Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments

The assembly and disassembly of RecA-DNA nucleoprotein filaments on double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) are important steps for homologous recombination and DNA repair. The assembly and disassembly of the nucleoprotein filaments are sensitive to the reaction conditions. In this work, we investigated different morphologies of the formed nucleoprotein filaments at low temperature under different solution conditions by atomic force microscopy (AFM). We found that low temperature and long keeping time could induce the incomplete disassembly of the formed nucleoprotein filaments. In addition, when the formed filaments were kept at -20 degrees C for 20 h with 1,4-dithiothreitol (DTT), the integrated filaments disassembled. It was similar to the case under the same condition without anything added. However, when glycerol was used as a substitute for DTT, there was no obvious disassembly at the same condition. Oppositely, when the formed filaments were kept at 4 degrees C for 20 h, the disassembly with additional DTT was not as obvious as the case at -20 degrees C for 20 h, whereas the case with additional glycerol disassembled. The experiments indicated the effect of cold denaturation on the interaction of DNA and RecA. Meanwhile, the study of these phenomena can supply guidelines for the property and stability of RecA as well as the relevant roles of influencing factors to RecA and DNA in further theoretical studies.     

Microwave synthesis of electrically conductive gold nanowires on DNA scaffolds

Biological molecules, in particular DNA, have shown great potential to be used as interconnects of nanodevices and computational elements. In this research, we synthesized electrically conductive gold nanowires for the first time exploiting an electroless and microwave heating method for 120-180 s. Our results indicate that DNA serves as a reducing and nonspecific capping agent for the growth of nanowires. The current voltage ( I- V) characteristics of the Au nanowires are continuous, exhibiting Ohmic behavior having low contact resistance with the gold electrodes. The nanowires have a diameter of 10-15 nm in solution and of 20-30 nm in immobilized DNA with resistivity comparable to pure metals. The method is highly selective with deposition confined to the DNA itself. The nanowires we fabricated can be used as building blocks for functional nanodevices, sensors, and optoelectronics.     

Engineering Hierarchical Nanostructures by Elastocapillary Self‐Assembly

Surfaces coated with nanoscale filaments such as silicon nanowires and carbon nanotubes are potentially compelling for high‐performance battery and capacitor electrodes, photovoltaics, electrical interconnects, substrates for engineered cell growth, dry adhesives, and other smart materials. However, many of these applications require a wet environment or involve wet processing during their synthesis. The capillary forces introduced by these wet environments can lead to undesirable aggregation of nanoscale filaments, but control of capillary forces can enable manipulation of the filaments into discrete aggregates and novel hierarchical structures. Recent studies suggest that the elastocapillary self‐assembly of nanofilaments can be a versatile and scalable means to build complex and robust surface architectures. To enable a wider understanding and use of elastocapillary self‐assembly as a fabrication technology, we give an overview of the underlying fundamentals and classify typical implementations and surface designs for nanowires, nanotubes, and nanopillars made from a wide variety of materials. Finally, we discuss exemplary applications and future opportunities to realize new engineered surfaces by the elastocapillary self‐assembly of nanofilaments.     

Direct evaluation of a mechanism for activation of the RecA nucleoprotein filament

The RecA protein of Escherichia coli controls the SOS response for DNA damage tolerance and plays a crucial role in recombinational DNA repair. The formation of a RecA.ATP.ssDNA complex initiates all RecA activities, and yet this process is not understood at the molecular level. An analysis of RecA.DNA interactions was performed using both a mutant RecA protein containing a tryptophan (Trp) reporter and oligodeoxyribonucleotides (ODNs) containing a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Experiments using fluorescent ODNs allowed structurally distinct nucleoprotein filaments, formed in the absence and presence of ATPgammaS (a slowly hydrolyzed analogue of ATP), to be differentiated directly. Stopped-flow spectrofluorometry, combined with presteady-state kinetic analyses, revealed unexpected differences in the rates of RecA.ODN and RecA.ATPgammaS.ODN complex assembly. This is the first demonstration that such intrinsically fluorescent synthetic DNAs can be used to characterize definitively the real-time assembly and activation of RecA.ssDNA complexes. Surprisingly, the ssDNA binding event is almost 50-fold slower in the presence of the activating ATPgammaS cofactor. Furthermore, a combination of time-dependent emission changes from 6MI and Trp allowed the first direct chemical test of whether an inactive filament can isomerize to the active state. The results revealed that, unlike the hexameric motor proteins, the inactive RecA filament cannot directly convert to the active state upon ATPgammaS binding. These results have implications for understanding how a coincidence of functions--an ATP-communicated signal-like activity and an ATP-driven motorlike activity--are resolved within a single protein molecule.     

