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At least 973 records · Page 54Linked to original sources
PubMed2003

A rational study of crystal engineering of supramolecular assemblies of 1,2,4,5-benzenetetracarboxylic acid.

Supramolecular assemblies of 1,2,4,5-benzenetetracarboxylic acid, 1, with aza donor molecules such as 1,10-phenanthroline, 2, 1,7-phenanthroline, 3, phenazine, 4, 4-(N,N-dimethylamino)pyridine, 5, 1,2-bis(4-pyridyl)ethene, 6, and 1,2-bis(4-pyridyl)ethane, 7, have been synthesized and characterized by single-crystal X-ray diffraction methods. All the complexes crystallize in the triclinic, Ponemacr; space group. In the complexes of 2 and 4, water is also present in the resultant assembly, but the complexes of 5, 6, and 7 crystallize without any water molecules or solvent of crystallization. However, 3 forms two types of complexes, a hydrate and a nonhydrate complex, depending upon whether water is used as a solvent or not. These assemblies divide into two classes, host-guest systems (with aza molecules being in the channels created by the acid molecules) and assemblies with infinite molecular tapes. While the assemblies of the compounds 2, 4, and 5 belong to the former class, the assemblies of compounds 6 and 7 form molecular tapes, which are arranged in two dimensions to form sheet structures. The two structures of 3, in fact, bridge the two classes with each one falling into different categories.

Journal Article↗
PubMed2006

Self-assembly of molecular nanoball: design, synthesis, and characterization.

The design and self-assembly of two new flexible supramolecular nanoballs are described. These assemblies incorporate two flexible tritopic amide and ester building blocks and were prepared in excellent yields (96-97%) via coordination driven self-assembly. The first resulted from the reaction of 4 equiv of a new tritopic ester ligand N,N',N' '-tris(4-pyridylmethyl) trimesic ester and 3 equiv of C4 symmetric Pd(NO3)2. The second analogous structure was obtained by the self-assembly of a flexible N,N',N' '-tris(3-pyridylmethyl) trimesic amide and Pd(NO3)2. The assemblies were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, elemental analysis, and TGA. Mass spectrometry along with NMR data and TEM view confirms the existence of the two assemblies. MM2 force field simulations of the cages showed a ball shape with the diameter of the inner cavity of about 2.1 and 1.8 nm for 2a and 2b, respectively, which were also corroborated by TEM analysis.

Journal Article↗
PubMed2005

Assembling and orientation of polyfluorenes in solution controlled by a focused near-infrared laser beam.

Ordered fibril- and particle-like assemblies of poly(2,7-(9,9-bis(2-ethylhexyl)fluorene)) can be formed by photon force of a focused near-infrared laser beam during the drying process of its tetrahydrofuran solution on a glass substrate. These formations have been achieved controllably by combining laser irradiation with convection in the cast solution; that is, when viscous drag of the solution in the convection is stronger than the photon force, the fibril-like assemblies can be formed. Molecular orientation in the assemblies differs from that in self-assembled fibril-like structures, and maybe it can be controlled by the polarization direction of the focused laser beam. We have demonstrated that the length and width of the assemblies can be controlled by the irradiation time, the laser power, the concentration of the solution, and the convection rate in the solution. On the other hand, when the viscous drag of the solution in the convection is weak compared to the photon force, particle-like assemblies in which molecular orientation is controlled by polarization direction are formed.

Journal Article↗
PubMed2005

Kinetic and thermodynamic assessments of the mediator-template assembly of nanoparticles.

The understanding of kinetic and thermodynamic factors governing the assembly of nanoparticles is important for the design and control of functional nanostructures. This paper describes a study of the kinetic and thermodynamic factors governing the mediator-template assembly of gold nanoparticles into spherical assemblies in solutions. The study is based on spectrophotometric measurements of the surface plasmon (SP) resonance optical property. Gold nanoparticle cores ( approximately 5 nm) encapsulated with tetraoctylammonium bromide shells were studied as a model system. The mediator-template assembly involves a thioether-based multidentate ligand (e.g., MeSi(CH2SMe)3) which functions as a mediator, whereas the tetraoctylammonium bromide capping molecules function as template agents. On the basis of the temperature dependence of the SP optical property in the mediator-template assembly process, the kinetic and thermodynamic parameters such as the reaction rate constant and reaction enthalpy have been determined. The results led to two important findings. First, the mediator-template assembly of nanoparticles is an enthalpy-driven process. Second, the enthalpy change (-1.3 kcal/mol) is close to the magnitude of the van der Waals interaction energy for alkyl chains and the condensation energy of hydrocarbons. Implications of the findings to the understanding of the interparticle interactions have also been discussed.

