Conductive metal nanowires templated by the nucleoprotein filaments, complex of DNA and RecA protein

Development of preprogrammable conductive nanowires is a requisite for the future fabrication of nanoscale electronics based on molecular assembly. Here, we report the synthesis of conductive metal nanowires from nucleoprotein filaments, complexes of single- or double-stranded DNA and RecA protein. A genetically engineered RecA derivative possessing a reactive and surface accessible cysteine residue was reacted with functionalized gold particles, resulting in nucleoprotein filaments with gold particles attached. The template-based gold particles were enlarged by chemical deposition to form uniformly metallized nanowires. The programming information can be encoded in DNA sequences so that an intricate electrical circuit can be constructed through self-assembly of each component. As the RecA filament has higher degree of stiffness than double-stranded DNA, it provides a robust scaffold that allows us to fabricate more reliable and well-organized electrical circuitry at the nanoscale. Furthermore, the function of homologous pairing provides sequence-specific junction formation as well as sequence-specific patterning metallization.     

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.     

Reversible control of assembly and disassembly of interlocked supermolecules

Two kinds of interlocked supramolecular complexes that display stimulus-responsive assembly and disassembly have been described. One is a pseudorotaxane driven by hydrogen-bonding interactions between rings 2a and 2b and rods 1a and 1b. The rods contain a binding site for the ring as well as a stimulus-responsive diazo group, both of which are conformationally constrained in parallel by connecting them to a rigid xanthene skeleton. The trans isomer of 1a bearing a rigid binding site cannot form the pseudorotaxanes with the rings 2a and 2b because the neighboring diazophenyl group sterically shields the binding site. However, when trans-1a was converted to the corresponding cis-1a by UV light, the pseudorotaxanes are immediately formed with association constants of 70 +/- 10 M(-1) and (1.1 +/- 0.1) x 10(3) M(-1) for 2a and 2b, respectively, in CDCl3 at 24 +/- 1 degrees C. The pseudorotaxanes are completely disassembled into their molecular component when heated at 80-85 degrees C for 20 min. The assembly and disassembly processes can be reversibly cycled by repeating irradiation and heating alternatively. In the case of the rod 1b that possesses a flexible binding site, both cis and trans isomers can form the corresponding pseudorotaxanes with association constants of (2.0 +/- 0.3) x 10(2) M(-1) for 2a and trans-1b and of (7.4 +/- 0.5) x 10(2) M(-1) for 2a and cis-1b in CDCl3 at 24 +/- 1 degrees C. In this system, therefore, external stimuli can modulate the relative distribution of the pseudorotaxane and its components. Finally, the work was extended to the construction of a kinetically more stable molecular machine based on a rotaxane-like complex 10.11 between a metallocycle 11 and a dumbbell 10. In this system, the complex and its components showed separate sets of the signals, not the averaged, in 1H NMR spectroscopy as expected by the increased kinetic stability.     

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.     

Assembly of DNA-functionalized gold nanoparticles studied by UV/Vis-spectroscopy and dynamic light scattering

The DNA mediated assembly of complementary DNA-functionalized gold nanoparticles (DNA-AuNP) was investigated by means of UV/Vis-spectroscopy and Dynamic Light Scattering (DLS). The melting temperature of the aggregates was determined to be T(m) = 31 degrees C. Characterization of the assembly at 20 degrees C, 25 degrees C and 30 degrees C showed a decrease of the initial assembly growth rate with increasing temperature. The correlation of the wavelengths at the absorbance maxima lambda(max) and the hydrodynamic radii R(h) of the AuNP assemblies proved the dependence of the optical properties on the assembly size while at higher assembly temperature (30 degrees C) a larger redshift of lambda(max) with increasing R(h) was observed than at lower temperatures. This tendency might give information about the dependence of the internal structure of the DNA-AuNP assemblies on assembly temperature. It is assumed that at higher temperatures more compact assemblies are built than at lower temperatures of 20 degrees C and 25 degrees C. To the best of our knowledge, this is the first systematic time-resolved in situ investigation of DNA-mediated AuNP assembly by UV/Vis-spectroscopy and DLS.     

Reversible self-organization of a UV-responsive PEG-terminated malachite green derivative: vesicle formation and photoinduced disassembly

This paper describes the assembly and disassembly of vesicles formed by a UV-responsive poly(ethylene glycol) terminated malachite green derivative. The UV-responsive amphiphile with both a hydrophobic malachite green group and a hydrophilic PEG group can self-organize into vesicles in water before UV irradiation. However, upon UV irradiation, the photochromic moiety can be ionized to its corresponding cation, leading to the disassembly of these vesicles. In addition, the cation can thermally recover its electrically neutral form, and the disassembled species can form vesicles reversibly on the basis of a thermal reverse reaction. The reverse reaction is temperature-controlled and can be speeded up by thermal treatment. By using various characterization techniques, e.g., transmission electron microscopy, dynamic light scattering, UV-visible spectroscopy, and NMR spectroscopy, we have confirmed that the vesicle structures can be formed, disassembled, and recovered by the above-mentioned treatments. It is anticipated greatly that this line of research may provide new insights into the mechanism behind stimuli-responsive formation and rupture of molecular assemblies, facilitating the design and synthesis of new surface active molecules for the fabrication of stimuli-responsive materials with designed functions.     

