfer in DNA. In the case of hole transfer in DNA, detailed mechanisms and dynamical parameters have been estimated by means of time-resolved spectroscopic methods and product analysis. On the other hand, detailed dynamics of excess electron transfer have not been established yet, although several aspects have been revealed by the continuous efforts of various research groups. In the present Perspective, studies on the charge transfer dynamics in DNA are summarized.     

A model for electrochemical electron transfer with strong electronic coupling

Electron exchange between a metal or semiconducting electrode and a solvated reactant is calculated by Green-function techniques. In the wide band approximation the time development of a system prepared in a definite electronic state can be calculated exactly. The results are valid for all coupling strengths, and are applied both to photoexcited and to thermally-induced transfer.     

Estimation of electronic coupling for intermolecular electron transfer from cross-reaction data

Sixty-five electron-transfer reactions including 27 new 0, +1 couples have been added to our data set of cross-reactions between 0 and +1 couples, bringing it to 206 reactions involving 72 couples that have been studied by stopped-flow kinetics in acetonitrile containing supporting electrolyte at 25 degrees C, formal potentials determined by cyclic voltammetry, and analyzed using Marcus cross-rate theory. Perhaps surprisingly, a least-squares analysis demonstrates that intrinsic rate constants exist that predict the cross-rate constants to within a factor of 2 of the observed ones for 93% of the reactions studied, and only three of the reactions have a cross-rate constant that lies outside of the factor of 3, that corresponds to a factor of 10 uncertainty in the rate constant for an unknown couple. Many triarylamines, which have very high intrinsic reactivity, are included among the newly studied couples. The enthalpy contribution to the Marcus reorganization energy, lambda'v, has been calculated for 46 of the couples studied, at the (U)B3LYP/6-31+G (or for the larger and lower barrier compounds, at the less time-consuming (U)B3LYP/6-31G) level. In combination with a modified Levich and Dogodnadze treatment that assumes that the rate constant is proportional to (KeHab2/lambda1/2) exp[-DeltaG/RT], this allows estimation of the electronic coupling (Hab) at the transition state for intermolecular electron transfer, (more properly H'ab, the product of the square root of the encounter complex formation constant times Hab) for these couples. Although the principal factor affecting intermolecular electron-transfer rate constants is clearly lambda, H'ab effects are easily detectable, and the dynamic range in our estimates of them is over a factor of 600.     

Reductive electron transfer and transport of excess electrons in DNA

In principle, DNA-mediated charge transfer processes can be categorized as either oxidative hole transfer or reductive electron transfer. In research on DNA damage, major efforts have focused on the investigation of oxidative hole transfer or transport, resulting in insights on the mechanisms. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology. Yet the mechanistic details of this type of charge transfer chemistry were unclear. In the last two years this mechanism has been addressed in gamma-pulse radiolysis studies with randomly DNA-bound electron acceptors or traps. The major disadvantage of this experimental setup is that the electron injection and trapping is not site-selective. More recently, new photochemical assays for the chemical and spectroscopic investigation of reductive electron transfer and electron migration in DNA have been published which give new insights into these processes. Based on these results, an electron-hopping mechanism is proposed which involves pyrimidine radical anions as intermediate electron carriers.     

Efficient interstrand excess electron transfer in PNA:DNA hybrids

PNA:DNA strands were prepared containing a flavin electron donor and a thymine dimer acceptor, which gives a strand break upon single electron reduction. With these constructs, it was confirmed that an excess electron transfer through the base stack can be efficient in an interstrand fashion. The effect of an increased distance, a changed sequence, and stacking was explored.     

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.     

Investigation of the pathways of excess electron transfer in DNA with flavin-donor and oxetane-acceptor modified DNA hairpins

Oxetane is a potential intermediate that is enzymatically formed during the repair of (6-4) DNA lesions by special repair enzymes (6-4 DNA photolyases). These enzymes use a reduced and deprotonated flavin to cleave the oxetane by single electron donation. Herein we report synthesis of DNA hairpin model compounds containing a flavin as the hairpin head and two different oxetanes in the stem structure of the hairpin. The data show that the electron moves through the duplex even over distances of 17 A. Attempts to trap the moving electron with N2O showed no reduction of the cleavage efficiency showing that the electron moves through the duplex and not through solution. The electron transfer is sequence dependent. The efficiency is reduced by a factor of 2 in GC rich DNA hairpins.     

