Charge separation in acridine- and phenothiazine-modified DNA

The formation of the long-lived, charge-separated state in DNA upon visible light irradiation is of particular interest in molecular-scale optoelectronics, sensor design, and other areas of nanotechnology. However, the efficient generation of the charge-separated state is hampered by fast charge recombination within a contact ion pair, which limits the application of DNA for photoelectrochemical sensors and devices. In this study, a series of protonated 9-alkylamino-6-chloro-2-methoxyacridine (Acr+)- and phenothiazine (Ptz)-modified DNAs were synthesized for the further understanding of the mechanism of charge separation in DNA to generate a long-lived, charge-separated state with a high quantum yield (Phi). The Acr+ serves as a photosensitizer to produce a hole on guanine (G), and the G-C base pairs were used as a hole-transporting pathway to separate a hole from Acr* (the one-electron-reduced form of Acr+) to be trapped at Ptz. Since Acr+ oxides only G upon photoexcitation, the A-T base pair can be used as a spacer between Acr+ and the G-C base pair to avoid the formation of a contact ion pair. The charge injection dynamics was investigated by steady-state fluorescence spectra and fluorescence lifetime measurements, and the Phi and the lifetime of the charge-separated state produced upon photoirradiation were assessed by nanosecond laser flash photolysis of the Acr+- and Ptz-modified DNA. A long-lived, charge-separated state was successfully formed upon visible-light irradiation, and the Phi was the highest for the DNA having a single intervening A-T base pair between Acr+ and the G-C base pair. These results clearly demonstrated that the charge separation process in DNA can be refined by putting a redox-inactive intervening base pair as a spacer between a photosensitizer and the nucleobase to be oxidized to slow down the charge recombination rate.     

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.     

Charge separation in mesoporous aluminosilicates

EPR spectroscopy has been used to investigate spontaneous and/or photo-induced electron transfer between adsorbed organic molecules and the mesoporous aluminosilicate MCM-41 host. Spontaneous electron transfer occurs from the host to electron acceptor molecules with sufficiently favourable reduction potentials (TCNE, TCNQ, 1,4-benzoquinone, 1,4-naphthaquinone and 1,4-anthraquinone), provided the MCM-41 contains aluminium and the radical anion yield correlates with the aluminium content of the host. The semiquinone radical anions are interacting strongly with exposed Al³⁺ sites, whereas the TCNE and TCNQ radical anions are loosely bound and can be washed from the host. Radical cation formation is observed when electron donor molecules with favourable oxidation potentials are adsorbed in MCM-41 containing aluminium, and the radical cations formed interact with exposed Al³⁺ sites. This work shows that aluminium-containing MCM-41 contains both electron donating and electron accepting sites which may intervene in intra-molecular charge separation processes in adsorbed organic molecules.     

Cross-linking of a DNA conjugate tethering a cis-bifunctional platinated complex to a target DNA duplex

Tethering an ethylene diamine linker to the 5' terminus of an oligothymidine sequence provides a ligand for complexation with K2PtCl4. Post-synthetic reaction of the platinum reagent with the diamino oligothymidine generates the diamino dichloro platinum-DNA conjugate that can be used for DNA duplex targeting by oligodeoxyncleotide-mediated triplex formation. Cross-linking between the third strand and the duplex occurs exclusively with the duplex target strand directly involved in triplex formation. No examples of cross-linking to the complementary target strand or cases of cross-linking to both target strands are observed. Most efficient cross-linking occurs when the dinucleotide d(GpG) is present in the target strand and no cross-linking occurs with the corresponding 7-deazaG dinucleotide target. Cross-linking is also observed when dC or dA residues are present in the target strand, or even with a single dG residue, but it is not observed in any cases to dT residues. Triplex formation provides the ability to target specific sequences of double-stranded DNA; conjugates of the type described here offer the potential of delivering a platinum complex to a specific DNA site.     

