Rapid long-distance hole transfer through consecutive adenine sequence

Long-distance hole transfer via A-hopping over a long A sequence in DNA has been studied by time-resolved transient absorption measurements. DNA modified with naphthalimide (NI) and phenothiazine (PTZ), in which two molecules are separated by a consecutive A sequence, was synthesized to investigate the hole transfer process via A-hopping. After the laser-pulse excitation of NI, an NI radical anion and PTZ radical cation were produced within the laser pulse duration (8 ns) even in the case of an A30 sequence. Hole transfer efficiency from A adjacent to NI to PTZ was weakly distance dependent, showing that the hole transfer process through a consecutive A sequence proceeds via a multistep mechanism. These results clearly suggest that the hole transfer via A-hopping in DNA takes place efficiently and rapidly.     

Mechanism of charge separation in DNA by hole transfer through consecutive adenines

To investigate the mechanism of charge separation in DNA with consecutive adenines adjacent to a photosensitizer (Sens), a series of naphthalimide (NI) and 5-bromouracil ((br)U)-modified DNAs were prepared, and the quantum yields of formation of the charge-separated states (Phi) upon photo-excitation of the Sens NI in DNA were measured. The Phi was modulated by the incorporation site of (br)U, which changes the oxidation potential of its complementary A through hydrogen bonding and the hole-transfer rates between adenines. The results were interpreted as charge separation by means of the initial charge transfer between NI in the singlet excited state and the second- and third-nearest adenine to the NI. In addition, the oxidation of the A nearest to NI leads to the rapid charge recombination within a contact ion pair. This suggests that the charge-separation process can be refined to maximize the Phi by putting a redox-inactive spacer base pair between a photosensitizer and an A-T stretch.     

HOMO energy gap dependence of hole-transfer kinetics in DNA

DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).     

Dynamics and energetics of single-step hole transport in DNA hairpins

The dynamics of single-step hole transport processes have been investigated in a number of DNA conjugates possessing a stilbenedicarboxamide electron acceptor, a guanine primary donor, and several secondary donors. Rate constants for both forward and return hole transport between the primary and secondary donor are obtained from kinetic modeling of the nanosecond transient absorption decay profiles of the stilbene anion radical. The kinetic model requires that the hole be localized on either the primary or the secondary donor and not delocalized over both the primary and the secondary donor. Rate constants for hole transport are found to be dependent upon the identity of the secondary donor, the intervening bases, and the location of the secondary donor in the same strand as the primary donor or in the complementary strand. Rate constants for hole transport are much slower than those for the superexchange process used to inject the hole on the primary donor. This difference is attributed to the larger solvent reorganization energy for charge transport versus charge separation. The hole transport rate constants obtained in these experiments are consistent with experimental data for single-step hole transport from other transient absorption studies. Their relevance to long-distance hole migration over tens of base pairs remains to be determined. The forward and return hole transport rate constants provide equilibrium constants and free energies for hole transport equilibria. Secondary GG and GGG donors are found to form very shallow hole traps, whereas the nucleobase deazaguanine forms a relatively deep hole trap. This conclusion is in accord with selected strand cleavage data and thus appears to be representative of the behavior of holes in duplex DNA. Our results are discussed in the context of current theoretical models of hole transport in DNA.     

Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.     

Photoinduced electron transfer processes in 1,8-naphthalimide-linker-phenothiazine dyads

Photoinduced electron transfer (PET) processes of 1,8-naphthalimide-linker-phenothiazine (NI-L-PTZ) dyads have been investigated using the nanosecond- and picosecond-transient absorption measurements. Two kinds of linker were introduced, i.e., polymethylene-linked dyad (NI-C8-PTZ and NI-C11-PTZ) and a poly(ethyl ether)-linked one (NI-O-PTZ). The 355 nm pulsed laser excitation of NI-C8-PTZ, NI-C11-PTZ, and NI-O-PTZ in acetonitrile produced NI radical anion (NI*-) and PTZ radical cation (PTZ*+) with the absorption bands around 420 and 520 nm, respectively, through charge transfer from PTZ to NI in the singlet excited state (NI(S1)) as well as in the triplet excited states (NI(T1)) in acetonitrile. On the other hand, the charge transfer process occurred only from NI(S1) in nonpolar solvents. The rates of charge transfer and charge recombination processes largely depended on the solvent polarity and they are affected by the length of linkers and electronic coupling through polyether linker. The PET mechanism is discussed in terms of the free energy change for the charge transfer.     

