Recent developments of charge injection and charge transfer in DNA

The question of whether and how electrons migrate through DNA was a matter of controversial discussion over the last ten years. Today, there is no doubt that long distance charge migration through DNA exists and most scientists explain this process by a multistep hopping mechanism. This feature article presents recent developments of our group on the injection of a positive charge into DNA bases and the transfer of the charge between the DNA bases. The influence of the donor, the nature of the bridge, and the distance between the donor and the acceptor are discussed.     

Development of donor-acceptor modified DNA hairpins for the investigation of charge hopping kinetics in DNA

Investigation of hole or excess electron hopping in DNA is mostly performed based on yield studies, in which an injector modified DNA duplex is irradiated to continuously inject either holes or electrons into the duplex. Observed is a chemical reaction of a "probe" molecule, which can be either one of the two purine bases or a different trap molecule positioned at various distances. The next step in the field will be the direct time resolution of the hole or electron transfer kinetics in DNA. Herein we describe the development of defined donor-DNA-acceptor systems, with properties that may allow time resolved electron and hole transfer studies in stably folded DNA structures.     

Excess electron transfer in flavin-capped,thymine dimer-containing DNA hairpins

The transfer of an excess electron through DNA was investigated with DNA hairpins, which contain a flavin cap functioning as an electron donor. A thymine dimer with an open backbone acts as the electron acceptor. The dimer translates the electron capture into a strand break, which is readily detectable by HPLC. Analysis of four hairpins, in which the distance between the flavin donor and the dimer acceptor was systematically increased, revealed a flat distance dependence of the repair efficiency supporting the view that excess electrons hop through DNA using intermediate A-T base pairs as temporary charge carriers.     

Hole and excess electron transfer dynamics in DNA

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

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).     

Theoretical study of boron nitride nanotubes with defects in nitrogen-rich synthesis

On the basis of calculations using the density functional theory, it is shown that BNNT synthesis could produce tubes deprived of one (B1 hole) or two (B2 hole) boron atoms under the condition where nitrogen atoms exist in excess throughout this study. The relative populations of various isomers of defective tubes will depend on the chirality of the tube. Interestingly, calculations show that B2 holes are much more favored than B1 holes, particularly in armchair tubes. Electronic properties are modified in such a way that the band gap is decreased through the introduction of defect states inside the gap. Magnetic properties will also be dependent on the chirality. The majority of armchair tubes with B2 holes will be nonmagnetic, while the majority of zigzag tubes with defects will exhibit magnetism. Contrary to the case of defect-free BNNT, the defective tubes are expected to be easily subject to reduction by accommodating excess electrons in the presence of Li atoms. In addition, the defect sites will show a higher affinity toward hydrogenation than the defect-free sites.     

Evidence of impurities in thiolated single-stranded DNA oligomers and their effect on DNA self-assembly on gold

The diversity of techniques used in the synthesis, treatment, and purification of the single-stranded DNA oligomers containing a thiol anchor group (SH-ssDNA) has led to a significant variation in the purity of commercially available SH-ssDNA. In this work, we use X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study how the impurities present in commercially synthesized SH-ssDNA oligomers affected the structure of the resulting DNA films on Au. XPS results indicate that two of the purchased SH-ssDNA oligomers contain excess carbon and sulfur. The molecular fragmentation patterns obtained with ToF-SIMS were used to determine the identity of several contaminants in the DNA films, including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules. In particular, the ToF-SIMS results determined that the excess sulfur detected by XPS was due to the presence of dithiothreitol, a reductant often used to cleave disulfide precursors. Furthermore, we found that the SH-ssDNA self-assembly process is affected by the presence of these contaminants. When relatively pure SH-ssDNA is used to prepare the DNA films, the P, N, O, and C atomic percentages were observed by XPS to increase over a 24-h time period. In contrast, surfaces prepared using SH-ssDNA containing higher levels of contaminants did not follow this trend. XPS result indicates that, after the initial SH-ssDNA adsorption, the remaining material incorporated into these films was due to contamination.     

Excess electron interactions with solvated DNA nucleotides: strand breaks possible at room temperature

When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C(3')-O(3') bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.     