Parameters for excess electron transfer in DNA. Estimation using unoccupied Kohn-Sham orbitals and TD DFT

We show that the energetics and electronic couplings for excess electron transfer (EET) can be accurately estimated by using unoccupied Kohn-Sham orbitals (UKSO) calculated for neutral pi stacks. To assess the performance of different DFT functionals, we use MS-PT2 results for seven pi stacks of nucleobases as reference data. The DFT calculations are carried out by using the local spin density approximation SVWN, two generalized gradient approximation functionals BP86 and BLYP, and two hybrid functionals B3LYP and BH&HLYP. Best estimations within the UKSO approach are obtained by the B3LYP and SVWN methods. TD DFT calculations provide less accurate values of the EET parameters as compared with the UKSO data. Also, the excess charge distribution in the radical anions is well described by the LUMOs of neutral systems. In contrast, spin-unrestricted DFT calculations of radical anions considerably overestimate delocalization of the excess electron. The excellent results obtained for the ground and excited states of the radical anions (excitation energy, transition dipole moment, electronic coupling, and excess electron distribution) by using UKSO of neutral dimers suggest an efficient strategy to calculate the EET parameters for DNA pi stacks.     

Semiclassical treatments of electron transfer rate from weak to strong electronic coupling regime

Electron transfer (ET) rate is a fundamental parameter to characterize ET processes in physical, chemical, material and biologic sciences. It is affected by a number of quantum phenomena, such as nuclear tunneling, curve crossing, quantum interference, and the coupling to the environment. It is thus a challenge to accurately evaluate the ET rate since one has to incorporate both quantum effects and dissipation. In this review article, we present several semiclassical theories proposed in our group to cover the regime from weak to strong electronic coupling. Their applications to some concrete systems are also shown.     

Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA

Charge transfer in DNA is an essential process in biological systems because of its close relation to DNA damage and repair. DNA is also an important material used in nanotechnology for wiring and constructing various nanomaterials. Although hole transfer in DNA has been investigated by various researchers and the dynamic properties of this process have been well established, the dynamics of a negative charge, that is, excess electron, in DNA have not been revealed until now. In the present paper, we directly measured the rate of excess electron transfer (EET) through a consecutive thymine (T) sequence in nicked-dumbbell DNAs conjugated with a tetrathiophene derivative (4T) as an electron donor and diphenylacetylene (DPA) as an electron acceptor at both ends. The selective excitation of 4T by a femtosecond laser pulse caused the excess electron injection into DNA, and led to EET in DNA by a consecutive T-hopping mechanism, which eventually formed the DPA radical anion (DPA(?-)). The rate constant for the process of EET through consecutive T was determined to be (4.4 ± 0.3) × 10(10) s(-1) from an analysis of the kinetic traces of the ΔO.D. during the laser flash photolysis. It should be emphasized that the EET rate constant for T-hopping is faster than the rate constants for oxidative hole transfers in DNA (10(4) to 10(10) s(-1) for A- and G-hopping).     

Excited-state electronic coupling and photoinduced multiple electron transfer in two related ligand-bridged hexanuclear mixed-valence compounds

The synthesis, characterization, electrochemical, photophysical, and photochemical properties of two hexanuclear mixed-valence compounds are reported. Each supramolecular species consists of two cyano-bridged [(NC)(5)Fe(II)-CN-Pt(IV)(NH(3))(3)L-NC-Fe(II)(CN)(5)] triads that are linked to each other through a Pt(IV)-L-Pt(IV) bridge, where L = 4,4'-dipyridyl (bpy) or 3,3'-dimethyl-4,4'-dipyridyl (dmb). The major difference between the two compounds is the electronic nature of the bridging ligand between the two Pt atoms. Both species exhibit a broad Fe(II) --> Pt(IV) intervalent (IT) absorption band at 421 nm with an oscillator strength that is approximately four times that for [(NC)(5)Fe(II)-CN-Pt(IV)(NH(3))(5)] and twice that for [(NC)(5)Fe(II)-CN-Pt(IV)(NH(3))(4)-NC-Fe(II)(CN)(5)].(4-) When L = bpy, the resonance Raman spectrum obtained by irradiating the IT band at 488 nm exhibits several dipyridyl ring modes at 1604, 1291, and 1234 cm(-1) which are not present in the spectrum when L = dmb. In addition, femtosecond pump-probe spectroscopy performed at 400 nm yields a transient bleach of the IT absorption band with a single exponential decay of 3.5 ps for L = bpy, compared with only 1.8 ps for L = dmb and 2.1 ps for [(NC)(5)Fe(II)-CN-Pt(IV)(NH(3))(4)-NC-Fe(II)(CN)(5)].(4-) Last, prolonged irradiation of the complexes at 488 nm leads to the formation of 4 equiv of ferricyanide with a quantum efficiency of 0.0014 for L = bpy and 0.0011 for L = dmb. The transient absorption, resonance Raman, and photochemical data suggest that the degree of excited electronic coupling in these compounds is tunable by changing the electronic nature of the Pt-L-Pt bridging ligand.     