DNA-templated assembly of nanoscale wires and protein-functionalized nanogap contacts

The use of DNA to template the assembly of nanoscale wires and protein-functionalized nanogap contacts is described: Specifically, the use of DNA to template the assembly of gold nanowires between conventionally patterned gold contacts on a silicon wafer substrate. Also described is the use of DNA to template the assembly of protein-functionalized nanogap gold contacts on a silicon wafer substrate. Of particular significance is the finding that suitably modified gold nanoparticles recognize and bind selectively the protein-functionalized nanogap and are localized there.     

Nanoparticle-DNA conjugates bearing a specific number of short DNA strands by enzymatic manipulation of nanoparticle-bound DNA

Self-assembling of metallic nanoparticles to form well-defined nanostructured structures is a field that has been receiving considerable research interest in recent years. In this field, DNA is a commonly used linker molecule to direct the assembly of the nanoscale building blocks because of its unique recognition capabilities, mechanical rigidity, and physicochemical stability. This study reported our novel approach to generate gold nanoparticle-DNA conjugates bearing specially designed DNA linker molecules that can be used as building blocks to construct nanoassemblies with precisely controlled structure or as nanoprobes for quantitative DNA sequence detection analysis. In our approach, gold nanoparticle-DNA conjugates bearing a specific number of long double-stranded DNA strands were prepared by gel electrophoresis. A restriction endonuclease enzyme was then used to manipulate the length of the nanoparticle-bound DNA. This enzymatic cleavage was confirmed by gel electrophoresis, and digestion efficiency of 90% or more was achieved. With this approach, nanoparticle conjugates bearing a specific number of strands of short DNA with less than 20-base can be achieved.     

DNA-templated assembly and electropolymerization of aniline on gold surface

Biomolecule template gives new opportunities for the fabrication of novel materials with special features. Here we report a route to the formation of DNA–polyaniline (PAn) complex, using immobilized DNA as a template. A gold electrode was first modified with monolayer of 2-aminoethanethiol by self-assembly. Thereafter, by simply immersing the gold electrode into DNA solution, DNA molecules can be attached onto the gold surface, followed by the DNA-templated assembly and electropolymerization of protonated aniline. The electrostatic interactions between DNA and aniline can keep the aniline monomers aligning along the DNA strands. Investigations by surface plasmon resonance (SPR), electrochemistry and reflection–absorption UV/Vis–Near IR spectroscopy substantially convince that PAn can be electrochemically grown around DNA template on gold surface. This work may be provides fundamental aspects for building PAn nanowires with DNA as template on solid surface if DNA molecules can be individually separated and stretched.     

Construction of Heterojunction Nanowires from Polythiophene/Polypyrrole for Applications as Efficient Switches

The design and fabrication of PTh–PPY heterojunction nanowires that exhibits smart responses to electrochemical redox potentials is described. In their oxidized state, PTh–PPY nanowires act as resistors, whilst in their reduced state, they acts as diodes. Furthermore, the electrical transport mode can be reversibly changed by alternately exposing the nanowires to negative and positive potentials. Constructing full‐organic heterojunction nanowires with smart, controllable properties will contribute to the development of intelligent organic devices and organic–electronic circuits on the nanoscale.     