Electron and hole transfer from indium phosphide quantum dots

Electron- and hole-transfer reactions are studied in colloidal InP quantum dots (QDs). Photoluminescence quenching and time-resolved transient absorption (TA) measurements are utilized to examine hole transfer from photoexcited InP QDs to the hole acceptor N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) and electron transfer to nanocrystalline titanium dioxide (TiO2) films. Core-confined holes are effectively quenched by TMPD, resulting in a new approximately 4-ps component in the TA decay. It is found that electron transfer to TiO2 is primarily mediated through surface-localized states on the InP QDs.     

Role of bridge energetics on the preference for hole or electron transfer leading to charge recombination in donor-bridge-acceptor molecules

The impact of donor-acceptor electronic coupling and bridge energetics on the preference for hole or electron transfer leading to charge recombination in a series of donor-bridge-acceptor (D-B-A) molecules was examined. In these systems, the donor is 3,5-dimethyl-4-(9-anthracenyl)-julolidine (DMJ-An) and acceptor is naphthalene-1,8:4,5-bis(dicarboximide) (NI), while the bridges are either oligo(p-phenyleneethynylene) (PE(n)P, where n = 1-3) 1-3 or oligo(2,7-fluorenone) (FN(n), where n = 1-3) 4-6. Photoexcitation of 1-3 and 4-6 produces DMJ(+?)-An-PE(n)P-NI(-?) and DMJ(+?)-An-FN(n)-NI(-?), respectively, which undergo radical pair intersystem crossing followed by charge recombination to yield both (3*)An and (3*)NI, which are observed by time-resolved electron paramagnetic resonance (TREPR) spectroscopy. (3*)NI is produced by hole transfer from DMJ(+?) to NI(-?), while (3*)An is produced by electron transfer from NI(-?) to DMJ(+?), using the agency of the bridge HOMOs and LUMOs, respectively. By monitoring the initial population of (3*)NI and (3*)An in 1-6, the data show that charge recombination occurs preferentially by selective hole transfer when the bridge is PE(n)P, while it occurs by preferential electron transfer when the bridge is FN(n). Over time, the initial population of (3*)NI decreases, while that of (3*)An increases, indicating that triplet-triplet energy transfer (TEnT) occurs. The observed distance dependence of TEnT from (3*)NI to An is weakly exponential with a decay parameter β = 0.08 ?(-1) for the PE(n)P series and β = 0.03 ?(-1) for the FN(n) series. In the PE(n)P series, this weak distance dependence is attributed to a transition from the superexchange regime to hopping transport as the energy gap for triplet energy injection onto the bridge becomes significantly smaller as n increases, while in the FN(n) series the corresponding energy gap is small for all n resulting in triplet energy transport by the hopping mechanism.     

Proton-coupled hole transfer in X-irradiated doped crystalline cytosine.H2O

Following exposure to X-irradiation at low temperatures, the main reactions taking place in single crystals of cytosine monohydrate doped with minute amounts of 2-thiocytosine are hole transfer (HT) from the electron-loss centers to the dopant and recombination of oxidation and reduction products, assumedly by electron transfer. A huge deuterium kinetic isotope effect (KIE; >102-103) at 100 K, together with the kinetic curves obtained and density functional theory (DFT) calculations of equilibrium energy changes, indicates that these reactions proceed through a concerted proton-coupled electron/hole transfer where the proton transfer occurs between hydrogen-bonded cytosine molecules. The temperature dependence of these reaction rates between 10 and 150 K in normal and partially deuterated samples was investigated by monitoring the growth and decay of the various radical species over time using electron paramagnetic resonance (EPR) spectroscopy. By assuming a random distribution of the hole donors and acceptors in the crystals, the data are consistent with an exponential distance-dependent rate, giving a distance decay constant (beta) around 1 A-1 for the HT, which indicates that a long-range single-step superexchange mechanism mediates the charge transfer. The reactions undergo a transition from a slow, weakly temperature-dependent rate to an Arrhenius-type rate at 40-50 K, presumably being activated by excitation of low-frequency intermolecular vibrations that couple to the process. Below this transition temperature, the transfer probability might be dominated by temperature-independent nuclear tunneling. A similar beta value in both temperature regions suggests that hopping is not activated.     

