Intermolecular vs. intramolecular photoinduced electron transfer from nucleotides in DNA to acridinium ion derivatives in relation with DNA cleavage

Photoirradiation of various 10-methylacridinium ions (AcrR⁺, R = H, ⁱPr, and Ph) intercalated in DNA results in ultrafast intramolecular electron transfer, followed by rapid back electron transfer between AcrR⁺ and nucleotides in DNA. The electron-transfer dynamics in DNA were monitored by femtosecond time-resolved transient absorption spectroscopy. Both acridinyl radical and nucleotide radical cations, formed in the photoinduced electron transfer in DNA, were successfully detected in an aqueous solution. These transient absorption spectra were assigned by the comparison with those of DNA nucleotide radical cations, which were obtained by the intermolecular electron-transfer oxidation of nucleotides with the electron-transfer state of 9-mesityl-10-methylacridinium ion (Acr–Mes⁺) produced upon photoexcitation of Acr⁺–Mes. Photoinduced cleavage of DNA with various acridinium ions (AcrR⁺, R = H, ⁱPr, Ph, and Mes) has also been examined by agarose gel electrophoresis, which indicates that the rapid intramolecular back electron transfer between acridinyl radical and nucleotide radical cation in DNA suppresses the DNA cleavage as compared with the intermolecular electron-transfer oxidation of nucleotides with Acr–Mes⁺.     

Regioselective hydroxylation of phenols by simultaneous photochemical generation of phenol cation-radical and hydroxyl radical

Substituted phenols having pendant isoquinoline N-oxide were synthesized and their photochemical and luminiscent properties studied. Photolysis in an acid medium was found to yield the related photohydroxylation products, in a regioselective process, in addition to the isoquinoline deoxygenated precursor. Photoinduced electron transfer from the donor phenols to the protonated form of the first excited singlet state (S₁) of the pendant isoquinoline N-oxide acting as acceptor leads to a red-shifted emissive charge transfer (CT) state that is in fact a radical/cation-radical pair. Homolysis of the N-OH bond restores the aromatic isoquinoline nucleus and produces a hydroxyl radical that can couple to the required ring carbon in the phenol cation-radical to give the photohydroxylation products in a regioselective process controlled by the spin density of the phenol cation-radical. These photohydroxylation processes efficiently compete with the reported tendency to deprotonation in phenol cation-radicals. The photohydroxylation process by itself, and its regioselectivity, exclude a proton-coupled electron transfer mechanism or a consecutive electron transfer/deprotonation reaction. By contrast, the phenol cation-radical exists long enough to undergo the hydroxyl radical coupling reaction that leads to the photohydroxylation products.     

Sequence‐Dependent Photocurrent Generation through Long‐Distance Excess‐Electron Transfer in DNA

Given its well‐ordered continuous π stacking of nucleobases, DNA has been considered as a biomaterial for charge transfer in biosensors. For cathodic photocurrent generation resulting from hole transfer in DNA, sensitivity to DNA structure and base‐pair stacking has been confirmed. However, such information has not been provided for anodic photocurrent generation resulting from excess‐electron transfer in DNA. In the present study, we measured the anodic photocurrent of a DNA‐modified Au electrode. Our results demonstrate long‐distance excess‐electron transfer in DNA, which is dominated by a hopping mechanism, and the photocurrent generation is sequence dependent.     

Coexistence of Different Electron‐Transfer Mechanisms in the DNA Repair Process by Photolyase

DNA photolyase has been the topic of extensive studies due to its important role of repairing photodamaged DNA, and its unique feature of using light as an energy source. A crucial step in the repair by DNA photolyase is the forward electron transfer from its cofactor (FADH^?) to the damaged DNA, and the detailed mechanism of this process has been controversial. In the present study, we examine the forward electron transfer in DNA photolyase by carrying out high‐level ab initio calculations in combination with a quantum mechanical/molecular mechanical (QM/MM) approach, and by measuring fluorescence emission spectra at low temperature. On the basis of these computational and experimental results, we demonstrate that multiple decay pathways exist in DNA photolyase depending on the wavelength at excitation and the subsequent transition. This implies that the forward electron transfer in DNA photolyase occurs not only by superexchange mechanism but also by sequential electron transfer.     

Theoretical study of excitation energy transfer in DNA photolyase

Photolyase (PL) is a DNA repair enzyme which splits UV light-induced thymine dimers on DNA by an electron transfer reaction occurring between the photoactivated FADH(-) cofactor and the DNA dimer in the DNA/PL complex. The crystal structure of the DNA/photolyase complex from Anacystis nidulans has been solved. Here, using the experimental crystal structure, we re-examine the details of the repair electron transfer reaction and address the question of energy transfer from the antenna HDF to the redox active FADH(-) cofactor. The photoactivation of FADH(-) immediately preceding the electron transfer is a key step in the repair mechanism that is largely left unexamined theoretically. An important butterfly thermal motion of flavin is identified in ab initio calculations; we propose its role in the back electron transfer from DNA to photolyase. Molecular dynamics simulation of the whole protein/DNA complex is carried out to obtain relevant cofactor conformations for ZINDO/S spectroscopic absorption and fluorescence calculations. We find that significant thermal broadening of the spectral lines, due to protein dynamics, as well as the alignment of the donor HDF and the acceptor FADH(-) transition dipole moments both contribute to the efficiency of energy transfer. The geometric factor of F?rster's dipolar coupling is calculated to be 1.82, a large increase from the experimentally estimated 0.67. Using F?rster's mechanism, we find that the energy transfer occurs with remarkable efficiency, comparable with the experimentally determined value of 98%.     