DNA Assisted Assembly of Multisegmented Nanowires

This work demonstrates a highly specific and selective assembly of multisegmented nanowires on prepatterned gold electrodes using DNA hybridization. Multisegmented Au/Pd/Au nanowires were synthesized using template‐directed electrodeposition. Two complementary single‐stranded DNAs modified with thiol tags adsorb on gold electrodes and gold segments of nanowires, and enable the nanowires to assemble across electrodes. The assembled nanowires show ohmic contact with minimum contact resistance. Using these nanowires, the temperature dependent electrical resistance and the sensing performance toward hydrogen were investigated. The temperature coefficient of resistance of nanowires was lower than bulk polycrystalline counterpart, because of higher electron scattering at the surface and grain boundaries of nanowires. The nanowires were sensitive toward hydrogen gas at room temperature with a detection limit of 0.5%.     

Polymer-like conformation and growth kinetics of Bi2S3 nanowires

One-dimensional inorganic crystals (i.e., crystalline nanowires) are one of the most intensely investigated classes of materials of the past two decades. Despite this intense effort, an important question has yet to be answered: do nanowires display some of the unique characteristics of polymers as their diameter is progressively decreased? This work addresses this question with three remarkable findings on the growth and form of ultrathin Bi(2)S(3) nanowires. (i) Their crystallization in solution is quantitatively describable as a form of living step-growth polymerization: an apparently exclusive combination of addition of "monomer" to the ends of the nanowires and coupling of fully formed nanowires "end-to-end", with negligible termination and initiation. (ii) The rate constants of these two main processes are comparable to those of analogous processes found in polymerization. (iii) The conformation of these nanowires is quantitatively described as a worm-like conformation analytically analogous to that of semiflexible polymers and characterized by a persistence length of 17.5 nm (shorter than that of double-stranded DNA) and contour lengths of hundreds of micrometers (longer than those of most synthetic polymers). These findings do not prove a chemical analogy between crystals and polymers (it is unclear if the monomer is a molecular entity tout court) but demonstrate a physical analogy between crystallization and polymerization. Specifically, they (i) show that the crystallization of ensembles of nanoscale inorganic crystals can be conceptually analogous to polymerization and can be described quantitatively with the same experimental and mathematical tools, (ii) demonstrate that one-dimensional nanocrystals can display topological characteristics of polymers (e.g., worm-like conformation in solution), (iii) establish a unique experimental model system for the investigation of polymer-like topological properties in inorganic crystals, and (iv) provide new heuristic guidelines for the synthesis of polymer-like nanowires.     

Nanoparticle arrays patterned by electron-beam writing: structure, composition, and electrical properties

Direct electron beam writing in nanoparticle films is employed to create nanoscale wires between prepatterned gold electrodes on SiO(2)/Si wafers. Characterization of these nanowires using AFM, SEM, and EDX reveals a core/sheath morphology, where a gold-rich core is surrounded by a sheath which is mainly of carbon. Z-contrast STEM images indicate that the central core consists of a distribution of metal cores in a carbon network. The results suggest that the nanoparticle network is created through cross-linking of the ligands of adjacent particles. The high resistivities obtained in conductivity measurements are consistent with this picture. The work illustrates the ability to generate patterned nanoparticle arrays which can be addressed electrically.     

Synthesis, manipulation and conductivity of supramolecular polymer nanowires

The synthesis of supramolecular conducting nanowires can be achieved by using DNA and pyrrole. Oxidation of pyrrole in DNA-containing solutions yields a material that contains both the cationic polypyrrole (PPy) and the anionic DNA polymers. Intimate interaction of the two polymer chains in the self-assembled nanowires is indicated by FTIR spectroscopy. AFM imaging shows individual nanowires to be continuous, approximately 5 nm high and conformationally flexible. This feature allows them to be aligned by molecular combing in a similar manner to bare DNA and provides a convenient method for fabricating a simple electrical device by stretching DNA/PPy strands across an electrode gap. Current-voltage measurements confirm that the nanowires are conducting, with values typical for a polypyrrole-based material. In contrast to polymerisation of pyrrole on a DNA template in bulk solution, attempts to form similar wires by polymerisation at surface-immobilised DNA do not give a continuous coverage; instead, a beads-on-a-string appearance is observed suggesting that immobilisation inhibits the assembly process.     

