Contributions of the distance-dependent reorganization energy and proton-transfer to the hole-transfer process in DNA

A kinetic study of the single-step hole transfer in DNA was performed by measuring time-resolved transient absorption. DNA molecules with various sequences were designed and conjugated with naphthalimide (NI) and phenothiazine (PTZ) to investigate the sequence and distance dependence of the single-step hole transfer between guanines (Gs). Hole injection into DNA was accomplished by excitation of the NI site with a 355 nm laser pulse, and the kinetics of the hole-transfer process were investigated by monitoring the transient absorption of the PTZ radical cation (PTZ.+). Kinetic analysis of the time profile of PTZ.+ based on the kinetic model showed that the distance dependence of the hole-transfer process was significantly influenced by the DNA sequence. Results of temperature- and isotope-effect experiments demonstrated that the activation energy increased as the number of bridge bases separating the Gs increased. This is because of the distance-dependent reorganization energy and contribution of the proton-transfer process to the hole transfer in DNA.     

Charge separation in DNA via consecutive adenine hopping

Charge transfer in DNA is of current interest because of the involvement of charge transfer in oxidative DNA damage and electronic molecular devices. We have investigated the charge separation process via the consecutive adenine (A)-hopping mechanism using laser flash photolysis of DNA conjugated with naphthaldiimide (NDI) as an electron acceptor and phenothiazine (PTZ) as a donor. Upon the 355-nm laser flash excitation of NDI, the charge separation and recombination process between NDI and PTZ was observed. The yields of the charge separation via the consecutive A-hopping were slightly dependent upon the number of A bases between the two chromophores, while the charge recombination rate was strongly dependent upon the distance. The charge-separated state persisted over 300 micros when NDI was separated from PTZ by eight A bases. Furthermore, the rate constant of the A-hopping process was determined to be 2 x 10(10) s(-1) from an analysis of the yield of the charge separation depending on the number of A-hopping steps.     

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.     

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*+.     

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).     

Hole transfer in DNA and photosensitized DNA damage: importance of adenine oxidation

Photosensitized DNA damage reactions were investigated for two well-known DNA-damaging photosensitizers (Sens), naphthalimide (NI) and napthaldiimide (NDI), which have similar photophysical properties but differ in their redox properties. NI and NDI derivatives (NIN, NDIN), which have cationic side chains and electrostatically binding to DNA due to favorable electrostatic interactions between the negatively charged phosphate groups of DNA and cationic groups, and NIP and NDIP, which possess phosphate groups and do not bind to DNA, were synthesized. NIN and NDIN can oxidize A and G via their singlet excited state, and NDIP oxidizes A and G via its triplet excited state, whereas NIP oxidizes only G. A combination of laser flash photolysis kinetic studies and quantitative HPLC analyses of photosensitized DNA damage was performed for several DNA sequences in the presence of Sens. NIN, NDIN, and NDIP, which oxidizes A, caused significant DNA damage upon photoirradiation, and DNA damage yield increased with the length of the consecutive A stretch. In contrast, NIP, which oxidizes only G, caused only moderate damage to DNA and showed no preference for the consecutive A sequences. These results clearly demonstrate the importance of A-oxidation, especially in consecutive A sequences, which triggers the rapid hole transfer between A's.     

Highly oxidizing excited states of one-electron-oxidized guanine in DNA: wavelength and pH dependence

Excited states of one-electron-oxidized guanine in DNA are known to induce hole transfer to the sugar moiety and on deprotonation result in neutral sugar radicals that are precursors of DNA strand breaks. This work carried out in a homogeneous aqueous glass (7.5 M LiCl) at low temperatures (77-175 K) shows the extent of photoconversion of one-electron-oxidized guanine and the associated yields of individual sugar radicals are crucially controlled by the photon energy, protonation state, and strandedness of the oligomer. In addition to sugar radical formation, highly oxidizing excited states of one-electron-oxidized guanine are produced with 405 nm light at pH 5 and below that are able to oxidize chloride ion in the surrounding solution to form Cl(2)(?-) via an excited-state hole transfer process. Among the various DNA model systems studied in this work, the maximum amount of Cl(2)(?-) is produced with ds (double-stranded) DNA, where the one-electron-oxidized guanine exists in its cation radical form (G(?+):C). Thus, via excited-state hole transfer, the dsDNA is apparently able to protect itself from cation radical excited states by transfer of damage to the surrounding environment.     