Photocontrolled DNA Origami Assembly by Using Two Photoswitches

Stimuli-responsive switching molecules have been widely investigated for the purpose of the mechanical control of biomolecules. Recently developed arylazopyrazole (AAP) shows photoisomerization activity, displaying a faster response to light-induced conformational changes and unique absorption spectral properties compared with those of conventionally used azobenzene. Herein, it is demonstrated that AAP can be used as a photoswitching molecule to control photoinduced assembly and disassembly of DNA origami nanostructures. An AAP-modified DNA origami has been designed and constructed. It is observed that the repeated assembly and disassembly of AAP-modified X-shaped DNA origami and hexagonal origami with complementary strands can be achieved by alternating UV and visible-light irradiation. Closed and linear assemblies of AAP-modified X-shaped origami were successfully formed by photoirradiation, and more than 1 μm linear assemblies were formed. Finally, it is shown that the two photoswitches, AAP and azobenzene, can be used in tandem to independently control different assembly configurations by using different irradiation wavelengths. AAP can extend the variety of available wavelengths of photoswitches and stably result in the assembly and disassembly of various DNA origami nanostructures.     

Disassembly of Multicompartment Polymer Micelles in Spatial Sequence Using an Electrostatic Field and Its Application for Release in Chronological Order

Multicompartment micelles (MCPs), comprising sequences of repeated elemental discoid parts connected by fasciculus, were formed by self‐assembly of polystyrene‐block‐poly(2‐vinyl pyridine)‐block‐poly(ethylene oxide). Using an electrostatic field, the MCPs can be disassembled through consequent release of small spherical micelles. During this disassembly process, release of loaded species can be achieved from the micelles in chronological order. Two location‐selected cargos (mitoxantrone (MTNT) and fluorescein isothiocyanate (FITC)) in the outer and inner compartments of the micelles can be released in chronological order. Under the applied electrostatic field (intensity: 16 kV cm^?1), the loaded MTNT was rapidly released with more than 80 % release, whereas the loaded FITC was slowly released with less than 20 % release in 12 h. At a later stage (after more than 12 h), the loaded MTNT was slowly released with less than 20 % release, while the loaded FITC was rapidly released with more than 80 % release.     

Surface Assembly of DNA Origami on a Lipid Bilayer Observed Using High-Speed Atomic Force Microscopy

The micrometer-scale assembly of various DNA nanostructures is one of the major challenges for further progress in DNA nanotechnology. Programmed patterns of 1D and 2D DNA origami assembly using specific DNA strands and micrometer-sized lattice assembly using cross-shaped DNA origami were performed on a lipid bilayer surface. During the diffusion of DNA origami on the membrane surface, the formation of lattices and their rearrangement in real-time were observed using high-speed atomic force microscopy (HS-AFM). The formed lattices were used to further assemble DNA origami tiles into their cavities. Various patterns of lattice–tile complexes were created by changing the interactions between the lattice and tiles. For the control of the nanostructure formation, the photo-controlled assembly and disassembly of DNA origami were performed reversibly, and dynamic assembly and disassembly were observed on a lipid bilayer surface using HS-AFM. Using a lipid bilayer for DNA origami assembly, it is possible to perform a hierarchical assembly of multiple DNA origami nanostructures, such as the integration of functional components into a frame architecture.     

Synthesis and characterization of mesoporous ceria/alumina nanocomposite materials via mixing of the corresponding ceria and alumina gel precursors

Mesoporous ceria/alumina, CeO(2)/Al(2)O(3), composites containing 10, 20 and 30% (w/w) ceria were prepared by a novel gel mixing method. In the method, ceria gel (formed via hydrolysis of ammonium cerium(IV) nitrate by aqueous ammonium carbonate solution) and alumina gel (formed via controlled hydrolysis of aluminum tri-isopropoxide) were mixed together. The mixed gel was subjected to subsequent drying and calcination for 3 h at 400, 600, 800 and 1000 degrees C. The uncalcined (dried at 110 degrees C) and the calcined composites were investigated by different techniques including TGA, DSC, FTIR, XRD, SEM and nitrogen adsorption/desorption isotherms. Results indicated that composites calcined for 3 h at 800 degrees C mainly kept amorphous alumina structure and gamma-alumina formed only upon calcinations at 1000 degrees C. On the other hand, CeO(2) was found to crystallize in the common ceria, cerinite, phase and it kept this structure over the entire calcination range (400-1000 degrees C). Therefore, high surface areas, stable surface textures, and non-aggregated nano-sized ceria dispersions were obtained. A systematic texture change based on ceria ratio was observed, however in all cases mesoporous composite materials exposing thermally stable texture and structure were obtained. The presented method produces composite ceria/alumina materials that suit different applications in the field of catalysis and membranes technology, and throw some light on physicochemical factors that determine textural morphology and thermal stability of such important composite.     