Preparation of high quality electrical insulator self-assembled monolayers on gold. Experimental investigation of the conduction mechanism through organic thin films

Self-assembled monolayers (SAMs) form highly ordered, stable dielectrics on conductive surfaces. Being able to attach larger-area contacts in a MIM (metal-insulator-metal) diode, their electrical properties can be determined. In this paper, the electrical conduction through thiolate SAMs of different alkyl chain lengths formed on gold surfaces were studied and discussed. The influence of the headgroup with respect to the surface quality and prevention of short circuits is investigated. Phenoxy terminated alkanethiols were found to form high quality SAMs with perfect insulating properties. Synthesis of the required terminally substituted long chain thiols have been developed. The I(V) characteristics of MIM structures formed with these SAMs are measured and simulated according to theoretical tunneling models for electrical conductivity through thin organic layers. SAM based electronic devices will become especially important for future nanoscale applications, where they can serve as insulators, gate dielectric of FETs, resistors, and capacitor structures.     

Morphology control in self-assembled monolayers written by dip pen nanolithography

Here, we describe the effect of writing speed in dip pen nanolithography on the morphology (height and density) of self-assembled monolayers of alkanethiols on gold surfaces. The analysis of atomic force microscopy images of written monolayers shows that molecules assemble according to a nucleation and growth mechanism. Slow writing speeds lead to dense monolayers that can be used either to direct the self-assembly of metal nanoparticles or as masks for selective etching of conductive gold nanowires.     

High density germanium nanowire assemblies: contact challenges and electrical characterization

The conductive properties of vertically aligned germanium nanowires, with mean diameters of 50 and 100 nm, within anodized aluminum oxide (AAO) templates have been characterized by conductive atomic force microscopy (C-AFM) and macrocontact measurements. C-AFM was used to determine the electrical transport properties of individual nanowires within the arrays, while macrocontacts were used to measure the mean current-voltage characteristics of groups of nanowires. Contact resistance between the nanowires and metal macrocontacts was minimized by polishing and gradual etching of the AAO surface, to expose the nanowires, prior to deposition of the contacts. Impedance measurements were used to analyze the importance of defects on the charge transport properties of the germanium nanowire arrays. Conductivity data from C-AFM and macrocontact measurements were found to be comparable suggesting that both methods are inherently suitable for evaluating the electrical transport properties of encapsulated nanowires within a matrix. These results are significant as the ability to make good ohmic contacts to nanowires, within well-defined arrays, is key for the future "bottom-up" fabrication of multilayered device architectures for future electronic and optoelectronic devices.     

Nanowire-based nanogap electrodes by annealing of multisegmented Pt/Au/Pt nanowires in air

A simple thermally lithographic method for fabricating nanowire-based metallic nanogap electrodes is presented, in which the multisegmented Pt/Au/Pt nanowires were electrodeposited in the pores of porous anodic aluminum oxide (AAO) templates first and then thermally annealed to form a nanoscale gap at the interface of Au/Pt. We proposed that the breaking of the multisegmented Pt/Au/Pt nanowires is due to the chemical and physical transformations of the Au segment with O₂. These electrodes are ideally suited for electron-transport studies of chemically synthesized nanostructures, and their utility is demonstrated here by measuring the electronic conduction of short (54-base-pairs) double-stranded (ds) DNA molecules in a dry state.     

What is the structure of the RecA-DNA filament?

