基于新型DNA金属化工艺银纳米线的制备

随着DNA金属化工艺逐渐发展, 以DNA为模板进行金属纳米线的制备, 使得生物与微细加工技术的结合变得可能. 我们将DNA模板金属化工艺加以改进, 利用半导体材料——硅作为样品衬底, 并在硅片上利用Parafilm疏水膜斜向拉伸排列DNA分子, 采用化学还原反应, 成功地进行了银纳米线的制备. 改进后的金属化工艺对DNA分子金属化程度较好, 而且制备出了金属纳米网状结构. 基于DNA构筑复杂纳米图形的实现, 进行相关的金属化, 有望构筑纳米集成电路.     

Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications

In biology, DNA is the central molecule that stores the genetic information. DNA also has attractive physicochemical features for use as materials in molecular assemblies. DNA is chemically stable and can be prepared in nearly any length and sequence by chemical and enzymatic syntheses. Auxiliary functional groups can be built into the backbone as amidite reagents using automated DNA synthesizers. In addition, we can choose an appropriate method from abundant chemistries for post-modifications. The structures of DNA complexes can be rationally designed by bottom-up self-assembly. Therefore, functional groups can be positioned on the DNA scaffold in distinct distance and spatial arrangements.In the last decade, a number of DNA-based allosteric molecular systems have been reported. Some of the systems function as signal transducers, amplifiers, and chemical catalysts. These systems are rather exciting as fundamental achievements of the studies for nanomachines or nanodevices. They should also be useful as robust molecular sensors for sensitive bioassays. In this review, we will cover the photochemically relevant DNA-based molecular systems. They are classified into three groups: (i) DNA-templated molecular/ion assemblies; (ii) DNA-directed complexation; and (iii) chemical transformations accelerated on DNA.     

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.     

Electroless deposition of nickel on fluoropolymers modified by surface graft copolymerization

Surface modification of Ar plasma-pretreated poly(tetrafluoroethylene) (PTFE) and poly(vinylidene fluoride) (PVDF) films via UV-induced graft copolymerization with 4-vinylpyridine (4VP), 2-vinylpyridine (2VP) or 1-vinylimidazole (VIDz) was carried out. Electroless deposition of nickel could be carried out on these graft-modified fluoropolymer surfaces after PdCl₂ activation. The surface compositions of the graft-modified films were studied by X-ray photoelectron spectroscopy. The adhesion strength between the surface graft-copolymerized fluoropolymer film and the electrolessly deposited nickel was affected by the type of monomers used for graft copolymerization and the graft concentration. The optimum T-peel adhesion strengths of the electrolessly deposited Ni on the 4VP graft-copolymerized PTFE and PVDF surfaces were about 7 and 13 N/cm, respectively. The metal/fluoropolymer assemblies delaminated by cohesive failure inside the fluoropolymer substrates. The enhanced adhesion between the electrolessly deposited Ni and the surface-modified fluoropolymers is attributable to the interfacial charge transfer interactions between the grafted polymer chains and the deposited metals (Pd and Ni), the spatial distribution of the graft chains into the metal matrix and the covalent tethering of the graft chains on the fluoropolymer surface.     

DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.     

DNA-templated nanotube localization

Carbon nanotubes are nanometer-scale materials with important properties, but their use in nanofabrication will require further development of methods for controlled positioning at well-defined locations on surfaces. We have devised an approach for specifically localizing single-walled carbon nanotubes (SWNTs) onto 1-pyrenemethylamine (PMA)-decorated lambda-DNA molecules aligned on Si surfaces. PMA is used as a bridging compound because its amine group is attracted electrostatically to the negatively charged phosphate backbone of DNA, while the pyrenyl group in PMA interacts with SWNT surfaces through pi-stacking forces. From a total of 60 atomic force microscopy images obtained on three different substrates, we determined that 63% of SWNTs observed on the surfaces were anchored along DNA, and these nanotubes covered approximately 5% of the total DNA length. DNA-templated nanopositioning offers intriguing possibilities for the bottom-up assembly of materials at the nanometer scale.     

DNA-templated fluorescent silver nanoclusters

In this review, we discuss the synthesis and applications of DNA-templated fluorescent silver nanoclusters in aqueous solution. Various oligonucleotide sequences or conformations have been utilized to synthesize silver nanoclusters with excellent fluorescence properties. The range of applications has expanded greatly, from live cell staining and the detection of metal ions and small biomolecules to the detection of DNA or proteins.     