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.     

Direct observation of the preference of hole transfer over electron transfer for radical ion pair recombination in donor-bridge-acceptor molecules

Understanding how the electronic structures of electron donor-bridge-acceptor (D-B-A) molecules influence the lifetimes of radical ion pairs (RPs) photogenerated within them (D+*-B-A-*) is critical to designing and developing molecular systems for solar energy conversion. A general question that often arises is whether the HOMOs or LUMOs of D, B, and A within D+*-B-A-* are primarily involved in charge recombination. We have developed a new series of D-B-A molecules consisting of a 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) electron donor linked to a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor via a series of Phn oligomers, where n = 1-4, to give DMJ-An-Phn-NI. The photoexcited charge transfer state of DMJ-An acts as a high-potential photoreductant to rapidly and nearly quantitatively transfer an electron across the Phn bridge to produce a spin-coherent singlet RP 1(DMJ+*-An-Phn-NI-*). Subsequent radical pair intersystem crossing yields 3(DMJ+*-An-Phn-NI-*). Charge recombination within the triplet RP then gives the neutral triplet state. Time-resolved EPR spectroscopy shows directly that charge recombination of the RP initially produces a spin-polarized triplet state, DMJ-An-Phn-3*NI, that can only be produced by hole transfer involving the HOMOs of D, B, and A within the D-B-A system. After the initial formation of DMJ-An-Phn-3*NI, triplet-triplet energy transfer occurs to produce DMJ-3*An-Phn-NI with rate constants that show a distance dependence consistent with those determined for charge separation and recombination.     

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.     

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

Introduction ElectrontransferoxidationofDNAbytripletartifi cialphotonucleaserevealsabrightprospectofitsappli cationinbiologyandmedicine.Bothmolecularorbital calculationandlaserexperimentshaveindicatedthat thehomoguaninesequenceshouldbethefinallocaliza tio…     

Lifetime regulation of the charge-separated state in DNA by modulating the oxidation potential of guanine in DNA through hydrogen bonding

A series of naphthalimide (NI)- and 5-bromocytosine ((br)C)-modified oligodeoxynucleotides (ODNs) were prepared, and their lifetimes of the charge-separated states during the photosensitized one-electron oxidation of DNA were measured. Various lifetimes of the charge-separated states were observed depending on the sequence and the incorporation sites of (br)C, and the oxidation potential of G in the (br)C:G base-pair relative to that of G in the C:G base-pair and in the GGG sequence was determined by comparing the lifetimes of the charge-separated states. The change in the cytosine C5 hydrogen to bromine resulted in a 24 mV increase in the oxidation potential of G in the (br)C:G base-pair as compared to that of G in the C:G base-pair, the value of which is comparable to a 58 mV decrease in the oxidation potential of G in the GGG sequence. These results clearly demonstrate that hole transfer in DNA can be controlled through hydrogen bonding by introducing a substituent on the cytosine.     