Journal Article↗
PubMed2004

Self-organization of self-assembled tetrameric porphyrin arrays on surfaces.

The incorporation of designed self-assembled supramolecular structures into devices requires deposition onto surfaces with retention of both structure and function. This remains a challenge and can present a significant barrier to developing devices using self-organizing materials. To examine the role of peripheral groups in the self-organization of self-assembled multiporphyrinic arrays on surfaces, Pd(II)-linked square and Pt(II)-linked trapezoidal tetrameric porphyrin arrays with peripheral tert-butylphenyl or dodecyloxyphenyl functionalities were investigated using various spectroscopies and atomic force microscopy. The Pd(II) assembled squares disassemble upon deposition on glass surfaces, while the Pt(II) assembled trapezoids are more robust and can be routinely cast on these surfaces. The orientation and length of the peripheral alkyl substituents influence the resultant structures on surfaces. The tert-butylphenyl-substituted porphyrin array forms discrete columnar stacks, which assemble in a vertical direction via pi-stacking interactions among the macrocycles. The tetrameric porphyrin array with dodecyloxyphenyl groups forms a continuous film via van der Waals interactions among the peripheral hydrocarbon chains. The super-molecules with liquid crystal-forming moieties also form three-dimensional crystalline structures at higher deposition concentrations. These observations clearly demonstrate that the number, position, and nature of the peripheral groups and the supramolecular structure and dynamics, as well as the energetics of interactions with the surface, are of key importance to the two-dimensional and three-dimensional self-organization of assemblies such as porphyrin arrays on surfaces.

Dimerization↗
PubMed2005

Programmed hyperhelical supramolecular assembly of nickel phthalocyanine bearing enantiopure 1-(p-tolyl)ethylaminocarbonyl groups.

The present paper reports uniqueness of a simple, programmed design of disk-shaped homochiral nickel phthalocyanine (Pc) molecules bearing four enantiomerically pure 1-(p-tolyl)ethylaminocarbonyl groups at their peripheral positions, (Pc-(R) and Pc-(S)), and their controlled self-organization into mesoscopic supramolecular helical fibers with a preferential handedness in solution and onto solid surfaces. A combination of four fundamental intermolecular interactions, including quadruple hydrogen bonding, pi-pi stacking, homochiral interactions of the enantiopure bulky aralkyl entities, and noncoordinating nature of nickel ion of the Pc molecules afforded a high thermal stability of the Pc self-assembly in chloroform (CHCl(3)), tetrahydrofuran, and o-dichlorobenzene and onto hydrophilic mica and hydrophobic HOPG surfaces. A higher-ordered helical self-assembly of Pc disks was observed in these solutions (approximately 200 Pc molecules), while the self-assembly was completely dissociated into monomeric species in N,N-dimethylformamide due to a loss of hydrogen-bonding interactions between Pc molecules. Supramolecular chirality in the hierarchical self-assembly of Pc molecules originated from the presence of (R)- or (S)-chiral centers in the peripheral tails, which rotate noncovalently linked molecular building blocks to effectively form the helical architectures. The helical Pc nanofibers dissolved in CHCl(3), estimated to be ca. 70 nm from peak molecular weight obtained by SEC analysis, acts as a building block for higher-order helical fibers (ca. 1 microm) at single molecular level on the solid surfaces, as demonstrated by the dynamic force mode atomic force microscopy. Regardless of hydrophilic and hydrophobic substrates, the interaction between these Pc molecules and the solid surfaces could not affect the morphology of helical assemblies, indicating a unique robustness of these assemblies.

Biopolymers↗
PubMed2005

Thermodynamic properties of the unique self-assembly of {Mo72Fe30} inorganic macro-ions in salt-free and salt-containing aqueous solutions.

Static and dynamic laser light scattering techniques are used to monitor the slow self-assembly of 2.5-nm-diameter, hollow spherical, fully hydrophilic heteropolyoxometalate {Mo72Fe30} macro-ions into single-layer vesicle-like "blackberries" (averaging approximately 50-60 nm in diameter) in dilute salt-free and salt-containing aqueous solutions, to obtain the thermodynamic properties of the unique self-assembly. A very high activation energy is observed during the transition from the single ion (general solute state) to blackberries (so-called "second solute state"), which might be responsible for the interestingly slow self-assembly process in dilute solutions. The thermodynamic parameters of the blackberry formation can be affected by adding simple electrolytes into the solution, because the electrostatic interactions are responsible for the unique self-assembly, and the effects of various anions and cations (in the low salt concentration regimes) are discussed. Multivalent anions make the single {Mo72Fe30} macro-ions more stable and make the blackberry formation more difficult. Small cations carrying more charges tend to accelerate the self-assembly process. This is the first study on the thermodynamic properties of the novel self-assembly in dilute solutions and the equilibrium and transition between the two solute states of macro-ions in solution.

