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.     

Watson–Crick Base Pairing Controls Excited‐State Decay in Natural DNA

Excited‐state dynamics are essential to understanding the formation of DNA lesions induced by UV light. By using femtosecond IR spectroscopy, it was possible to determine the lifetimes of the excited states of all four bases in the double‐stranded environment of natural DNA. After UV excitation of the DNA duplex, we detected a concerted decay of base pairs connected by Watson–Crick hydrogen bonds. A comparison of single‐ and double‐stranded DNA showed that the reactive charge‐transfer states formed in the single strands are suppressed by base pairing in the duplex. The strong influence of the Watson–Crick hydrogen bonds indicates that proton transfer opens an efficient decay path in the duplex that prohibits the formation or reduces the lifetime of reactive charge‐transfer states.     

双链DNA分子内电荷转移超交换机理

设计并合成了一系列寡聚核苷酸组成的双链DNA分子,通过检测样品中二氨基嘌呤(Ap)荧光峰强度和相对荧光量子产率来研究DNA分子内电荷转移.实验中直接分辨和观测到双链DNA分子内电荷转移超交换机理,超交换机理在近距离起作用；而电荷转移跳跃机理,可能是通过极子运动形式体现.     

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.     

Direct Detection of DNA and DNA‐Ligand Interaction by Impedance Spectroscopy

In this work we present an impedimetric detection system for DNA‐ligand interactions. The sensor system consists of thiol‐modified single‐stranded DNA chemisorbed to gold. Impedance measurements in the presence of the redox system ferri‐/ferrocyanide show an increase in charge transfer resistance (R_ct) after hybridisation of a complementary target. Different amounts of capture strands, used for gold electrode modification, result in surface coverages between 3 and 15 pmol/cm² ssDNA. The relative change in R_ct upon hybridisation increases with increasing amount of capture probe on the electrode from 1.5‐ to 4.5‐fold. Impedimetric detection of binding events of a metal‐intercalator ([Ru(phen)₃]²⁺) and a groove binder (spermine) to double‐stranded DNA is demonstrated. Binding of [Ru(phen)₃]²⁺ and spermine exhibits a decrease in charge transfer resistance. Here, the ligand’s interaction leads to electrostatic shielding of the negatively charged DNA backbone. The impedance changes have been evaluated in dependence on the concentration of both DNA binders. Furthermore, the association of a single‐stranded binding protein (SSBP) is found to cause an increase in charge transfer resistance only when incubated with single‐stranded DNA. The specific binding of an anti‐dsDNA antibody to the dsDNA‐modified electrode surface decreases in contrast the interfacial impedance.     

Controlling Electron Rebound within Four‐Base π‐Stacks in Z‐DNA by Changing the Sugar Moiety from Deoxy‐ to Ribonucleotide

Charge transfer through DNA is of great interest because of the potential of DNA to be a building block for nanoelectronic sensors and devices. The photochemical reaction of 5‐halouracil has been used for probing charge‐transfer processes along DNA. We previously reported on unique charge transfer following photochemical reaction of 5‐bromouracil within four‐base π‐stacks in Z‐DNA. In this study, we incorporated a guanosine instead of a deoxyguanosine into Z‐DNA, and found that electron transfer occurs in a different mechanism through four‐base π‐stacks.     

Ultrafast Dynamics of Solvation and Charge Transfer in a DNA‐Based Biomaterial

Charge migration along DNA molecules is a key factor for DNA‐based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA‐based materials for the intactness of the DNA structure and their dynamic role in the charge‐transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA–cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well‐known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as‐prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature‐dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2‐ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge‐transfer dynamics.     

DNA‐Based Oligochromophores as Light‐Harvesting Systems

The chromophores ethynyl pyrene as blue, ethynyl perylene as green and ethynyl Nile red as red emitter were conjugated to the 5‐position of 2′‐deoxyuridine via an acetylene bridge. Using phosphoramidite chemistry on solid phase labelled DNA duplexes were prepared that bear single chromophore modifications, and binary and ternary combinations of these chromophore modifications. The steady‐state and time‐resolved fluorescence spectra of all three chromophores were studied in these modified DNA duplexes. An energy‐transfer cascade occurs from ethynyl pyrene over ethynyl perylene to ethynyl Nile red and subsequently an electron‐transfer cascade in the opposite direction (from ethynyl Nile red to ethynyl perylene or ethynyl pyrene, but not from ethynyl perylene to ethynyl pyrene). The electron‐transfer processes finally provide charge separation. The efficiencies by these energy and electron‐transfer processes can be tuned by the distances between the chromophores and the sequences. Most importantly, excitation at any wavelength between 350 and 700 nm finally leads to charge separated states which make these DNA samples promising candidates for light‐harvesting systems.     