The bacterial RecA protein has been a model system for understanding how a protein can catalyze homologous genetic recombination. RecA-like proteins have now been characterized from many organisms, from bacteriophage to humans. Some of the RecA-like proteins, including human RAD51, appear to function as helical filaments formed on DNA. However, we currently have high resolution structures of inactive forms of the protein, and low resolution structures of the active complexes formed by RecA-like proteins on DNA in the presence of ATP or ATP analogs. Within a crystal of the E. coli RecA protein, a helical polymer exists, and it has been widely assumed that this polymer is quite similar to the active helical filament formed on DNA. Recent developments have suggested that this may not be the case.     

模板合成法制备金纳米线的研究

近年来,利用化学和物理方法制备各种高度有序的纳米结构材料已经成为学术界的研究热点之一．其中,在特定的模板中沉积各种材料而构建纳米点阵的方法,具有制备简便,成本较低等优点,而且在尺度上可以突破刻蚀技术的局限性,具有广泛的应用前景［１］．常用的模板有阳极氧化多孔铝（ＡＡＯ）、多孔硅和聚合物等,其中ＡＡＯ模板具有耐高温,绝缘性好,孔洞分布均匀有序,而且大小可控等特点［２］,是使用较为广泛的一种．利用阳极氧化铝为模板,采用电化学方法［３～７］或压差注入法［８］制备有序的纳米粒子点阵,已经在润滑［９］、电…     

Formation process of two-dimensional networked gold nanowires by citrate reduction of AuCl4- and the shape stabilization

Gold nanowires with a two-dimensional (2-D) network structure were formed by citrate reduction of AuCl4- with a low concentration of citrate. The structure change during the growth processes was observed by transmission electron microscopy (TEM) and the variation in concentrations of gold species in the aqueous solution was monitored by UV-vis spectra and Inductively Coupled Argon Plasma Emission Spectrophotometer (ICAP). The formation of 2-D gold nanowires was induced by the small amount of reducing agent because the preliminary gold nanoparticles formed by reduction of AuCl4- were thermodynamically unstable in the aqueous solution due to the insufficient capping of citrate. One of the key points of nanowire formation is the preferential adsorption of AuCl4- instead of citrate ions on the surface of the preliminary gold particles, which results in an attracting force between gold nanoparticles. We propose a hit-to-stick-to-fusion model, in which gold nanoparticles adhere by the attraction force and stick together, causing selective deposition of reduced gold metallic species on the concave surface of the two sticking particles, followed by fusion into nanowires. Nanowires then connect with each other, forming a network structure. The evidence obtained from TEM observation of transformation from gold nanowires on a TEM grid to large nanoparticles by hydrogen gas reduction and time-resolved measurements of gold ions suggest that gold ions not only are crucial for the growth of gold nanowires but also play an important role in stabilizing the shape of gold nanowires during the formation process. This method for synthesizing 2-D gold nanowires is simple and relatively easy application to the synthesis of other metallic nanowires such as silver or platinum is expected.     

Label-free and sequence-specific DNA detection down to a picomolar level with carbon nanotubes as support for probe DNA

This study describes a simple and label-free electrochemical impedance spectroscopic (EIS) method for sequence-specific detection of DNA by using single-walled carbon nanotubes (SWNTs) as the support for probe DNA. SWNTs are confined onto gold electrodes with mixed self-assembly monolayers of thioethanol and cysteamine. Single-stranded DNA (ssDNA) probe is anchored onto the SWNT support through covalent binding between carboxyl groups at the nanotubes and amino groups at 5′ ends of ssDNA. Hybridization of target DNA with the anchored probe DNA greatly increases the interfacial electron-transfer resistance (R_et) at the double-stranded DNA (dsDNA)-modified electrodes for the redox couple of Fe(CN)₆^3−/4−, which could be used for label-free and sequence-specific DNA detection. EIS results demonstrate that the utilization of SWNTs as the support for probe DNA substantially increases the surface loading of probe DNA onto electrode surface and thus remarkably lowers the detection limit for target DNA. Under the conditions employed here, R_et is linear with the concentration of target DNA within a concentration range from 1 to 10 pM with a detection limit down to 0.8 pM (S/N = 3). This study may offer a novel and label-free electrochemical approach to sensitive sequence-specific DNA detection.