Journal Article↗
PubMed2005

Covalent molecular assembly of oligoimide ultrathin films in supercritical and liquid solvent media.

An ultrathin film of oligoimide has been fabricated on amine-modified substrates of silicon and quartz through alternate layer-by-layer (LBL) assembly of pyromellitic dianhydride (PMDA) and diaminodiphenyl ether (DDE), with interlayer links established by covalent bonds. The assembly was formed in supercritical carbon dioxide (SCCO2) and in solution (dimethyl acetamide, DMAc), and the imidization reaction was performed by thermal and chemical methods, in benzene and in the supercritical medium. X-ray photoelectron and UV-visible absorption spectroscopies, atomic force microscopy (AFM), and ellipsometry were employed to study the interfacial chemistry, growth, morphology, and thickness of the assembled film. XPS analysis confirmed the sequential deposition of PMDA and DDE through formation of amic acids. At each deposition step, surface functionalities for the assembly of the next layer were generated. The interfacial chemical reaction was almost complete in the SCF (supercritical fluid) medium, as compared to the conversions observed in conventional assembly. Both the PMDA and DDE molecules were assembled in an organized manner, resulting in uniform surface morphology. Uniform film growth was revealed from the increase of UV absorption intensity and film thickness. The overall growth and quality of the films in SCF medium were greater than that for films formed in DMAc. The results of this novel study show that an environmentally friendly solvent can be used to obtain mechanically robust and thermally stable ultrathin films with little loss of material during the imidization step. In contrast to conventional deposition of the molecular layers that utilizes liquid solvents, use of SCCO(2) avoids solvent effects and posttreatment for solvent removal, while ensuring facile transport during contact.

Benzoates↗
PubMed2006

Directed assembly of surface-supported bilayers with transmembrane helices.

The lateral assembly of transmembrane (TM) helices gives rise to membrane proteins with complex folds, which play important roles in biochemical processes. Therefore, the assembly of surface-supported bilayers containing TM helices is the first step toward the development of functional biomembrane mimetics. Here we report novel directed assembly of surface-supported lipid bilayers with laterally mobile TM helices. The TM helices were incorporated into lipid monolayers at the air/water interface, and the monolayers were then transferred onto glass substrates using Langmuir-Blodgett (LB) deposition. Finally, bilayers were assembled using lipid vesicle fusion on top of the LB monolayers. The novelty is the incorporation of the peptides into the monolayer at the first step of bilayer assembly, which allows control over the peptide concentration and orientation. The transmembrane orientation of the peptides was confirmed using oriented circular dichroism (OCD), lateral mobility was assessed using fluorescence recovery after photobleaching (FRAP), and diffusion coefficients were determined using a novel boundary profile evolution (BPE) method. The described directed-assembly approach can be used to develop versatile bilayer platforms for studying membrane proteins interactions in native bilayer environments.

Amino Acid Sequence↗
PubMed2006

Supramolecular assemblies with tunable morphologies from homopolymeric and small organic molecular building blocks.

This work demonstrates the formation of micrometer-sized supramolecular assemblies with tunable morphologies using a homopolymer, poly(4-vinylpyridine), and a small organic acid, 5,7-dodecadiynedioic acid, as the building molecules. Three different morphologies (hollow spheres, solid spheres, and rods) were obtained, depending on the molar ratio of the building molecules. It is proposed that hydrogen bonding between P4VP and DCDA and the pi-pi stacking of the diacetylenic moieties are responsible for the formation of these assemblies. Interestingly, ordered hexagonal and lamellar mesostructures were also formed within the microstructure during the co-assembly process. As a result, UV irradiation of the supramolecular assemblies polymerized the diacetylenic moieties, resulting in cross-linked and responsive blue polydiacetylenic assemblies that can change color to red upon external stimuli (e.g., thermal stimuli). This work provides a novel concept of the synthesis of responsive supramolecular assemblies from a homopolymer and small organic molecules.

Fatty Acids↗
PubMed2007

Visualization of flow-aligned type I collagen self-assembly in tunable pH gradients.