On the Mechanism of Long-Range Electron Transfer through DNA

Hopping between bases of similar redox potentials is the mechanism by which charge transport occurs through DNA. This was shown by rate measurements performed with double strands 1 – 3 . This mechanism explains why hole transfer displays a strong sequence dependence, and postulates that electron transfer in unperturbed DNA should not be dependent on the sequence.     

Competition between superexchange-mediated and sequential electron transfer in a bridged donor-acceptor system

The temperature- and solvent-dependence of photoinduced electron-transfer reactions in a porphyrin-based donor-bridge-acceptor (DBA) system is studied by fluorescence and transient absorption spectroscopy. Two competing processes occur: sequential and direct superexchange-mediated electron transfer. In a weakly polar solvent (2-methyltetrahydrofuran), only direct electron transfer from the excited donor to the appended acceptor is observed, and this process has weak temperature dependence. In polar solvents (butyronitrile and dimethylformamide), both processes are observed and the sequential electron transfer shows strong temperature dependence. In systems where both electron transfer processes are observed, the long-range superexchange-mediated process is more than two times faster than the sequential process, even though the donor-acceptor distance is significantly larger in the former case.     

Kinetics of weak distance-dependent hole transfer in DNA by adenine-hopping mechanism

The kinetics of hole transfer in DNA by adenine-hopping mechanism was investigated by the combined pulse radiolysis-laser flash photolysis method. The hole transfer from Ptz*+* to oxG across the (A)n-bridge preceded by the A-hopping mechanism and the weak distance-dependent hole transfer with the rates faster than 108 s-1 over the distance range of 7-22 A was demonstrated. In contrast, hole transfer from oxG*+ to Ptz followed the single-step super exchange mechanism. Thus, two different processes for the hole transfer across the identical (A)n-bridge in DNA have been demonstrated. The results clearly show that the mechanism of hole transfer in DNA strongly depends on the redox nature of the oxidant, whether it produces only G*+ or both A*+ and G*+.     

Electron Transfer Reaction Between Desoxyadenosine and Triplet 2-Methyl-1,4-naphthaquinone:A Laser Photolysis Study

Introduction ElectrontransferoxidationofDNAbytripletartifi cialphotonucleaserevealsabrightprospectofitsappli cationinbiologyandmedicine.Bothmolecularorbital calculationandlaserexperimentshaveindicatedthat thehomoguaninesequenceshouldbethefinallocaliza tio…     

A Charge‐Stabilizing,Multimodular, Ferrocene–Bis(triphenylamine)–Zinc‐porphyrin–Fullerene Polyad

A novel multimodular donor–acceptor polyad featuring zinc porphyrin, fullerene, ferrocene, and triphenylamine entities was designed, synthesized, and studied as a charge‐stabilizing, photosynthetic‐antenna/reaction‐center mimic. The ferrocene and fullerene entities, covalently linked to the porphyrin ring, were distantly separated to accomplish the charge‐separation/hole‐migration events leading to the creation of a long‐lived charge‐separated state. The geometry and electronic structures of the newly synthesized compound was deduced by B3LYP/3‐21G(*) optimization, while the energy levels for different photochemical events was established using data from the optical absorption and emission, and electrochemical studies. Excitation of the triphenylamine entities revealed singlet‐singlet energy transfer to the appended zinc porphyrin. As predicted from the energy levels, photoinduced electron transfer from both the singlet and triplet excited states of the zinc porphyrin to fullerene followed by subsequent hole migration involving ferrocene was witnessed from the transient absorption studies. The charge‐separated state persisted for about 8.5 μs and was governed by the distance between the final charge‐transfer product, that is, a species involving a ferrocenium cation and a fullerene radical anion, with additional influence from the charge‐stabilizing triphenylamine entities located on the zinc‐porphyrin macrocycle.     

A novel 1,8-naphthalimide probe: synthesis and interactions with nucleic acid and its precursor

Three novel, water-soluble N-substituted 1,8-naphthalimides as the spectroscopic probes of nucleic acid, N-(2-hydroxyethyl)-1,8-naphthalimide (NI1), 1,8-naphthalimide-N-acetic acid (NI2) and 1,8-naphthalimide-N-caproic acid (NI3), were synthesized and photophysically characterized. The steady-state fluorescence quenching of the NI probes with nucleic acids (NA) and their precursors (nucleobases and nucleosides) were studied by Stern–Volmer correlation. The rate constants for bimolecular quenching were obtained in Tris buffer solution. The transient absorption spectroscopy by nanosecond laser flash photolysis were explored to identify the transient species and to determine the kinetics. The dynamic interaction mechanism was attributed to electron transfer (ET) and energy transfer via ³NI.     