Excess electron transfer from an internally conjugated aromatic amine to 5-bromo-2'-deoxyuridine in DNA

DNA duplexes containing an N,N,N',N'-tetramethyl-1,5-diaminonaphthalene analogue and 5-bromo-2'-deoxyuridine (BrdU) provide a readily accessible system for investigating excess electron transfer in DNA. Photoexcitation of the aromatic amine (lambda > 335 nm) induces reductive electron transfer as observed by strand cleavage adjacent to the BrdU residue. The weak exponential distance dependence (0.3 A-1) of electron transfer determined for this system of mixed dA-T and dG-dC base pairs suggests that thermally activated electron hopping is competitive with proton transfer within the dG.dC radical anion. The UV-dependent transfer of excess electrons and subsequent strand cleavage proceeds equivalently under anaerobic and aerobic conditions and is not sensitive to e-(aq) or hydroxyl radical trapping agents.     

Radiation effects, energy storage and its release in solid rare gases

An irradiation of solid argon sample by electrons ionizes the Ar atoms, and part of the beam energy is stored in the solid mainly in the form of self-trapped Ar(2)(+) holes. The pre-irradiated samples are investigated by methods of the so called "activation spectroscopy". During their controlled warm-up three thermally stimulated effects are observed and, in our experiments, simultaneously monitored: a VUV emission resulting from neutralization of the Ar(2)(+) holes by electrons, an anomalous desorption of surface atoms, and an exoelectron emission. A comparison of experiments with linear and step-wise sample heating shows clearly that all three processes are intimately connected. The heating detraps electrons, which neutralize the Ar(2)(+) holes resulting in a bound-free emission of argon dimers, centered around 9.7 eV. The excess energy set free during this process may dislodge surface atoms leading to an anomalous, low temperature, pressure rise. Some of the electrons can also be directly extracted from the sample and detected as an exoelectron current. The experiments provide information about the depth of electron traps, and indicate that there is a nearly continuous distribution of trapping energies.     

Biomolecule-nanoparticle hybrid systems for bioelectronic applications

Recent advances in nanobiotechnology involve the use of biomolecule-nanoparticle (NP) hybrid systems for bioelectronic applications. This is exemplified by the electrical contacting of redox enzymes by means of Au-NPs. The enzymes, glucose oxidase, GOx, and glucose dehydrogenase, GDH, are electrically contacted with the electrodes by the reconstitution of the corresponding apo-proteins on flavin adenine dinucleotide (FAD) or pyrroloquinoline quinone (PQQ)-functionalized Au-NPs (1.4 nm) associated with electrodes, respectively. Similarly, Au-NPs integrated into polyaniline in a micro-rod configuration associated with electrodes provides a high surface area matrix with superior charge transport properties for the effective electrical contacting of GOx with the electrode. A different application of biomolecule-Au-NP hybrids for bioelectronics involves the use of Au-NPs as carriers for a nucleic acid that is composed of hemin/G-quadruplex DNAzyme units and a detecting segment complementary to the analyte DNA. The functionalized Au-NPs are employed for the amplified DNA detection, and for the analysis of telomerase activity in cancer cells, using chemiluminescence as a readout signal. Biomolecule-semiconductor NP hybrid systems are used for the development of photoelectrochemical sensors and optoelectronic systems. A hybrid system consisting of acetylcholine esterase (AChE)/CdS-NPs is immobilized in a monolayer configuration on an electrode. The photocurrent generated by the system in the presence of thioacetylcholine as substrate provides a means to probe the AChE activity. The blocking of the photocurrent by 1,5-bis(4-allyldimethyl ammonium phenyl)pentane-3-one dibromide as nerve gas analog enables the photoelectrochemical analysis of AChE inhibitors. Also, the association CdS-NP/double-stranded DNA hybrid systems with a Au-electrode, and the intercalation of methylene blue into the double-stranded DNA, generates an organized nanostructure of switchable photoelectrochemical functions. Electrochemical reduction of the intercalator to the leuco form, -0.4 V vs. SCE, results in a cathodic photocurrent as a result of the transfer of photoexcited conduction-band electrons to O(2) and the transport of electrons to the valance-band holes by the reduced intercalator units. The oxidation of the intercalator, E 0 V (vs. SCE), yields in the presence of triethanolamine, TEOA, as sacrificial electron donor, an anodic photocurrent by the transport of conduction-band electrons, through intercalator units, to the electrodes, and filling the valance-band holes with electrons supplied by TEOA. The systems reveal potential-switchable directions of the photocurrents, and reveal logic gate functions.     