Collagen is a major component of the extracellular matrix that exhibits unique hierarchical organization at multiple length scales ranging from nano to macroscale. Despite numerous methods to create collagen-based biomaterials, the self-assembly process of collagen ex vivo is poorly understood. Here, we describe a system that uses a microfluidic method to investigate the dynamics of collagen self-assembly. A main inlet stream of semidilute soluble collagen-I is hydrodynamically focused by two side inlet streams, which gradually increases the pH in the main stream. This enables dynamic nonequilibrium investigation of the self-assembly process simultaneously at different positions and therefore different stages in the assembly process within the same system. The device is designed for in situ monitoring and characterization of collagen assembly using polarization microscopy and X-ray diffraction: the continuous extensional flow provides highly ordered phases of the macromolecules over a large distance in the outlet microchannel and allows for data collection without material damage. We further demonstrate that finite element method simulations provide a good description of our experimental results regarding the diffusive phenomena, flow profile, and pH distribution. Our approach has broad impact, since it provides a powerful means of controlling and investigating the dynamic self-assembly process of biomacromolecules.

Animals↗
PubMed2002

Evidence of an assembly pheromone in the black-legged deer tick, Ixodes scapularis.

The responses of Irodes scapularis (Acari: Ixodidae) nymphs and adults to extracts of cast larval skins were tested in a Petri dish bioassay. Assembly was elicited in nymphs and adults in the presence of skins, exudate from ticks, and filter paper exposed to ticks compared to untreated controls. Assembly was noted by 1 hr after exposure with little change between 1 and 24 hr. The assembly response increased in the presence of an increased number of skins. Similar assembly was elicited in nymphs and adults in the presence of cast larval skins and a saline (0.95% NaCl) skin extract. Methanol and hexane extracts were not attractive. When chemical standards were tested against nymphs, they responded to guanine, uric acid, hypoxanthine, xanthine, inosine, and hematin. Adults were tested against guanine, inosine, and xanthine, and all elicited significant assembly. Responses of nymphs increased significantly with increase in dose of uric acid and guanine. Responses of nymphs to a mixture of guanine, xanthine, and adenine (25:1:1 ratio) were similar to responses to cast skins. This study provides the first evidence of an assembly pheromone in I. scapularis.

Animals↗
PubMed1998

Regulation of SNARE complex assembly by an N-terminal domain of the t-SNARE Sso1p.

The fusion of intracellular transport vesicles with their target membranes requires the assembly of SNARE proteins anchored in the apposed membranes. Here we use recombinant cytoplasmic domains of the yeast SNAREs involved in Golgi to plasma membrane trafficking to examine this assembly process in vitro. Binary complexes form between the target membrane SNAREs Sso1p and Sec9p; these binary complexes can subsequently bind to the vesicle SNARE Snc2p to form ternary complexes. Binary and ternary complex assembly are accompanied by large increases in alpha-helical structure, indicating that folding and complex formation are linked. Surprisingly, we find that binary complex formation is extremely slow, with a second-order rate constant of approximately 3 M(-1) s(-1). An N-terminal regulatory domain of Sso1p accounts for slow assembly, since in its absence complexes assemble 2,000-fold more rapidly. Once binary complexes form, ternary complex formation is rapid and is not affected by the presence of the regulatory domain. Our results imply that proteins that accelerate SNARE assembly in vivo act by relieving inhibition by this regulatory domain.

Circular Dichroism↗
PubMed2000

The polarity and dynamics of microtubule assembly in the budding yeast Saccharomyces cerevisiae.

Microtubule assembly in Saccharomyces cerevisiae is initiated from sites within spindle pole bodies (SPBs) in the nuclear envelope. Microtubule plus ends are thought to be organized distal to the SPBs, while minus ends are proximal. Several hypotheses for the function of microtubule motor proteins in force generation and regulation of microtubule assembly propose that assembly and disassembly occur at minus ends as well as at plus ends. Here we analyse microtubule assembly relative to the SPBs in haploid yeast cells expressing green fluorescent protein fused to alpha-tubulin, a microtubule subunit. Throughout the cell cycle, analysis of fluorescent speckle marks on cytoplasmic astral microtubules reveals that there is no detectable assembly or disassembly at minus ends. After laser-photobleaching, metaphase spindles recover about 63% of the bleached fluorescence, with a half-life of about 1 minute. After anaphase onset, photobleached marks in the interpolar spindle are persistent and do not move relative to the SPBs. In late anaphase, the elongated spindles disassemble at the microtubule plus ends. These results show for astral and anaphase interpolar spindle microtubules, and possibly for metaphase spindle microtubules, that microtubule assembly and disassembly occur at plus, and not minus, ends.