Electrophoretic behavior of DNA‐methyl‐CpG‐binding domain protein complexes revealed by capillary electrophoreses laser‐induced fluorescence

The free solution electrophoretic behavior of DNA‐protein complexes depends on their charge and mass in a certain experimental condition, which are two fundamental properties of DNA‐protein complexes in free solution. Here, we used CE LIF to study the free solution behavior of DNA‐methyl‐CpG‐binding domain protein (MBD2b) complexes through exploring the relationship between the mobilities, charge, and mass of DNA‐protein complexes. This method is based on the effective separation of free DNA and DNA‐protein complexes because of their different electrophoretic mobility in a certain electric field. In order to avoid protein adsorption, a polyacrylamide‐coated capillary was used. Based on the evaluation of the electrophoretic behavior of formed DNA‐MBD2b complexes, we found that the values of (μ₀/μ)‐1 were directly proportional to the charge‐to‐mass ratios of formed complexes, where the μ₀ and μ are the mobility of free DNA probe and DNA‐protein complex, respectively. The models were further validated by the complex mobilities of protein with various lengths of DNA probes. The deviation of experimental and calculated charge‐to‐mass ratios of formed complexes from the theoretical data was less than 10%, suggesting that our models are useful to analyze the DNA‐binding properties of the purified MBD2b protein and help to analyze other DNA‐protein complexes. Additionally, this study enhances the understanding of the influence of the charge‐to‐mass ratios of formed DNA‐protein complexes on their separation and electrophoretic behaviors.     

Photocurrent Generation through Charge‐Transfer Processes in Noncovalent Perylenediimide/DNA Complexes

The charge‐transfer process in noncovalent perylenediimide (PDI)/DNA complexes has been investigated by using nanosecond laser flash photolysis (LFP) and photocurrent measurements. The PDI/DNA complexes were prepared by inclusion of cationic PDI molecules into the artificial cavities created inside DNA. The LFP experiments showed that placement of the PDI chromophore at a specific site and included within the base stack of DNA led to the efficient generation of a charge‐separated state with a long lifetime by photoexcitation. When two PDI chromophores were separately placed at different positions in DNA, the yield of the charge‐separated state with a long lifetime was dependent upon the number of A–T base pairs between the PDIs, which was explained by electron hopping from one PDI to another. Photocurrent generation of the DNA‐modified electrodes with the complex was also dependent upon the arrangement of the PDI chromophores. A good correlation was obtained between observed charge separation and photocurrent generation on the PDI/DNA‐modified electrodes, which demonstrated the importance of the defined arrangement and assembly of organic chromophores in DNA for efficient charge separation and transfer in multichromophore arrays.     

A Novel DNA‐Enrichment Technology Based on Amino‐Modified Functionalized Silica Nanoparticles

Abstract

In this paper we report a novel DNA‐enrichment technology based on amino‐modified functionalized silica nanoparticles. The approach takes advantage of the amino‐modified silica nanoparticles that have been prepared in one step by the controlled synchronous hydrolysis of tetraethoxysilane and N‐(β‐amimoethyl)‐γ‐aminopropyltriethoxysilane in water nanodroplets of water‐in‐oil microemulsions. The functionalized silica nanoparticles display a positive surface charge at neutral pH due to the presence of amino groups on the surface of these nanoparticles. DNA‐enrichment has been realized in the form of nanoparticle–DNA complexes that is accomplished through electrostatic binding between the positive charge of the amino group and the negative charge of the phosphate groups of the nucleic acid. These nanoparticles have high affinity to bind DNA. The results show that 1 mg of nanoparticles can bind 97.2 µg of plasmid DNA with 4.3 kb. This novel DNA‐enrichment technology has been used successfully in gene delivery.     