A Horizontal Magnetic Tweezers for Studying Single DNA Molecules and DNA-Binding Proteins

We report data from single molecule studies on the interaction between single DNA molecules and core histones using custom-designed horizontal magnetic tweezers. The DNA-core histone complexes were formed using λ-DNA tethers, core histones, and NAP1 and were exposed to forces ranging from ~2 pN to ~74 pN. During the assembly events, we observed the length of the DNA decrease in approximate integer multiples of ~50 nm, suggesting the binding of the histone octamers to the DNA tether. During the mechanically induced disassembly events, we observed disruption lengths in approximate integer multiples of ~50 nm, suggesting the unbinding of one or more octamers from the DNA tether. We also observed histone octamer unbinding events at forces as low as ~2 pN. Our horizontal magnetic tweezers yielded high-resolution, low-noise data on force-mediated DNA-core histone assembly and disassembly processes.     

pH-Responsive Reversible DNA Self-assembly Mediated by Zwitterion

pH-Responsive DNA assembles have drawn growing attentions owing to their great potential in diverse areas.However,pH-responsive motifs are limited to specific DNA sequences and annealing is usually needed for DNA assemblies;therefore,sequence-independent pH-responsive DNA assembly at room temperature is highly desired as a more general way.Here,we propose a reversible pH-responsive DNA assembly strategy at room-temperature using zwitterion,glycine betaine(GB),as charge-regulation molecules.The reversible assembly and disassembly of DNA nanostructures could be achieved by alternatively regulating the acidic and basic environments in the presence of GB,respectively.In an acidic environment,carboxylate group in GB was protonated and GB was positively charged,which facilitated to shield the inherent electrostatic repulsion of DNA strands.Molecular simulation showed that the newly formed carboxyl group in protonated GB could form hydrogen bonds with bases in DNA to promote the assembly of DNA strands.In a basic solution,carboxylate group in GB was deprotonated and GB was neutral,thus inducing the dissociation of DNA assembly.     

Polyelectrolyte adsorption and layer-by-layer assembly: Electrochemical control

Thin films formed via the adsorption or layer-by-layer assembly of charged polymers are important in many sensing, energy, and biomedical applications. When the underlying substrate is a (semi)conductor, the opportunity exists to influence film formation and film properties through an applied electric potential. The recent literature on electrochemical influence of polyelectrolyte-based films is reviewed, with a focus on monolayer and multilayer film assembly and disassembly. Of particular interest are monolayer films grown to a tailored thickness on the 10–100 nm scale, and polyelectrolyte multilayer films controllably disassembled, upon application of a modest electric potential. Experimental observations are discussed in terms of governing factors such as interfacial pH and ionic composition, counter-ion correlations, charge regulation, dielectric discontinuity, and short-range polymer–polymer interactions. Recent modeling efforts are also briefly addressed.     

Foaming properties of monoglycerol fatty acid esters in nonpolar oil systems

Foaming properties of monoglycerol fatty acid esters that have different alkyl chain lengths were studied in different nonpolar oils, namely liquid paraffin (LP 70), squalane, and squalene. The effect of the hydrocarbon chain length of the surfactant, the concentration, the nature of the oil, and the temperature on the nonaqueous foam stability was mainly studied. Five weight percent of glycerol alpha-monododecanoate (monolaurin) formed highly stable foams in squalane at 25 degrees C, and the foams were stable for more than 14 h. Foam stability of the monolaurin/LP 70 and the monolaurin/squalene systems are almost similar, and the foams were stable for more than 12 h. Foam stability was decreased as the hydrocarbon chain length of the monoglyceride decreased. In the glycerol alpha-monodecanoate (monocaprin)-oil systems, the foams were stable only for 3-4 h, depending on the nature of the oil. However, the foams formed in the glycerol alpha-monooctanoate (monocaprylin)-oil systems coarsened very quickly, leading to the progressive destruction of foam films, and all of the foams collapsed within a few minutes. Foam stability decreased when the oil was changed from squalane to squalene, in both monocaprin and monolaurin systems. It was observed that, in the dilute regions, these monoglycerides form fine solid dispersions in the aforementioned oils at 25 degrees C. At higher temperatures, the solid melts to isotropic single-liquid or two-liquid phases and the foams formed collapsed within 5 min. Judging from the wide-angle X-ray scattering (WAXS) and the foaming test, it is concluded that the stable foams are mainly caused by the dispersion of the surfactant solids (beta-crystal) and foam stability is largely influenced by the shape and size of the dispersed solid particles.     