Driving force and electronic coupling effects on photoinduced electron transfer in a fullerene-based molecular triad

Tuning thermodynamic driving force and electronic coupling through structural modifications of a carotene (C) porphyrin (P) fullerene (C60) molecular triad has permitted control of five electron and energy transfer rate constants and two excited state lifetimes in order to prepare a high-energy charge-separated state by photoinduced electron transfer with a quantum yield of essentially unity (> or = 96%). Excitation of the porphyrin moiety of C-P-C60 is followed by a combination of photoinduced electron transfer to give C-P(.+)-C60.- and singlet-singlet energy transfer to yield C-P-1C60. The fullerene excited state accepts an electron from the porphyrin to also generate C-P(.+)-C60.-. Overall, this initial state is formed with a quantum yield of 0.97. Charge shift from the carotenoid to yield C(.+)-P-C60.- is at least 60 times faster than recombination of C-P(.+)-C60.-, leading to the overall quantum yield near unity for the final state. Formation of a similar charge-separate species from the zinc analog of the triad with a yield of 40% is also observed. Charge recombination of C(.+)-P-C60.- in 2-methyltetrahydrofuran yields the carotenoid triplet state, rather than the ground state. Comparison of the results for this triad with those for related triads with different structural features provides information concerning the effects of driving force and electronic coupling on each of the electron transfer steps.     

Probing the contribution of electronic coupling to the directionality of electron transfer in photosynthetic reaction centers

Subpicosecond transient absorption studies are reported for a set of Rhodobacter (R.) capsulatus bacterial photosynthetic reaction centers (RCs) designed to probe the origins of the unidirectionality of charge separation via one of two electron transport chains in the native pigment-protein complex. All of the RCs have been engineered to contain a heterodimeric primary electron donor (D) consisting of a bacteriochlorophyll (BChl) and a bacteriopheophytin (BPh). The BPh component of the M heterodimer (Mhd) or L heterodimer (Lhd) is introduced by substituting a Leu for His M200 or His L173, respectively. Previous work on primary charge separation in heterodimer mutants has not included the Lhd RC from R. capsulatus, which we report for the first time. The Lhd and Mhd RCs are used as controls against which we assess RCs that combine the heterodimer mutations with a second mutation (His substituted for Leu at M212) that results in replacement of the native L-side BPh acceptor with a BChl (beta). The transient absorption spectra reveal clear evidence for charge separation to the normally inactive M-side BPh acceptor (H(M)) in Lhd-beta RCs to form D+H(M)- with a yield of approximately 6%. This state also forms in Mhd-beta RCs but with about one-quarter the yield. In both RCs, deactivation to the ground state is the predominant pathway of D decay, as it is in the Mhd and Lhd single mutants. Analysis of the results indicates an upper limit ofV2L/V2m < or = 4 for the contribution of the electronic coupling elements to the relative rates of electron transfer to the L versus M sides of the wild-type RC. In comparison to the L/M rate ratio (kL/kM) approximately 30 for wild-type RCs, our findings indicate that electronic factors contribute approximately 35% at most to directionality with the other 65% deriving from energetic considerations, which includes differences in free energies, reorganization energies, and contributions of one- and two-step mechanisms on the two sides of the RC.     

Photoinduced reductive repair of thymine glycol: implications for excess electron transfer through DNA containing modified bases

Photoinduced reduction of thymine glycol in oligodeoxynucleotides was investigated using either a reduced form of flavin adenine dinucleotide (FADH(-)) as an intermolecular electron donor or covalently linked phenothiazine (PTZ) as an intramolecular electron donor. Intermolecular electron donation from photoexcited flavin (FADH(-)) to free thymidine glycol generated thymidine in high yield, along with a small amount of 6-hydroxy-5,6-dihydrothymidine. In the case of photoreduction of 4-mer long single-stranded oligodeoxynucleotides containing thymine glycol by *FADH(-), the restoration yield of thymine was varied depending on the sequence of oligodeoxynucleotides. Time-resolved spectroscopic study on the photoreduction by laser-excited N,N-dimethylaniline (DMA) suggested elimination of a hydroxyl ion from the radical anion of thymidine glycol with a rate constant of approximately 10(4) s(-1) generates 6-hydroxy-5,6-dihydrothymidine (6-HOT(*)) as a key intermediate, followed by further reduction of 6-HOT(*) to thymidine or 6-hydroxy-5,6-dihydrothymdine (6-HOT). On the other hand, an excess electron injected into double-stranded DNA containing thymine glycol was not trapped at the lesion but was further transported along the duplex. Considering redox properties of the nucleobases and PTZ, competitive excess electron trapping at pyrimidine bases (thymine, T and cytosine, C) which leads to protonation of the radical anion (T(-)(*), C(-)(*)) or rapid back electron transfer to the radical cation of PTZ (PTZ(+)(*)), is presumably faster than elimination of the hydroxyl ion from the radical anion of thymine glycol in DNA.     