DNA sensors using a ferrocene-oligonucleotide conjugate

Using the redox-active DNA conjugate (ferrocene-modified oligonucleotide 12 mer) as a probe, the novel electrochemical gene sensor, which is sensitive, convenient, and not relying on radio isotope, has been developed. Oligonucleotide (16 mer) complementary to the target (19 mer) was immobilized onto gold electrode through the specific chemisorption of successive phosphorothioates which were introduced into 5'-end of the oligonucleotide. The sequence of the conjugate was designed to be also complementary to another site of the target. Therefore, the conjugate and the oligonucleotide anchoring on the electrode formed a sandwich-type ternary complex with a target DNA to give electric currents based on the ferrocene oxidation. By using this system, we have distinguished the mutant that has one base substitution from the fully complementary target.     

Charge separation and ion-pair formation in cations subsequent to electron-impact

Investigation of metastable ion transitions shows, that spontaneous charge separations (loss of an electron from a cation) and ion-pair formations (loss of negative ions from positive ones)are taking place in conventional mass spectrometry. Such processes may be important factors in formation of doubly charged ions.     

Charge reversal of the conjugate base of formamide

Charge reversal collisional activation mass spectremetry of negative ions has been used in conjunction with positive ion collisional activation to investigate several isomeric [H₂, C, N, O]⁺ ions. Generation of m/z 44 ions from formamide, acetamide, JV-methylformamide, acetaldoxime and by charge reversal of the [M–1]^? ion formed from formamide yields several different isomeric structures. Charge reversal of the conjugate base of formamide appears to yield a mixture of singlet and triplet H₂NC?O⁺ ions; experiments with deuterium-labeled compounds have been used to support this. Ab initio molecular orbital calculations indicate that the triplet ion is a stable structure, existing in a potential minimum 390.6 kJ mol^?1 above the ground state singlet.     

NMR structural analysis of a modular threading tetraintercalator bound to DNA

The synthesis and NMR structural studies are reported for a modular threading tetraintercalator bound to DNA. The tetraintercalator design is based on 1,4,5,8-tetracarboxylic naphthalene diimide units connected through flexible peptide linkers. Aided by an overall C(2) symmetry, NMR analysis verified a threading polyintercalation mode of binding, with linkers alternating in the order minor groove, major groove, minor groove, analogous to how a snake might climb a ladder. This study represents the first NMR analysis of a threading tetraintercalator and, as such, structurally characterizes a new topology for molecules that bind to relatively long DNA sequences with extensive access to both DNA grooves.     

DNA separation by EFFF in a microchannel

This paper theoretically explores the application of electric field flow fractionation (EFFF) for the size-based separation of DNA strands in a microchannel. An axial electric field cannot separate DNA strands in solution because the electrical mobility of the strands is independent of the length. However, lateral electric fields coupled with an axial Poiseuille flow can separate the DNA strands of different sizes. By using regular perturbation analysis, we obtain the effective diffusivity and the mean velocity of the DNA molecules that are undergoing a pressure driven Poiseuille flow in a 2D channel in presence of a lateral electric field. The mean velocities and the dispersion coefficients are then utilized to determine the scaling for length of the channel and the time required for separation of DNA molecules in different parameter regimes. The results show that EFFF can separate DNA strands in the range of 10 kbp that differ in size by about 2.5 kbp in about half an hour in a 1 cm long channel. While DNA strands can be separated by EFFF, the performance of devices based on EFFF seems to be at best comparable to other techniques such as entropic trapping.     

Enantioselective DNA alkylation by a pyrrole-imidazole S-CBI conjugate

Conjugates 12S and 12R of N-methylpyrrole (Py)-N-methylimidazole (Im) seven-ringed hairpin polyamide with both enantiomers of 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) were synthesized, and their DNA alkylating activity was examined. High-resolution denaturing gel electrophoresis revealed that 12S selectively and efficiently alkylated at one match sequence, 5'-TGACCA-3', in 450-bp DNA fragments. The selectivity and efficiency of the DNA alkylation by 12S were higher than those of the corresponding cyclopropapyrroloindole (CPI) conjugate, 11. In sharp contrast, another enantiomer, 12R, showed very weak DNA alkylating activity. Product analysis of the synthetic decanucleotide confirmed that the alkylating activity of 12S was comparable with 11 and that 12S had a significantly higher reactivity than 12R. The enantioselective reactivity of 12S and 12R is assumed to be due to the location of the alkylating cyclopropane ring of the CBI unit in the minor groove of the DNA duplex. Since the CBI unit can be synthesized from commercially available 1,3-naphthalenediol, the present results open up the possibility of large-scale synthesis of alkylating Py-Im polyamides for facilitating their use in future animal studies.     