Intramolecular exciplex and intermolecular excimer formation of 1,8-naphthalimide-linker-phenothiazine dyads

Steady-state fluorescence spectra were measured for 1,8-naphthahlimide-linker-phenothiazine dyads (NI-L-PTZ, where L = octamethylenyl ((CH2)8) and 3,6,9-trioxaundecyl ((CH2CH2O)3C2H4)), NI-C8-PTZ and NI-O-PTZ, as well as the NI derivatives substituted on the nitrogen atom with various linker groups without PTZ as the reference NI molecule in n-hexane. Normal fluorescence peaks were observed at 367-369 nm in all NI molecules together with a broader emission around 470 nm, which is assigned to the excimer emission between the NI in the singlet excited state (1NI*) and the NI moiety of another NI molecule (1[NI/NI]*). In addition, a broad peak around 600 nm was observed only for NI-L-PTZ, which is assigned to an intramolecular exciplex emission between donor (PTZ) and acceptor (NI) moieties in the excited singlet state, 1[NI-L-NI]*. The formation of an intramolecular exciplex corresponds to the existence of a conformer with a weak face-to-face interaction between the NI and PTZ moieties in the excited state because of the long and flexible linkers. The excited-state dynamics of the NI molecules in n-hexane were established by means of time-resolved fluorescence spectroscopy.     

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.     

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.     

Synthesis and photooxidation of oligodeoxynucleotides containing 5-dimethylaminocytosine as an efficient hole-trapping site in the positive-charge transfer through DNA duplexes

We have designed and synthesized DNA duplexes containing 5-dimethylaminocytosine ((DMA)C) to investigate the effects of C(5)-substituted cytosine bases on the transfer and trapping of positive charge (holes) in DNA duplexes. Fluorescence quenching experiments revealed that a (DMA)C base is more readily one-electron oxidized into a radical cation intermediate as compared with other natural nucleobases. Upon photoirradiation of the duplexes containing (DMA)C, the photosensitizer-injected hole migrated through the DNA bases and was trapped efficiently at the (DMA)C sites, where an enhanced oxidative strand cleavage occurred by hot piperidine treatment. The (DMA)C radical cation formed by hole transfer may undergo specific hydration and subsequent addition of molecular oxygen, thereby leading to its decomposition followed by a predominant strand cleavage at the (DMA)C site. This remarkable property suggests that the modified cytosine (DMA)C can function as an efficient hole-trapping site in the positive-charge transfer in DNA duplexes.     

Ruthenium-phenothiazine electron transfer dyad with a photoswitchable dithienylethene bridge: flash-quench studies with methylviologen

A molecular ensemble composed of a phenothiazine (PTZ) electron donor, a photoisomerizable dithienylethene (DTE) bridge, and a Ru(bpy)(3)(2+) (bpy = 2,2'-bipyridine) electron acceptor was synthesized and investigated by optical spectroscopic and electrochemical means. Our initial intention was to perform flash-quench transient absorption studies in which the Ru(bpy)(3)(2+) unit is excited selectively ("flash") and its (3)MLCT excited state is quenched oxidatively ("quench") by excess methylviologen prior to intramolecular electron transfer from phenothiazine to Ru(III) across the dithienylethene bridge. However, after selective Ru(bpy)(3)(2+1)MLCT excitation of the dyad with the DTE bridge in its open form, (1)MLCT → (3)MLCT intersystem crossing on the metal complex is followed by triplet-triplet energy transfer to a (3)π-π* state localized on the DTE unit. This energy transfer process is faster than bimolecular oxidative quenching with methylviologen at the ruthenium site (Ru(III) is not observed); only the triplet-excited DTE then undergoes rapid (10 ns, instrumentally limited) bimolecular electron transfer with methylviologen. Subsequently, there is intramolecular electron transfer with PTZ. The time constant for formation of the phenothiazine radical cation via intramolecular electron transfer occurring over two p-xylene units is 41 ns. When the DTE bridge is photoisomerized to the closed form, PTZ(+) cannot be observed any more. Irrespective of the wavelength at which the closed isomer is irradiated, most of the excitation energy appears to be funneled rapidly into a DTE-localized singlet excited state from which photoisomerization to the open form occurs within picoseconds.     