Theory and calculation for the electronic coupling in excitation energy transfer

Excitation energy transfer (EET) is a process where the electronically excitation is transferred from a donor to an acceptor. EET is widely seen in both natural and in artificial systems, such as light‐harvesting in photosynthesis, the fluorescence resonance energy transfer technique, and the design of light‐emitting molecular devices. In this work, we outline the theories describing both singlet and triplet EET (SEET and TEET) rates, with a focus on the physical nature and computational methods for the electronic coupling factor, an important parameter in predicting EET rates. The SEET coupling is dominated by the Coulomb coupling, and the remaining short‐range coupling is very similar to the TEET coupling. The magnitude of the Coulomb coupling in SEET can vary much, but the contribution of short‐range coupling has been found to be similar across different excited states in naphthalene. The exchange coupling has been believed to be the major physical contribution to the short‐range coupling, but it has been pointed out that other contribution, such as the orbital overlap effect is similar or even larger in strength. The computational aspects and the subsequent physical implication for both SEET and TEET coupling values are summarized in this work. © 2013 The Authors. International Journal of Quantum Chemistry Published by Wiley Periodicals, Inc.     

Conformer-dependent electronic coupling for long-range triplet energy transfer in donor-bridge-acceptor porphyrin dimers

The electronic coupling for triplet energy transfer is calculated by time-dependent density functional theory (TD-DFT) for a set of tri-chromophoric systems based on a zinc(II) porphyrin donor and the corresponding free base acceptor covalently connected by different hydrocarbon bridging chromophores. The calculated electronic coupling, for systems with identical donor acceptor distances, is sensitive to the bridge electronic structure and shows a significant dependence for the bridge and donor-bridge conformations. The computational results compare quantitatively to measurements of triplet energy transfer rates in the corresponding donor-bridge-acceptor systems.     

DNA double-helix-mediated long-range electron transfer

A theoretical analysis based upon large-scale self-consistent Hartree-Fock calculations at a semiempirical quantum theory level (CNDO/S) is performed to investigate long-range electron transfer in a donor-DNA-acceptor molecule, where the donor and acceptor moieties are tethered to the DNA. The π-stacked base pairs are found to dominate the long-range electronic coupling. Despite the π-electron mediated coupling, the exponential distance decay constant of the electron transfer rate is ∼ 1.2–1.6 Å⁻¹, values typical of electron transfer proteins. The calculated long-range electron transfer rate of the order of 10⁶ s⁻¹ for a metal-to-metal distance of 21 Å is found to be in agreement with kinetic measurements by Meade and Kayyem. Based on the current analysis, the π-electrons dominate the long-range electronic coupling interactions in DNA, but they do not lead to one-dimensional molecular wire-like properties. © 1996 John Wiley & Sons, Inc.     

Compatible injection and detection systems for studying the kinetics of excess electron transfer

[reaction: see text] A design for fast kinetic studies of electron transfer in radical anions is reported. alpha-Hydroxy radicals formed by 355 nm laser flash photolysis of alpha-phenacyl alcohols are deprotonated under basic conditions to give ketyl radical anions that serve as electron injectors in inter- and intramolecular electron-transfer reactions. The 2,2-diphenylcyclopropyl group serves as a reporter. When an electron is injected and transferred such that spin character is adjacent to the reporter, cyclopropyl ring opening gives a readily detected diphenylalkyl radical.     

Triplet state mechanism for electron transfer oxidation of DNA

The interaction of anthraquinone-2-sulfonate with nucleotides and DNA in acetonitrile and acetonitrile water solvent mixture have been studied using KrF laser photolysis aimed at elucidation of the reaction mechanism. Laser spectroscopy directly demonstrates that the initial species from interaction of anthraquinone-2-sulfonate with nucleotides are radical cations of nucleotides and radical anion of anthraquinone-2-sulfonate. In addition, formation of ion pair from interaction of any of nucleotides with anthraquinone-2-sulfonate is synchronous with decay of triplet anthraquinone-2-sulfonate, which has provided dynamic evidence for initiation of electron transfer from DNA bases to triplet anthraquinone-2-sulfonate. Moreover, direct observation of stabilized DNA guanyl radical cation from interaction of anthraquinone-2-sulfonate with DNA has provided initial evidence for selective cleavage of DNA at guanine moiety. The solvent-separated ion pairs in acetonitrile have evidently dissociated into free ions, thereby enabling independent study of the behavior of guanyl radical cations and radical anion of anthraquinone-2-sulfonate.