A Versatile Approach towards the Compaction,Decompaction, and Immobilization of DNA at Interfaces by Using Cyclodextrins

We investigate the temperature dependence of interactions of β‐cyclodextrin (CD)/hexadecyltrimethylammonium bromide (CTAB) self‐assemblies with DNA during the decompaction of DNA/CTAB complexes. By combining direct imaging techniques with density and sound‐velocity measurements, we can explain the decompaction process and suggest a suitable model. The DNA‐decompaction process by using CDs is accompanied by interactions with surfaces, such as glass or mica. The mechanism of β‐CD/CTAB self‐assembly is elucidated and the immobilization of DNA onto negatively charged surfaces is explained. Differences between the fractal dimensions of DNA that is adsorbed onto the surfaces are related to strong and weak binding, which permit the partial relaxation of DNA on the surfaces. The β‐CD/CTAB self‐assembled monolayers are demonstrated to be a facile and efficient route for surface functionalization, which allows for the immobilization of biomacromolecules in close proximity without any intermediate binding or deprotection steps. Moreover, this route is expected to show several advantages that might contribute to improving the performance of future biosensors as gentle immobilization‐limiting alteration of the protein structure, oriented immobilization, thereby allowing homogeneous accessibility, reversible immobilization, thereby allowing reutilizations, and high compatibility with various types of biomacromolecules.     

Nanoparticles as structural and functional units in surface-confined architectures

The nanoscale engineering of functional chemical assemblies has attracted recent research effort to provide dense information storage, miniaturized sensors, efficient energy conversion, light-harvesting, and mechanical motion. Functional nanoparticles exhibiting unique photonic, electronic and catalytic properties provide invaluable building blocks for such nanoengineered architectures. Metal nanoparticle arrays crosslinked by molecular receptor units on electrodes act as selective sensing interfaces with controlled porosity and tunable sensitivity. Photosensitizer/electron-acceptor bridged arrays of Au-nanoparticles on conductive supports act as photoelectrochemically active electrodes. Semiconductor nanoparticle composites on surfaces act as efficient light collecting systems, and nanoengineered semiconductor 'core-shell' nanocrystal assemblies reveal enhanced photoelectrochemical performance due to effective charge separation. Layered metal and semiconductor nanoparticle arrays crosslinked by nucleic acids find applications in the optical, electronic and photoelectrochemical detection of DNA. Metal and semiconductor nanoparticles assembled on DNA templates may be used to generate complex electronic circuitry. Nanoparticles incorporated in hydrogel matrices yield new composite materials with novel magnetic, optical and electronic properties.     

Soft functional polynuclear coordination compounds containing pyrimidine bridges

In this account, we describe the use of simple pyrimidine derivatives in combination with metal ions to build highly structured molecular architectures containing functional nanoenvironments, cavities and surfaces that can interact with additional species. The supramolecular structure of these systems can be rationally controlled by metal fragment geometry, reaction conditions and presence of templating agents. Thus, the use of transition metals with low coordination numbers or blocked bonding positions in combination with pyrimidines (e.g. 2-hydroxypyrimidine, 4-hydroxypyrimidine, 2,4-dihydroxypyrimidine, 2-aminopyrimidine) leads to the formation of either discrete assemblies, 1D polymers or helixes. When metal ions with higher coordination possibilities are applied instead, 2D and 3D networks are generated. Some of the assemblies built in this way possess functional cavities, pores and surfaces that can interact with additional species by means of hydrophobic, electrostatic, H-bonding interactions and coordinative bonds to give rise to recognition processes. The latter range from molecular recognition in homogeneous phase as well as clathrate formation, to heterogeneous solid-gas and solid-liquid adsorption phenomena. It should be noted that these materials are not rigid but able to undergo guest-induced reorganisation processes even in the solid state. Finally, some of these materials also combine additional interesting magneto-optical properties. Thus, dual systems can be envisaged in which two or more of these properties are present in the same material.     

Directing energy transfer in discrete one-dimensional oligonucleotide-templated assemblies

Monodisperse DNA-templated one dimensional dye assemblies have been constructed in which the energy transfer can be directed. Fluorescence experiments suggest an optimum transfer efficiency for stacks of 30 bases long.     

Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures

Spatially addressable DNA nanostructures facilitate the self-assembly of heterogeneous elements with precisely controlled patterns. Here we organized discrete glucose oxidase (GOx)/horseradish peroxidase (HRP) enzyme pairs on specific DNA origami tiles with controlled interenzyme spacing and position. The distance between enzymes was systematically varied from 10 to 65 nm, and the corresponding activities were evaluated. The study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Strongly enhanced activity was observed for those assemblies in which the enzymes were closely spaced, while the activity dropped dramatically for enzymes as little as 20 nm apart. Increasing the spacing further resulted in a much weaker distance dependence. Combined with diffusion modeling, the results suggest that Brownian diffusion of intermediates in solution governed the variations in activity for more distant enzyme pairs, while dimensionally limited diffusion of intermediates across connected protein surfaces contributed to the enhancement in activity for closely spaced GOx/HRP assemblies. To further test the role of limited dimensional diffusion along protein surfaces, a noncatalytic protein bridge was inserted between GOx and HRP to connect their hydration shells. This resulted in substantially enhanced activity of the enzyme pair.     

Stereoselectivity in DNA-templated organic synthesis and its origins

DNA-templated synthesis is a surprisingly general strategy for controlling chemical reactivity that enables synthetic products to be manipulated in ways previously available only to biological macromolecules. The chiral nature of the DNA template raises the possibility that DNA-templated synthesis can proceed stereoselectively. Here, we show that DNA-templated substitution reactions can exhibit stereoselectivity without the assistance of chiral groups other than those present in DNA. By characterizing changes in stereoselectivity as a result of systematic changes in the structure of the template-reagent complexes, we begin to reveal the origins of the observed stereoselectivity. We propose that the conformations of nucleotides adjacent to the reactants are largely responsible for stereoselectivity. Indeed, template and reagent sequences that can adopt either a left-handed Z-form DNA helix or a normal right-handed B-form DNA helix generate opposite stereoselectivities in the Z-form and B-form even though they share the same covalent structure and the same absolute stereochemistry. Our findings establish ways in which the chirality of an information carrier can be transmitted to the stereochemistry of encoded products through templated synthesis.     

Effects of template sequence and secondary structure on DNA-templated reactivity

DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. As the size of DNA-templated libraries increases, the possibility of forming intramolecularly base-paired structures within templates that impede templated reactions increases as well. To achieve uniform reactivity across many template sequences and to computationally predict and remove any problematic sequences from DNA-templated libraries, we have systematically examined the effects of template sequence and secondary structure on DNA-templated reactivity. By testing a series of template sequences computationally designed to contain different degrees of internal secondary structure, we observed that high levels of predicted secondary structure involving the reagent binding site within a DNA template interfere with reagent hybridization and impair reactivity, as expected. Unexpectedly, we also discovered that templates containing virtually no predicted internal secondary structure also exhibit poor reaction efficiencies. Further studies revealed that a modest degree of internal secondary structure is required to maximize effective molarities between reactants, possibly by compacting intervening template nucleotides that separate the hybridized reactants. Therefore, ideal sequences for DNA-templated synthesis lie between two undesirable extremes of too much or too little internal secondary structure. The relationship between effective molarity and intervening nucleic acid secondary structure described in this work may also apply to nucleic acid sequences in living systems that separate interacting biological molecules.     

Grafting acrylic polymers from flat nickel and copper surfaces by surface-initiated atom transfer radical polymerization

Acrylic polymers, including poly(methyl methacrylate), poly(2,2,2-trifluoroethyl methacrylate), poly( N,N'-dimethyaminoethyl methacrylate), and poly(2-hydroxyethyl methacrylate) were grafted from flat nickel and copper surfaces through surface-initiated atom transfer radical polymerization (ATRP). For the nickel system, there was a linear relationship between polymer layer thickness and monomer conversion or molecular weight of "free" polymers. The thickness of the polymer brush films was greater than 80 nm after 6 h of reaction time. The grafting density was estimated to be 0.40 chains/nm2. The "living" chain ends of grafted polymers were still active and initiated the growth of a second block of polymer. Block copolymer brushes with different block sequences were successfully prepared. The experimental surface chemical compositions as measured by X-ray photoelectron spectroscopy agreed very well with their theoretical values. Water contact angle measurements further confirmed the successful grafting of polymers from nickel and copper surfaces. The surface morphologies of all samples were studied by atomic force microscopy. This study provided a novel approach to prepare stable functional polymer coatings on reactive metal surfaces.     