Single‐Walled Carbon Nanotubes Modified Gold Electrodes as an Impedimetric DNA Sensor

A gold surface modified with a self‐assembled monolayer of 11‐amino‐1‐undecanethiol (AUT) was used for the covalent immobilization of oxidized single‐walled carbon nanotubes (SWNTs). The as‐described SWNTs‐modified substrate was subsequently used to attach single‐stranded deoxyribonucleic acid (ssDNA) used as a substrate for DNA hybridization. Electrochemical impedance spectroscopy measurements were performed to follow the DNA hybridization process by using the redox couple [Fe(CN)₆]^3−/4− as a marker ion. Specifically, changes in charge transfer resistance obtained from the Nyquist plots were used as the sensing parameter of DNA hybridization. The substrate sensitivity towards changes in target DNA concentration, its selectivity toward different DNA sequences and its reusability are successfully demonstrated in this report.     

Structure–Function Relationships of New Lipids Designed for DNA Transfection

Cationic liposome/DNA complexes can be used as nonviral vectors for direct delivery of DNA‐based biopharmaceuticals to damaged cells and tissues. To obtain more effective and safer liposome‐based gene transfection systems, two cationic lipids with identical head groups but different chain structures are investigated with respect to their in vitro gene‐transfer activity, their cell‐damaging characteristics, and their physicochemical properties. The gene‐transfer activities of the two lipids are very different. Differential scanning calorimetry and synchrotron small‐ and wide‐angle X‐ray scattering give valuable structural insight. A subgel‐like structure with high packing density and high phase‐transition temperature from gel to liquid‐crystalline state are found for lipid 7 (N′‐2‐[(2,6‐diamino‐1‐oxohexyl)amino]ethyl‐2,N‐bis(hexadecyl)propanediamide) containing two saturated chains. Additionally, an ordered head‐group lattice based on formation of a hydrogen‐bond network is present. In contrast, lipid 8 (N′‐2‐[(2,6‐diamino‐1‐oxohexyl)amino]ethyl‐2‐hexadecyl‐N‐[(9Z)‐octadec‐9‐enyl]propanediamide) with one unsaturated and one saturated chain shows a lower phase‐transition temperature and a reduced packing density. These properties enhance incorporation of the helper lipid cholesterol needed for gene transfection. Both lipids, either pure or in mixtures with cholesterol, form lamellar phases, which are preserved after addition of DNA. However, the system separates into phases containing DNA and phases without DNA. On increasing the temperature, DNA is released and only a lipid phase without intercalated DNA strands is observed. The conversion temperatures are very different in the two systems studied. The important parameter seems to be the charge density of the lipid membranes, which is a result of different solubility of cholesterol in the two lipid membranes. Therefore, different binding affinities of the DNA to the lipid mixtures are achieved.     

Excess‐Electron Injection and Transfer in Terthiophene‐Modified DNA: Terthiophene as a Photosensitizing Electron Donor for Thymine,Cytosine, and Adenine

Excess‐electron transfer (EET) in DNA has attracted wide attention owing to its close relation to DNA repair and nanowires. To clarify the dynamics of EET in DNA, a photosensitizing electron donor that can donate an excess electron to a variety of DNA sequences has to be developed. Herein, a terthiophene (3T) derivative was used as the photosensitizing electron donor. From the dyad systems in which 3T was connected to a single nucleobase, it was revealed that ¹3T* donates an excess electron efficiently to thymine, cytosine, and adenine, despite adenine being a well‐known hole conductor. The free‐energy dependence of the electron‐transfer rate was explained on the basis of the Marcus theory. From the DNA hairpins, it became clear that ¹3T* can donate an excess electron not only to the adjacent nucleobase but also to the neighbor one nucleobase further along and so on. From the charge‐injection rate, the possibilities of smaller β value and/or charge delocalization were discussed. In addition, EET through consecutive cytosine nucleobases was suggested.     

DNA‐Accelerated Catalysis of Carbene‐Transfer Reactions by a DNA/Cationic Iron Porphyrin Hybrid

A novel DNA‐based hybrid catalyst comprised of salmon testes DNA and an iron(III) complex of a cationic meso‐tetrakis(N‐alkylpyridyl)porphyrin was developed. When the N‐methyl substituents were placed at the ortho position with respect to the porphyrin ring, high reactivity in catalytic carbene‐transfer reactions was observed under mild conditions, as demonstrated in the catalytic enantioselective cyclopropanation of styrene derivatives with ethyl diazoacetate (EDA) as the carbene precursor. A remarkable feature of this catalytic system is the large DNA‐induced rate acceleration observed in this reaction and the related dimerization of EDA. It is proposed that high effective molarity of all components of the reaction in or near the DNA is one of the key contributors to this unique reactivity. This study demonstrates that the concept of DNA‐based asymmetric catalysis can be expanded into the realm of organometallic chemistry.     