Development of DNA computing and information processing based on DNA-strand displacement

DNA computing, currently a hot research field in information processing, has the advantages of parallelism, low energy consumption, and high storability, therefore, it has been applied to a variety of complicated computational problems. The emerging field of DNA nanotechnology has also developed quickly; within it, the method of DNA strand displacement has drawn great attention because it is self-induced, sensitive, accurate, and operationally simple. This article summarizes five aspects of the recent developments of DNA-strand displacement in DNA computing:(1) cascading circuits;(2) catalyzed reaction;(3) logic computation;(4) DNA computing on surfaces; and(5) logic computing based on nanoparticles guided by strand displacement. The applications and mechanisms of strand displacement in DNA computing are discussed and possible future developments are presented.     

Charge-transfer excited state dynamics in DNA hairpins substituted with an ethylenylpyrenyl-dU electron source and halo-dU traps

In this work nine DNA hairpins (HPs) are studied at room temperature to observe their pyrene(*+)/dU(*-) CT excited-state dynamics following photoexcitation at 355 nm with a 25 ps laser pulse. The HPs are 18-24 bases long, have a central tetra-T loop, and have a single U(PE) (5-(2-pyren-1-yl-ethylenyl)-2'-deoxyuridine) substitution in the central region of their stems. Three of the HPs are also substituted with 5-XdU traps, where X = Br or F, to learn about the effects of these traps on CT excited-state lifetimes and emission quantum yields in U(PE) substituted HPs. The combination of lengthened average CT lifetime and enhanced CT emission quantum yield in HPs with excess electron traps compared to HPs lacking traps strongly suggests that excess electrons are injected into the DNA stem at pyrimidine sites external to U(PE) as well via charge separation within U(PE) itself. Furthermore, the increased CT emission quantum yield in HPs with traps compared to HPs without traps implies that externally injected electrons can migrate to uracil in U(PE) (i.e., Py(*+)dU) and thus indirectly form the emissive Py(*+)dU(*-) CT state of U(PE).     

受主掺杂BaPbO3晶体的缺陷化学模型

以高温平衡电导法测定高温平衡电导率随氧分压的变化为基础, 具体分析了不同氧分压范围内主要缺陷类型——包括空穴、电子、氧离子空位、铅离子空位和杂质缺陷随氧分压的变化规律, 通过一定的理论假设, 建立了以空穴、电子、氧离子空位、铅离子空位和杂质缺陷为主要缺陷类型的受主掺杂BaPbO3材料的缺陷化学模型.     

Damage to model DNA fragments from very low-energy (<1 eV) electrons

Although electrons having enough energy to ionize or electronically excite DNA have long been known to cause strand breaks (i.e., bond cleavages), only recently has it been suggested that even lower-energy electrons (most recently 1 eV and below) can also damage DNA. The findings of the present work suggest that, while DNA bases can attach electrons having kinetic energies in the 1 eV range and subsequently undergo phosphate-sugar O-C sigma bond cleavage, it is highly unlikely (in contrast to recent suggestions) that electrons having kinetic energies near 0 eV can attach to the phosphate unit's P=O bonds. Electron kinetic energies in the 2-3 eV range are required to attach directly to DNA's phosphate group's P=O pi orbital and induce phosphate-sugar O-C sigma bond cleavages if the phosphate groups are rendered neutral (e.g., by nearby counterions). Moreover, significant activation barriers to C-O bond breakage render the rates of both such damage mechanisms (i.e., P=O-attached and base-attached) slow as compared to electron autodetachment and to other damage processes.     

Photocatalytic cleavage of single TiO2/DNA nanoconjugates

TiO(2)/DNA nanoconjugates were successfully fabricated by using the catechol moiety as a binding functional group, which was confirmed by steady-state absorption and fluorescence spectroscopies. Upon UV irradiation, the photocatalytic cleavage of the TiO(2)/DNA nanoconjugates was observed at the single-molecule level by using wide-field fluorescence microscopy. The decrease in the number of conjugates, which was estimated from the luminescent spots due to semiconductor quantum dots modified at the DNA strand, was significantly inhibited by a single A/C mismatch in the DNA sequences. This result strongly suggests that the migration of holes, which are injected from the photoexcited TiO(2) into the DNA, through the DNA bases plays an important role in the photocatalytic cleavage of the conjugates. The influences of the photogenerated reactive oxygen species (ROS) on the cleavage efficiency were also examined. According to the experimental results, it was concluded that oxidation of the catechol moiety and/or the DNA damage are key reactions in this process.     

Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.     

DNA sequencing

Determination of the sequence of DNA is one of the most important aspects of modern molecular biology. New sequencing methods currently being developed enable DNA sequence to be determined increasingly faster and more efficiently. One of the major advances in sequencing technology is the development of automated DNA sequencers. These utilize fluorescent rather than radioactive labels. A laser beam excites the fluorescent dyes, the emitted fluorescence is collected by detectors, and the information analyzed by computer. Robotic work stations are being developed to perform template preparation and purification, and the sequencing reactions themselves. Research is currently in progress to develop the technology of mass spectrometry for DNA sequencing. Success in this endeavor would mean that the gel electrophoresis step in DNA sequencing could be eliminated. A major innovation has been the application of polymerase chain reaction (PCR) technology to DNA sequence determination, which has led to the development of linear amplification sequencing (cycle sequencing). This very powerful yet technically simple method of sequencing has many advantages over conventional techniques, and may be used in manual or automated methods. Other recent innovations proposed recently to increase speed and efficiency include multiplex sequencing. This consists of pooling a number of samples and processing them as pools. After electrophoresis, the DNA is transferred to a membrane, and sequence images of the individual samples are obtained by sequential hybridizations with specific labeled oligonucleotides. Multiplex DNA sequencing has been used in conjunction with direct blotting electrophoresis to facilitate transfer of the DNA to a membrane. Chemiluminescent detection can also be used in conjunction with multiplex DNA sequencing to visualize the image on the membrane.     

Single-molecule studies on DNA and RNA.

DNA and RNA are the most individual molecules known. Therefore, single-molecule experiments with these nucleic acids are particularly useful. This review reports on recent experiments with single DNA and RNA molecules. First, techniques for their preparation and handling are summarised including the use of AFM nanotips and optical or magnetic tweezers. As important detection techniques, conventional and near-field microscopy as well as fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are touched on briefly. The use of single-molecule techniques currently includes force measurements in stretched nucleic acids and in their complexes with binding partners, particularly proteins, and the analysis of DNA by restriction mapping, fragment sizing and single-molecule hybridisation. Also, the reactions of RNA polymerases and enzymes involved in DNA replication and repair are dealt with in some detail, followed by a discussion of the transport of individual nucleic acid molecules during the readout and use of genetic information and during the infection of cells by viruses. The final sections show how the enormous addressability in nucleic acid molecules can be exploited to construct a single-molecule field-effect transistor and a walking single-molecule robot, and how individual DNA molecules can be used to assemble a single-molecule DNA computer.     

Adsorption of DNA into mesoporous silica

In these experiments, double-stranded, linear DNA sequences were adsorbed into the pores of spherically shaped acid-prepared mesoporous silica (APMS). The lengths of the sequences were either 760 base pairs or 2000 base pairs. DNA adsorption into the interior of the mesoporous material was confirmed using confocal microscopy of sequences containing fluorescently labeled DNA molecules. Additional characterization with N(2) physisorption and powder X-ray diffraction supported this finding. The extent of adsorption was measured at various concentrations using UV-visible spectrophotometry to establish adsorption isotherms. APMS alone adsorbed a negligible amount of DNA; however, exchanging divalent cations such as Mg(2+) and Ca(2+) into the pores of APMS prior to DNA uptake was found to cause a significant amount of DNA to be adsorbed. Using Na(+) caused a lower amount of DNA to be adsorbed. DNA adsorption was also dependent on the pore diameter of APMS. Adsorption increased upon expansion of the pore size of the metal ion-exchanged material from 34 to 54 A; however, no additional uptake was measured by further increasing the pore size to 100 A. The amount of DNA adsorbed could also be significantly increased by using (aminopropyl)triethoxysilane to covalently link ammonium ions to the surface. Postsynthetic modification of the silica surface with aminopropyl groups increased the maximum DNA adsorption to 15.7 microg/mg silica, for materials with pore diameters of 100 A, which is 2 to 3 times more adsorbed DNA than for metal ion-exchanged material. This indicated that DNA binds more strongly in the presence of the ammonium group compared to the metal counterions. Finally, calculation and comparison of Freundlich and Langmuir constants for these adsorption processes indicate that intermolecular interactions between the DNA molecules within the pores are significant when the effective pore diameter is small, including materials with larger pores that were modified with organosilane.