Reversible Assembly and Disassembly of Receptor‐Decorated Gold Nanoparticles Controlled by Ion Recognition

The controlled assembly of randomly dispersed colloidal particles can provide access to materials with advanced optical and electronic properties while providing fundamental insights into self‐assembly processes in nature and nanotechnology. Typically, self‐assembled nanoparticles are prepared by exploiting electrostatic interactions, lithographic techniques, and covalently linked molecular scaffolds. This results in static morphologies that cannot be disassembled easily. On the other hand, having access to systems that can be assembled or disassembled in a controlled manner could allow for in‐depth understanding of the nanoparticles as well as rational control over the morphology and fundamental properties of the resulting constructs. If the changes in aggregation are induced by a specific external chemical stimulus, it could also permit the development of new chemosensors. Here we demonstrate the reversible assembly and disassembly of gold nanoparticles achieved by modulating the noncovalent interactions between surface‐bound calix[4]pyrroles and added bis‐imidazolium cations. We also demonstrate the use of these nanoparticles in the selective sensing of anions.     

Naphthalene Imide Conjugates: Formation of Supramolecular Assemblies,and the Encapsulation and Release of Dyes through DNA‐Mediated Disassembly

We report the synthesis of two new amphiphilic conjugates 1 and 2 based on naphthalene di‐ and monoimide chromophores and the investigation of their photophysical, self‐assembly and DNA‐binding properties. These conjugates showed aqueous good solubility and exhibited strong interactions with DNA and polynucleotides such as poly(dG?dC)–poly(dG?dC) and poly(dA?dT)–poly(dA?dT). The interaction of these conjugates with DNA was evaluated by photo‐ and biophysical techniques. These studies revealed that the conjugates interact with DNA through intercalation with association constants in the order of 5–8×10⁴ M ^?1. Of these two conjugates, bolaamphiphile 1 exhibited a supramolecular assembly that formed vesicles with an approximate diameter of 220 nm in the aqueous medium at a critical aggregation concentration of 0.4 mM , which was confirmed by SEM and TEM. These vesicular structures showed a strong affinity for hydrophobic molecules such as Nile red through encapsulation. Uniquely, when exposed to DNA the vesicles disassembled, and therefore this transformation could be utilised for the encapsulation and release of hydrophobic molecules by employing DNA as a stimulus.     

Liquid crystal formation of RecA-DNA filamentous complexes

Spontaneous optical birefringence of RecA-bound linear and closed circular single-stranded DNA filaments, as well as RecA self-assembled polymer, was observed in aqueous buffer solutions, which demonstrates the formation of lyotropic liquid crystalline phases.     

Batch Fermentation Model of Propionic Acid Production by Propionibacterium acidipropionici in Different Carbon Sources

Propionic acid (PA) is widely used as additive in animal feed and also in the manufacturing of cellulose-based plastics, herbicides, and perfumes. Salts of propionic acid are used as preservative in food. PA is mainly produced by chemical synthesis. Nowadays, PA production by fermentation of low-cost industrial wastes or renewable sources has been an interesting alternative. In the present investigation, PA production by Propionibacterium acidipropionici ATCC 4965 was studied using a basal medium with sugarcane molasses (BMSM), glycerol or lactate (BML) in small batch fermentation at 30 and 36 degrees C. Bacterial growth was carried out under low dissolved oxygen concentration and without pH control. Results indicated that P. acidipropionici produced more biomass in BMSM than in other media at 30 degrees C (7.55 g l(-1)) as well as at 36 degrees C (3.71 g l(-1)). PA and biomass production were higher at 30 degrees C than at 36 degrees C in all cases studied. The best productivity was obtained by using BML (0.113 g l(-1) h(-1)), although the yielding of this metabolite was higher when using glycerol as carbon source (0.724 g g(-1)) because there was no detection of acetic acid. By the way, when using the other two carbon sources, acetic acid emerged as an undesirable by-product for further PA purification.     

Inhibition of Escherichia coli RecA by rationally redesigned N-terminal helix

Bacterial RecA promotes the development and transmission of antibiotic resistance genes by self-assembling into an ATP-hydrolyzing filamentous homopolymer on single-stranded DNA. We report the design of a 29mer peptide based on the RecA N-terminal domain involved in intermonomer contact that inhibits RecA filament assembly with an IC50 of 3 microM.