Anaphase↗
PubMed2004

Self-assembly of amphiphilic dendritic dipeptides into helical pores.

Natural pore-forming proteins act as viral helical coats and transmembrane channels, exhibit antibacterial activity and are used in synthetic systems, such as for reversible encapsulation or stochastic sensing. These diverse functions are intimately linked to protein structure. The close link between protein structure and protein function makes the design of synthetic mimics a formidable challenge, given that structure formation needs to be carefully controlled on all hierarchy levels, in solution and in the bulk. In fact, with few exceptions, synthetic pore structures capable of assembling into periodically ordered assemblies that are stable in solution and in the solid state have not yet been realized. In the case of dendrimers, covalent and non-covalent coating and assembly of a range of different structures has only yielded closed columns. Here we describe a library of amphiphilic dendritic dipeptides that self-assemble in solution and in bulk through a complex recognition process into helical pores. We find that the molecular recognition and self-assembly process is sufficiently robust to tolerate a range of modifications to the amphiphile structure, while preliminary proton transport measurements establish that the pores are functional. We expect that this class of self-assembling dendrimers will allow the design of a variety of biologically inspired systems with functional properties arising from their porous structure.

Biological Transport↗
PubMed2001

A multiprotein complex mediates the ATP-dependent assembly of spliceosomal U snRNPs.

The spliceosomal snRNPs U1, U2, U4 and U5 contain a common RNP structure termed the Sm core that is formed by the binding of Sm proteins onto the U snRNA. Although isolated Sm proteins assemble spontaneously onto U snRNAs in vitro, there is increasing evidence that SMN and its interactor Gemin2 are involved in this process in vivo. Here, we describe a cell-free assay system for the assembly of U snRNPs that closely reproduces in vivo conditions. Using this system, we show that assembly of U1 snRNP depends on ATP. Immunodepletion of SMN-Gemin2 from the extract abolished assembly even though the extract contained high levels of Sm proteins. An affinity-purified macromolecular SMN complex consisting of 16 components including all Sm proteins restored assembly in the immunodepleted extract. These data provide the first direct evidence that a complex containing SMN and Gemin2 mediates the active assembly of spliceosomal U snRNPs.

Adenosine Triphosphate↗
PubMed2025

Chromosome-level genome assembly and annotation of Pterygoplichthys pardalis.

Suckermouth catfishes, with their evolved powerful features, have become notorious invasive species, causing significant damage to aquatic ecosystems. However, the lack of high-quality genomes severely restricts research on this group within the field. In this study, we de novo assembled the chromosome-level genome assembly of Pterygoplichthys pardalis using multiple platforms of sequencing data, including Illumina short reads, Nanopore long reads, and Hi-C sequencing reads, resulting in a 1.51 Gb genome assembly. Multiple evaluations, including read mapping ratio (98.52%), transcript mapping ratio (99.61%), conserved BUSCO gene set (98.8%), and N50 score (49.47 Mb), indicated the high continuity and accuracy of the genome assembly we generated. Genome annotation found that 0.97 Gb of genome sequences are repetitive sequences, accounting for 64.47% of the genome assembly. Further, 23,859 protein-coding genes were successfully predicted, 92.92% of which could be annotated in functional databases. This high-quality genome assembly of P. pardalis provides a valuable resource for understanding the genetic underpinnings of P. pardalis's invasive success and offers critical data for future fisheries research and management.

Animals↗
PubMed2025

Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing.

Sinocyclocheilus jii, a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the most diverse group of cavefishes worldwide. However, the limited availability of genomic resources has limited investigations into the genetic basis of trait variations, phylogenetic relationships, and adaptive evolution in this genus. In this study, we assembled a chromosome-level reference genome for S. jii by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C sequencing data. Flow cytometry was used to estimate the genome size prior to assembly, providing a key step in technical validation. The final genome assembly spans 1.75 Gb with a contig N50 of 35.0 Mb. Using Hi-C sequencing data, the assembled scaffolds were successfully anchored to 50 chromosomes. The completeness of the chromosome-level assembly was estimated at 98.9% by BUSCO analysis. Genome annotation identified 855.5 Mb of repetitive sequences and predicted a total of 52,867 protein-coding genes, of which 51,932 genes were functionally annotated. This study presents a high-quality chromosome-level genome assembly and annotation of S. jii, providing a fundamental genomic resource for future phylogenetic and evolutionary studies.

Animals↗