Charge Transfer through the DNA Base Stack

Whether the DNA base pair stack might serve as a medium for efficient, long-range charge transfer has been debated almost since the first proposal of the double-helical structure of DNA. The consequences of long-range radical migration through DNA are important with respect to understanding carcinogenesis and mutagenesis. Double-helical DNA has in its core a stacked array of aromatic heterocyclic base pairs, and this molecular π stack represents a unique system in which to explore the chemistry of electron transfer. We designed a family of metal complexes which bind to DNA by intercalative stacking within the helix; these metallointercalators may be usefully applied in probing DNA-mediated electron transfer. Here we describe a range of electron transfer reactions we carried out which are mediated by the DNA base paired stack. In some cases, DNA serves as a bridge, and spectroscopic analyses permit us to probe how the π stack couples DNA-bound donors and acceptors. These studies point to the sensitivity of coupling to DNA intercalation. However, if the DNA π stack effectively bridges donors and acceptors, the base-pair stack itself might serve not only as a conduit for electron transfer in DNA, but also in reactions initiated from a remote position. We carried out a series of reactions involving oxidative damage to DNA arising from the remotely positioned oxidant on the helix. The implications of long-range charge migration through DNA to effect damage are substantial. As in other DNA-mediated charge transfers, these reactions are highly dependent on DNA intercalation and the integrity of the intervening base-pair stack, but not on molecular distance. Furthermore, a physiologically important DNA lesion, the thymine dimers, can be reversed in a reaction initiated by electron transfer. This repair reaction can also be promoted from a distance as a result of long-range charge migration through the DNA base pair stack.     

利用电子自旋共振技术捕捉烯类单体双光子聚合反应的自由基信号

<正>自1999年烯类单体的双光子聚合方法被发现以来[1],其产物在光开关制备[2]、光子晶体[3]、微机械[4]及三维微加工[5]等领域得到了广泛的应用.由此,烯类双光子聚合机理也成为人们研究的焦点[6].到目前为止,研究者们普遍认为烯类单体的双光子聚合反应属于自由基历程,各种利用双光子     

Ipso-amidation of arylboronic acids: Xenon difluoride-nitriles as efficient reagent systems

The xenon difluoride-mediated, ipso-amidation of boronic acids has been achieved for the first time under mild conditions. This method provides a simple, one-pot procedure for the direct synthesis of a series of anilides from the corresponding arylboronic acids and alkyl/aryl nitriles. Arylboronic acids bearing electron donating groups gave anilides in high yields, while moderate yields were observed for those bearing electron withdrawing groups. A plausible mechanism involving the formation of an aryl radical cation through single electron transfer by xenon difluoride, followed by the nucleophilic addition of the nitrile, is proposed.     

Reversed effects of DNA on hydride transfer and electron transfer reactions of acridinium and quinolinium ions

DNA inhibits hydride transfer from 1-benzyl-1,4-dihydronicotinamide to the 10-methylacridinium ion, whereas DNA accelerates photoinduced electron transfer from the excited state of Ru(bpy)3(2+) to the 1-methylquinolinium ion. The reason of such reversed effects of DNA on the hydride transfer and electron transfer reactions is clarified.     

The coordination chemistry of 1,2,4,5-tetrazines

1,2,4,5-Tetrazine and its 3,6-disubstituted derivatives exhibit a particular coordination chemistry, characterized by electron and charge transfer phenomena and by the ability of these heteroatom-rich ligands to bridge metal centers in various ways. A very low-lying π* orbital localized at the four nitrogen atoms is responsible for intense low-energy charge transfer absorptions, electrical conductivity of coordination polymers, unusual stability of paramagnetic radical or mixed-valent intermediates and for often well-resolved EPR hyperfine structure in the radical complexes. Substituted 1,4-dihydro-1,2,4,5-tetrazines have also been used as bridging ligands. The structural consequences of electron transfer as well as the capability for efficient and variable metal–metal bridging render the tetrazines as valuable components of supramolecular materials.     