Negative kinetic temperature effect on the hydride transfer from NADH analogue BNAH to the radical cation of N-benzylphenothiazine in acetonitrile

The reaction rates of 1-(p-substituted benzyl)-1,4-dihydronicotinamide (G-BNAH) with N-benzylphenothiazine radical cation (PTZ(*+)) in acetonitrile were determined. The results show that the reaction rates (k(obs)) decreased from 2.80 x 10(7) to 2.16 x 10(7) M(-1) s(-1) for G = H as the reaction temperature increased from 298 to 318 K. The activation enthalpies of the reactions were estimated according to Eyring equation to give negative values (-3.4 to -2.9 kcal/mol). Investigation of the reaction intermediate shows that the charge-transfer complex (CT-complex) between G-BNAH and PTZ(*+) was formed in front of the hydride transfer from G-BNAH to PTZ(*+). The formation enthalpy of the CT-complex was estimated by using the Benesi-Hildebrand equation to give the values from -6.4 to -6.0 kcal/mol when the substituent G in G-BNAH changes from CH(3)O to Br. Detailed thermodynamic analyses on each elementary step in the possible reaction pathways suggest that the hydride transfer from G-BNAH to PTZ(*+) occurs by a concerted hydride transfer via a CT-complex. The effective charge distribution on the pyridine ring in G-BNAH at the various stages-the reactant G-BNAH, the charge-transfer complex, the transition-state, and the product G-BNA(+)-was estimated by using the method of Hammett-type linear free energy analysis, and the results show that the pyridine ring carries relative effective positive charges of 0.35 in the CT-complex and 0.45 in the transition state, respectively, which indicates that the concerted hydride transfer from G-BNAH to PTZ(*+) was practically performed by the initial charge (-0.35) transfer from G-BNAH to PTZ(*+) and then followed by the transfer of hydrogen atom with partial negative charge (-0.65). It is evident that the present work would be helpful in understanding the nature of the negative temperature effect, especially on the reaction of NADH coenzyme with the drug phenothiazine in vivo.     

Rapid radical formation by DNA charge transport through sequences lacking intervening guanines

Using the flash-quench technique to probe DNA charge transport in assemblies containing a tethered ruthenium intercalator, the kinetics and yield of methylindole radical formation as a function of DNA sequence were studied by laser spectroscopy and biochemical methods. In these assemblies, the methylindole moiety serves as an artificial base of low oxidation potential. Hole injection and subsequent formation of the methylindole radical cation were observed at a distance of over 30 A at rates >/=107 s-1 in assemblies containing no guanine bases intervening the ruthenium intercalator and GMG oxidation site. Radical yield was, however, strikingly sensitive to an intervening base mismatch; no significant methylindole radical formation was evident with an intervening AA mismatch. Also critical is the sequence at the injection site; this sequence determines initial hole localization and hence the probability of hole propagation. With guanine rather than inosine near the site of hole injection, decreased yields of radicals and long-range oxidative damage are observed. The presence of the low-energy guanine site in this case serves to localize the hole and therefore diminish charge transport through the base pair stack.     

On the Distance‐Independent Hole Transfer over Long (A⋅T)n‐Sequences in DNA

Electron holes can travel through DNA double strands over long distances in a multistep ‘hopping’ process. But the influence of the DNA sequence on this process is still not understood in all details. We have carried out new experiments to understand the recent observation that the efficiency of the hole transport between guanines (G), which are separated from each other by long adenine?thymine (A?T) sequences, is nearly independent of the length of the (A?T)_n sequence for n ≥ 4. For this purpose, a new synthesis of the modified adenosine 16 and its incorporation into a DNA double strand was worked out. Subsequent experiments demonstrated that the hole transport between GGG units and the H₂O trapping of the guanine radical cation display similar rates. We conclude that the charge must be already partially equilibrated before being trapped by H₂O. Thus, the weak distance effect is caused not only by the rate of the hole transport, but also by its equilibration over the (A ? T)_n sequence.