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.     

Charge recombination versus charge separation in donor-bridge-acceptor systems

Optimizing the ratio of the rates for charge separation (CS) over charge recombination (CR) is crucial to create long-lived charge-separated states. Mastering the factors that govern the electron transfer (ET) rates is essential when trying to achieve molecular-scale electronics, artificial photosynthesis, and also for the further development of solar cells. Much work has been put into the question of how the donor-acceptor distances and donor-bridge energy gaps affect the electronic coupling, V(DA), and thus the rates of ET. We present here a unique comparison on how these factors differently influence the rates for CS and CR in a porphyrin-based donor-bridge-acceptor model system. Our system contains three series, each of which focuses on a separate charge-transfer rate-determining factor, the donor-acceptor distance, the donor-bridge energy gap, and last, the influence of the electron acceptor on the rate for charge transfer. In these three series both CS and CR are governed by superexchange interactions which make a CR/CS comparative study ideal. We show here that the exponential distance dependence increases slightly for CR compared to that for CS as a result of the increased tunneling barrier height for this reaction, in accordance with the McConnell superexchange model. We also show that the dependence on the tunneling barrier height is different for CS and CR. This difference is highly dependent on the electron acceptor and thus cannot solely be explained by the differences in the frontier orbitals of the electron donor in these porphyrin systems.     

表面相结结构在促进光催化电荷分离中的应用

二十世纪八十年代以来,特别是近十年,光催化研究在利用可再生能源太阳能的道路上飞速发展。越来越多的研究表明,相结结构的构筑是有效提高半导体光催化剂性能的重要策略。其中, TiO2作为重要的模型光催化剂,其相关研究成果呈现出指数增长的趋势。本综述围绕TiO2模型光催化剂,主要介绍TiO2表面相结的研究成果,包括TiO2表面相的表征、锐钛矿：金红石TiO2相结用于光催化产氢研究、TiO2相结在光催化中作用的最新认识等。在表征方面,通过表面灵敏的紫外拉曼光谱研究了TiO2相变过程中表面相结构的变化,结合可见拉曼以及XRD表征揭示了TiO2独特的相变过程,即相变始于锐钛矿粒子的界面处,小粒子逐渐团聚为大粒子,致其相变从大粒子体相开始最终扩展到整个粒子。使用CO, CO2探针红外光谱,根据锐钛矿和金红石表面吸附物种的差异,进一步证实了锐钛矿：金红石表面相结结构,为紫外拉曼光谱的表面表征特性提供坚实证据。同时,利用发光光谱观察到锐钛矿晶相的可见发光带和金红石晶相的近红外发光带,并基于此给出了TiO2材料表面相结结构的荧光表征新方法。此外荧光光谱还提供了锐钛矿、金红石相中载流子动力学信息,揭示了束缚态在光催化中的作用。在光催化应用方面,观察到混相结构TiO2较单独锐钛矿及金红石相具有更高的光催化产氢活性,通过在较大金红石颗粒上担载纳米锐钛矿粒子,证明了相结结构在提高光催化活性中的核心作用,并首次提出了锐钛矿：金红石表面异相结结构概念,推断其对电荷分离的促进作用是最终提高反应活性的原因。之后将此概念应用到改善商品TiO2(P25)光催化活性中,通过可控热处理精细调控P25的表面相结构,在光催化重整生物质衍生物产氢实验中,成功将P25光催化产氢活性提高3?5倍。之后发展了新的TiO2表面控制方法,通过加入Na2SO4等相变控制剂,延缓了TiO2从锐钛矿向金红石的相变过程,在较高温度下实现TiO2相结结构的调控,最终可将P25光催化重整甲醇制氢的活性提高6倍,同时通过高分辨电镜清晰观察到锐钛矿：金红石相结的原子层生长接触。在相结作用机理方面,多种时间分辨光谱技术以及理论计算被用作探索锐钛矿：金红石相结处的电子转移机理。通过时间分辨红外光谱对TiO2表面相结结构作用的研究,特别是利用锐钛矿、金红石不同的瞬态吸收光谱特征,证明了锐钛矿：金红石相结处的载流子转移过程,存在锐钛矿向金红石的电子转移过程。模型光催化剂TiO2相结的研究成果,加深了对光催化机理的认识,促进新型高效光催化体系的设计合成。     