DNA内电子传递特性的研究现状*

DNA是生物体中储存和传递遗传信息的重要物质。双链DNA分子中碱基对的紧密堆积为电子传递提供了有利条件,DNA内的电子转移与许多生物学功能密切相关,可能诱发遗传信息的错读和引起DNA损伤,导致细胞的突变和癌变。本文介绍了DNA电子传递的多种可能机理,就DNA电子传递的各种理论模型进行了讨论,详细介绍了实验体系的设计和研究方法,分析了各种影响电子传递的因素,对近10多年来DNA电子传递的研究工作进行了综述。     

Electrochemical Approach to the Radical Anion Formation from 2′‐Hydroxy Chalcone Derivatives

Three 2′‐hydroxy chalcone derivatives were electrochemically reduced to the radical anion by a reversible one‐electron transfer followed by a chemical dimerization reaction. Under suitable conditions of the medium, the one‐electron reduction produces very well resolved cyclic voltammograms due to the formation of the radical anion. By using appropriately the wide versatility of the cyclic voltammetric technique, was possible to study the generation of the radical anion and its stability.     

Femtosecond electron-transfer reactions in mono- and polynucleotides and in DNA

Quenching of redox active, intercalating dyes by guanine bases in DNA can occur on a femtosecond time scale both in DNA and in nucleotide complexes. Notwithstanding the ultrafast rate coefficients, we find that a classical, nonadiabatic Marcus model for electron transfer explains the experimental observations, which allows us to estimate the electronic coupling (330 cm(-1)) and reorganization (8070 cm(-1)) energies involved for thionine-[poly(dG-dC)](2) complexes. Making the simplifying assumption that other charged, pi-stacked DNA intercalators also have approximately these same values, the electron-transfer rate coefficients as a function of the driving force, DeltaG, are derived for similar molecules. The rate of electron transfer is found to be independent of the speed of molecular reorientation. Electron transfer to the thionine singlet excited state from DNA obtained from calf thymus, salmon testes, and the bacterium, micrococcus luteus (lysodeikticus) containing different fractions of G-C pairs, has also been studied. Using a Monte Carlo model for electron transfer in DNA and allowing for reaction of the dye with the nearest 10 bases in the chain, the distance dependence scaling parameter, beta, is found to be 0.8 +/- 0.1 A(-1). The model also predicts the redox potential for guanine dimers, and we find this to be close to the value for isolated guanine bases. Additionally, we find that the pyrimidine bases are barriers to efficient electron transfer within the superexchange limit, and we also infer from this model that the electrons do not cross between strands on the picosecond time scale; that is, the electronic coupling occurs predominantly through the pi-stack and is not increased substantially by the presence of hydrogen bonding within the duplex. We conclude that long-range electron transfer in DNA is not exceptionally fast as would be expected if DNA behaved as a "molecular wire" but nor is it as slow as is seen in proteins, which do not benefit from pi-stacking.     

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).     

Photochemical radical cyclization of γ,δ-unsaturated ketone oximes to 3,4-dihydro-2H-pyrroles

3,4-Dihydro-2H-pyrroles are synthesized from γ, δ-unsaturated oximes by photochemical radical cyclization with 1,5-dimethoxynaphthalene (DMN) as the sensitizer. The cyclization of alkyl ketone O-acetyloximes proceeds via photosensitized electron transfer in the presence of acetic acid, while conjugated oximes of aryl and α,β-unsaturated ketones are cyclized via energy transfer.     

Coupling Electrochemical Adsorption and Long‐range Electron Transfer: Label‐free DNA Mismatch Detection with Ultramicroelectrode (UME)

A new electrochemical hybridization transduction pathway, obtained by coupling electrochemical adsorption and long‐range electron transfer through double‐stranded DNA, was investigated using ultramicroelectrode (UME). The results show that long‐range electron transfer does not occurs exclusively throws well‐packed and organized self‐assembled DNA monolayers. This approach is used to investigate long‐range electron transfer properties of both single‐ and double‐ stranded short synthetic DNA and DNA plasmids. Single mismatch electrochemical detection protocol of non‐labelled short synthetic DNA, without heating or probe labelling, in a 10 minutes protocol, was in fine performed.     

Peptide electron transfer: more questions than answers

Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.     

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity‐shaped hydrated electron state to a hydrated nucleobase (NB)‐bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron‐induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution‐structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120–200 fs in four aqueous NB solutions, depending on the electron‐binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*‐type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron‐binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure‐fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA‐damage mechanism in solution.     

Electron injection into DNA: synthesis and spectroscopic properties of pyrenyl-modified oligonucleotides

The nucleoside 5-(1-pyrenyl)-2'-deoxyuridine (1) was prepared by a Suzuki-Miyaura cross-coupling reaction and subsequently used as a DNA building block in order to prepare a range of modified oligonucleotides using phosphoramidite chemistry. The DNA duplexes contain a pyrenyl group covalently attached to the nucleobase uracil. Upon excitation at 340 nm an intramolecular electron transfer from the pyrenyl group to the uracil moiety takes place which represents an injection of an excess electron into the DNA base stack. Based on the results obtained by steady-state fluorescence and time-resolved pump-probe laser spectroscopy it was possible to show that base-to-base electron transfer can occur from the Py-dU group only to adjacent thymines.     

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.