Intermolecular photoinduced electron-transfer of 1,8-naphthalimides in protic polar solvents

The intermolecular photoinduced electron transfer (PET) processes of 1,8-naphthalimide (NI) derivatives including NI-linker-phenothiazine dyads were investigated in a protic H(2)O/CH(3)CN (v/v=1:1) solvent using ns-laser flash photolysis with 355 nm-laser excitation. NI derivatives are surrounded by H(2)O in the ground state in H(2)O/CH(3)CN. The T(1)-T(n) absorption band of (3)NI* was observed at around 470 nm. The transient absorption band at around 410 nm increased concomitantly with the decay of (3)NI* in H(2)O/CH(3)CN. This implies that hydrated NI anion radical (NI*(-)) is primarily generated via the quenching of (3)NI* by NI at the diffusion control rate. This intermolecular PET did not occur in aprotic CH(3)CN. The formation and decay times of NI*(-) showed strong dependence on the concentration of NI. Then, we suggest that NI*(-) could undergo proton abstraction to give ketyl radical species of NI [NI(H)*] in H(2)O/CH(3)CN.     

Hydrogen Bonding Effects on the Photophysical Properties of 2,3-dihydro-3-keto-1H-pyrido[3,2,1-kl]phenothiazine

Time-dependent density functional theory (TDDFT) and femtosecond transient absorption spectroscopy were used to investigate the photophysical properties of 2,3-dihydro-3-keto-1H-pyrido[3,2,1-kl]phenothiazine (PTZ4) and 3-keto-1H-pyrido[3,2,1-kl]phenothiazine (PTZ5). The calculated results obtained from TDDFT suggest that the red-shifts of the absorption spectra of these two fluorophores in methanol are due to the formation of hydrogen-bonded complexes at the ground state. Four conformers of PTZ4 were obtained by TDDFT. The two fluorescence peaks of PTZ4 in tetrahydrofuran (THF) came from the ICT states of the four conformers. The fluorescence of PTZ4 in THF showed a dependence on the excitation wavelength because of butterfly bending. The excited state dynamics of PTZ4 in THF and methanol were obtained by transient absorption spectroscopy. The lifetime of the excited PTZ4 in methanol was 53.8 ps, and its relaxation from the LE state to the ICT state was completed within several picoseconds. The short lifetime of excited PTZ4 in methanol was due to the formation of out-of-plane model hydrogen bonds between PTZ4 and methanol at the excited state.     

Base sequence effects on transport in DNA

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.     

Exponential distance dependence of photoinitiated stepwise electron transfer in donor-bridge-acceptor molecules: implications for wirelike behavior

Donor-bridge-acceptor (D-B-A) systems in which a 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) chromophore and a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor are linked by oligomeric 2,7-fluorenone (FN(n)) bridges (n = 1-3) have been synthesized. Selective photoexcitation of DMJ-An quantitatively produces DMJ(+?)-An(-?), and An(-?) acts as a high-potential electron donor. Femtosecond transient absorption spectroscopy in the visible and mid-IR regions showed that electron transfer occurs quantitatively in the sequence: DMJ(+?)-An(-?)-FN(n)-NI → DMJ(+?)-An-FN(n)(-?)-NI → DMJ(+?)-An-FN(n)-NI(-?). The charge-shift reaction from An(-?) to NI(-?) exhibits an exponential distance dependence in the nonpolar solvent toluene with an attenuation factor (β) of 0.34 ?(-1), which would normally be attributed to electron tunneling by the superexchange mechanism. However, the FN(n)(-?) radical anion was directly observed spectroscopically as an intermediate in the charge-separation mechanism, thereby demonstrating conclusively that the overall charge separation involves the incoherent hopping (stepwise) mechanism. Kinetic modeling of the data showed that the observed exponential distance dependence is largely due to electron injection onto the first FN unit followed by charge hopping between the FN units of the bridge biased by the distance-dependent electrostatic attraction of the two charges in D(+?)-B(-?)-A. This work shows that wirelike behavior does not necessarily result from building a stepwise, energetically downhill redox gradient into a D-B-A molecule.