Biosorption of nickel(II) and copper(II) ions from aqueous solution by Streptomyces coelicolor A3(2)

The biosorption of nickel(II) and copper(II) ions from aqueous solution by dried Streptomyces coelicolor A3(2) was studied as a function of concentration, pH and temperature. The optimum pH range for nickel and copper uptake was 8.0 and 5.0, respectively. At the optimal conditions, metal ion uptake was increased as the initial metal ion concentration increased up to 250 mg l(-1). At 250 mg l(-1) copper(II) ion uptake was 21.8% whereas nickel(II) ion uptake was found to be as high as 7.3% compared to those reported earlier in the literature. Metal ion uptake experiments were carried out at different temperatures where the best ion uptake was found to be at 25 degrees C. The characteristics of the adsorption process were investigated using Scatchard analysis at 25 degrees C. Scatchard analysis of the equilibrium binding data for metal ions on S. coelicolor A3(2) gave rise to a linear plot, indicating that the Langmuir model could be applied. However, for nickel(II) ion, divergence from the Scatchard plot was evident, consistent with the participation of secondary equilibrium effects in the adsorption process. Adsorption behaviour of nickel(II) and copper(II) ions on the S. coelicolor A3(2) can be expressed by both the Langmuir and Freundlich isotherms. The adsorption data with respect to both metals provide an excellent fit to the Freundlich isotherm. However, when the Langmuir isotherm model was applied to these data, a good fit was obtained for the copper adsorption only and not for nickel(II) ion.     

Chemo-genetic optimization of DNA recognition by metallodrugs using a presenter-protein strategy

The mode of action of precious metal anticancer metallodrugs is generally believed to involve DNA as a target. However, the poor specificity of such drugs often requires high doses and leads to undesirable side-effects. With the aim of improving the specificity of a ruthenium piano-stool complex towards DNA, we employed a presenter protein strategy based on the biotin-avidin technology. Guided by the X-ray structure of the assembly of streptavidin and a biotinylated piano-stool, we explored the formation of metallodrug-mediated ternary complexes with the presenter protein and DNA. The assemblies bound more strongly to telomere G-quadruplexes than to double-stranded DNA; chemo-genetic modifications (varying the complex or mutating the protein) modulated binding to these targets. We suggest that rational targeting of small molecules by presenter proteins could be exploited to bind metallodrugs to preferred macromolecular targets.     

Bending Nanofibers into Nanospirals: Coordination Chemistry as a Tool for Shaping Hydrophobic Assemblies

In the current work, we demonstrate how coordination chemistry can be employed to direct self‐assembly based on strong hydrophobic interactions. To investigate the influence of coordination sphere geometry on aqueous self‐assembly, we synthesized complexes of the amphiphilic perylene diimide terpyridine ligand with the first‐row transition‐metal centers (zinc, cobalt, and nickel). In aqueous medium, aggregation of these complexes is induced by hydrophobic interactions between the ligands. However, the final shapes of the resulting assemblies depend on the preferred geometry of the coordination spheres typical for the particular metal center. The self‐assembly process was characterized by UV/Vis spectroscopy, zeta potential measurements, and cryogenic transmission electron microscopy (cryo‐TEM). Coordination of zinc(II) and cobalt(II) leads to the formation of unique nanospiral assemblies, whereas complexation of nickel(II) leads to the formation of straight nanofibers. Notably, coordination bonds are utilized not as connectors between elementary building blocks, but as directing interactions, enabling control over supramolecular geometry.     

Translation of DNA into synthetic N-acyloxazolidines

The translation of DNA into synthetic molecules enables their manipulation by powerful evolution-based methods previously available only to proteins and nucleic acids. The development of increasingly sophisticated DNA-templated small-molecule syntheses is crucial to broadening the scope of this approach. Here, we report the translation of DNA templates into monocyclic and bicyclic N-acyloxazolidines using multistep DNA-templated organic synthesis. Second-generation template architectures, used for the first time in a multistep DNA-templated synthesis, together with reactions and linker cleavage strategies not previously described in a DNA-templated format, were crucial to the successful translation. The products generated in this work represent the most complex small molecules to date synthesized in a DNA sequence-programmed manner and provide the basis for DNA-templated synthetic heterocycle libraries.