Charge separation in ground-state 1,2,4,5-tetra-substituted benzene derivatives

The conditions required for a formal biradical to exist in a zwitterionic form in the ground state are discussed following the recent experimental observation of zwitterionic structure in the ground state of a quinoid molecule (di-tert-butyl derivative of 2,5-diamino-1,4-benzoquinonediimine, I). A unique characteristic of molecules of this class is the fact that they may be considered as being formed by the union of two radicals, each having an odd number of pi electrons. In the case of I, one fragment carries the two amino group having 7 pi electrons; it acts as the electron donor. The other fragment carries the two oxygen atoms (carrying 5 pi electrons) and acts as an electron acceptor. A model that predicts the properties of these systems is presented, based on previous work on non-Kekule hydrocarbons(2,3) and on the electron donating and attracting properties of the donor and acceptor groups, respectively. The zwitterion is formed by an electron transfer leading to two subunits carrying 6 pi electrons each and may become more stable than the triplet biradical even in the gas phase (i.e., in the absence of an external field) if the ionization potential of the donor is small (of the order of 3-4 eV). In some cases solvation in a polar solvent is required to make the zwitterionic form the lowest energy species on the ground-state surface. The 'spacer' between the donor and acceptor groups (which need not be necessarily derived from an aromatic structure) can be varied and influences the overall dipole moment that is calculated in some cases to be quite large (over 20 D in the gas phase).     

Hybridization thermodynamics of DNA bound to gold nanoparticles

Isothermal Titration Calorimetry (ITC) was used to study the thermodynamics of hybridization on DNA-functionalized colloidal gold nanoparticles. When compared to the thermodynamics of hybridization of DNA that is free in solution, the differences in the values of the Gibbs free energy of reaction, Δ_rG°, the enthalpy, Δ_rH°, and entropy, Δ_rS°, were small. The change in Δ_rG° between the free and bound states was always positive but with statistical significance outside the 95% confidence interval, implying the free DNA is slightly more stable than when in the bound state. Additionally, ITC was also able to reveal information about the binding stoichiometry of the hybridization reactions on the DNA-functionalized gold nanoparticles, and indicates that there is a significant fraction of the DNA on gold nanoparticle surface that is unavailable for DNA hybridization. Furthermore, the fraction of available DNA is dependent on the spacer group on the DNA that is used to span the gold surface from that to the probe DNA.     

DNA separation at a liquid-solid interface

We demonstrate that it is possible to separate a broad band of DNA on a solid substrate without topological obstacles. The mobility was found to scale with molecular size (N) as N(-0.25), while the resolution scaled as N(0.75) indicating that diffusivity on this substrate was minimal. By varying the buffer concentration we were able to show that the mobility for a given chain length scaled with the persistent length (p) as p(1/2). This could be shown to be related to the Gaussian conformation of the chains adsorbed on the surface. A two-dimensional corrugated surface of nonporous silica beads was produced using a self-assembling process at the air/water interface. Even though the surface corrugations were comparable to persistence length we show that they do not affect the mobility, indicating that surface friction rather than topological constraints are the predominant mechanism of separation on a surface.     

Charge Transport within a Three-Dimensional DNA Nanostructure Framework

Three-dimensional (3D) DNA nanostructures have shown great promise for various applications including molecular sensing and therapeutics. Here we report kinetic studies of DNA-mediated charge transport (CT) within a 3D DNA nanostructure framework. A tetrahedral DNA nanostructure was used to investigate the through-duplex and through-space CT of small redox molecules (methylene blue (MB) and ferrocene (Fc)) that were bound to specific positions above the surface of the gold electrode. CT rate measurements provide unambiguous evidence that the intercalative MB probe undergoes efficient mediated CT over longer distances along the duplex, whereas the nonintercalative Fc probe tunnels electrons through the space. This study sheds new light on DNA-based molecular electronics and on designing high-performance biosensor devices.