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.     

DFT approach to calculate electronic transfer through a segment of DNA double helix

The electronic structures of an entire segment of a DNA molecule were calculated in its single‐strand and double‐helix cases using the DFT method with an overlapping dimer approximation and negative factor counting method. The hopping conductivity of the segment was calculated by the random walk theory from the results of energy levels and wave functions obtained. The results of the single‐strand case show that the DFT method is quantitatively in agreement with that of the HF MP2 method. The results for the double helix are in good agreement with that of the experimental data. Therefore, the long‐range electron transfer through the DNA molecule should be caused by hopping of electronic charge carriers among different energy levels whose corresponding wave functions are localized at different bases of the DNA molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1109–1117, 2000     

Emerging Electron Microscopy Techniques for Probing Functional Interfaces in Energy Materials

Interfaces play a fundamental role in many areas of chemistry. However, their localized nature requires characterization techniques with high spatial resolution in order to fully understand their structure and properties. State‐of‐the‐art atomic resolution or in situ scanning transmission electron microscopy and electron energy‐loss spectroscopy are indispensable tools for characterizing the local structure and chemistry of materials with single‐atom resolution, but they are not able to measure many properties that dictate function, such as vibrational modes or charge transfer, and are limited to room‐temperature samples containing no liquids. Here, we outline emerging electron microscopy techniques that are allowing these limitations to be overcome and highlight several recent studies that were enabled by these techniques. We then provide a vision for how these techniques can be paired with each other and with in situ methods to deliver new insights into the static and dynamic behavior of functional interfaces.     

Real Time Electrochemical Monitoring of DNA/PNA Dissociation by Melting Curve Analysis

An immobilization‐free electrochemical method is reported for real‐time monitoring of the DNA hybrid dissociation between a ferrocene labeled peptide nucleic acid (PNA) and a fully‐complementary or single‐base‐mismatched DNA. This method takes advantages of electrostatic charge characteristics and interactions among the neutrally charged PNA, the negatively charged DNA and the negatively charged electrode surface made of indium tin oxide (ITO). When a ferrocene labeled PNA (Fc‐PNA) sequence is hybridized to a complementary DNA strand, electrostatic repulsion between the negatively charged PNA/DNA hybrid and the negative ITO surface retards the diffusion of the electroactive Fc to the electrode, resulting in a much reduced electrochemical signal. On the other hand, when the Fc‐PNA is dissociated from the hybrid at elevated temperatures, the neutrally charged Fc‐PNA easily diffuses to the electrode with an enhanced electrochemical signal. Therefore, an electrochemical melting curve of the Fc‐PNA/DNA hybrid can be obtained by measuring the Fc signal with the increasing temperature. This strategy allows monitoring of the dissociation of the DNA hybrid in real time, which might lead to a simple detection method for single nucleotide polymorphism (SNP) analysis.     

Determination of the Degree of Charge‐Transfer Contributions to Surface‐Enhanced Raman Spectroscopy

We explore the application of a previously suggested formula for determining the degree of charge transfer in surface‐enhanced Raman scattering (SERS). SERS is often described as a phenomenon which obtains its enhancement from three major sources, namely the surface plasmon resonance, charge‐transfer resonances as well as possible molecular resonances. At any chosen excitation wavelength, it is possible to obtain contributions from several sources and this has led to considerable confusion. The formula for the degree of charge transfer enables one to separate these effects, but it requires that spectra be obtained either at two or more different excitation wavelengths or as a function of applied potential. We apply this formula to several examples, which display rather large charge‐transfer contributions to the spectrum. These are p‐aminothiophenol (PATP), tetracyano‐ ethylene (TCNE) and piperidine. In PATP we can show that several lines of the same symmetry give the same degree of charge transfer. In TCNE we are able to identify the charge‐transfer transition, which contributes to the effect, and are able to independently determine the degree of charge transfer by wavenumber shifts. This enables a comparison of the two techniques of measurement. In piperidine, we present an example of molecule to metal charge transfer and show that our definition of charge transfer is independent of direction.