DNA-programmed assembly of nanostructures

DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.     

Supramolecular aptamer-thrombin linear and branched nanostructures

Alpha and beta conjugated bis-aptamers against thrombin act as bidentate "glue" for the self-assembly of thrombin nanowires; mixing the bidentate aptamer with a tripodal tridentate alpha aptamer construct yields branched thrombin nanowire structures.     

DNA-programmed modular assembly of cyclic and linear nanoarrays for the synthesis of two-dimensional conducting polymers

Nanometer-scale arrays of conducting polymers were prepared on scaffolds of self-assembling DNA modules. A series of DNA oligomers was prepared, each containing six 2,5-bis(2-thienyl)pyrrole (SNS) monomer units linked covalently to N4 atoms of alternating cytosines placed between leading and trailing 12-nucleobase recognition sequences. These DNA modules were encoded so the recognition sequences would uniquely associate through Watson-Crick assembly to form closed-cycle or linear arrays of aligned SNS monomers. The melting behavior and electrophoretic migration of these assemblies showed cooperative formation of multicomponent arrays containing two to five DNA modules (i.e., 12-30 SNS monomers). The treatment of these arrays with horseradish peroxidase and H(2)O(2) resulted in oxidative polymerization of the SNS monomers with concomitant ligation of the DNA modules. The resulting cyclic and linear arrays exhibited chemical and optical properties typical of conducting thiophene-like polymers, with a red-end absorption beyond 1250 nm. AFM images of the cyclic array containing 18 SNS units revealed highly regular 10 nm diameter objects.     

A modular approach to DNA-programmed self-assembly of macromolecular nanostructures

DNA-programmed organic reactions are new and powerful tools for assembling chemical compounds into predetermined complex structures and a brief review of their use is given. This approach is particular efficient for the selection and covalent coupling of multiple components. DNA-templated synthesis is used for polymerization of PNA tetramers and for copying of the connectivity information in DNA. Direct DNA-programmed multicomponent coupling of custom designed organic modules is described. The macromolecular structures obtained are highly conjugated potentially conducting nanoscaffolds. Some future developments in this area are discussed.     

TMV microarrays: hybridization-based assembly of DNA-programmed viral nanotemplates

The intrinsic ability of biological molecules to self-organize into complex structures has the potential to revolutionize methods for the assembly of nanomaterials and devices. In this work, nucleic acid hybridization was used to simultaneously assemble different Tobacco mosaic virus (TMV) nanotemplates onto a glass substrate patterned with address specific capture DNAs. To accomplish this, TMV-based nanotemplates were programmed with linker DNAs containing sequence specific addresses and hybridized directly to the capture DNAs. This assembly process proved to be a reliable, selective, and controllable means to assemble multiple TMV nanotemplates.     

Differences in electrophoretic behavior between linear and branched PEG‐conjugated proteins

The objective of this study was to characterize the differences in electrophoretic behavior between linear and branched PEG‐conjugated proteins. Human growth hormone and alpha‐lactalbumin modified by linear or branched PEGs with molecular weight of 10 kDa were analyzed by SEC, MALDI‐TOF MS, SDS‐PAGE, and microchip CGE (MCGE). Chromatographic and mass spectrometric differences between the linear and branched PEG‐proteins on SEC and MALDI‐TOF MS were small, but their electrophoretic behaviors on SDS‐PAGE and MCGE were significantly different. In particular, MCGE showed significant differences in the peak width and the migration times of linear and branched PEG‐proteins, in which the branched PEG‐proteins exhibited a narrower peak and longer migration time than the linear PEG‐proteins. This phenomenon may explain the longer circulation half‐life for the branched PEG‐proteins observed in previously reported in vivo studies. Consequently, this study indicates that MCGE may be a valuable tool for differentiating linear and branched PEG‐proteins.     

Synthesis of linear and tripoidal oligo(phenylene ethynylene)-based building blocks for application in modular DNA-programmed assembly

Rigid linear and tripoidal organic modules based on the oligo(phenylene ethynylene) backbone having salicylaldehyde-derived termini are synthesized. A highly functionalized 5-iodosalicyl aldehyde was prepared and coupled to each ethynyl group of 1,4-diethynylbenzene or 1,3,5-triethynylbenzene in Sonogashira couplings. The two or three termini of the compounds are functionalized for incorporation in linear and branched oligonucleotide strands. For the linear module (LM), the two termini are equipped with amide spacers, and one of these was functionalized with a DMTr (dimethoxytrityl)-protected hydroxy group and the other with a phosphoramidite. One of the tripoidal modules is prepared with DMTr groups in two of its three termini. A tripoidal module is also synthesized with three different groups on its hydroxy termini: a phosphoramidite, a DMTr group, and an Fmoc group. Extended studies have shown that these rigid linear and tripoidal organic modules can be incorporated into short oligonucleotides. Several of these modules can be applied for DNA-directed assembly and covalent coupling into structures of predetermined connectivity. Such structures have potential application for molecular electronics and nanotechnology.     

Synthesis of an elongated linear oligo(phenylene ethynylene)-based building block for application in DNA-programmed assembly

The synthesis of an elongated linear oligonucleotide-functionalised module (ELOM) is described. The ELOM structure is based on an oligo(phenylene ethynylene) backbone substituted with two decyloxy groups. The two termini constitute two salicylaldehyde moieties acting as chemical cross-linkers. Before incorporation into an oligonucleotide sequence the organic part of the module, the elongated linear module (ELM), is functionalised with a dimethoxytrityl group and a phosphoramidite group. This enables incorporation into the middle of 30-mer oligonucleotide sequences by automated DNA synthesis. The obtained ELOMs were characterised by polyacrylamide gel electrophoresis and MALDI-TOF mass spectrometry. In analogy with previously reported LOM and TOM structures the coupling reactions of the ELOM modules were tested.     

Synthesis of linear and branched oligodialkylalkylhydrosiloxanes

New linear and branched oligodialkylalkylhydrosiloxanes were prepared by hydrolytic cocondensation of various functional organosilanes with diethyl(dimethyl-)dichlorosilane, ethylhydro-(methylhydro-) dichlorosilane, and trimethylchlorosilane, followed by catalytic rearrangement in the presence of an electrophilic catalyst. The products are of interest as hydrophobizing agents and starting compounds for replacement of hydrogen atoms at silicon by other substituents.     

Modular assembly of elliptical mesogens

Discotic mesogens featuring a pyridine ring were synthesized, and were found either to form ordered hexagonal columnar liquid crystalline phases or melt directly from a crystal to an isotropic liquid, depending on the position of the pyridyl nitrogen atom. Binary mixtures of the mesogenic pyridine derivatives with a similar discotic mesogen having a carboxylic acid group resulted in the formation of modular elliptical complexes through hydrogen bonding. The binary mixtures were found to exhibit ordered hexagonal columnar or ordered rectangular columnar and nematic mesophases, depending on the length of the alkyl chains, and displayed dramatically different properties from their constituent components. Binary mixtures of the non-mesogenic pyridine derivatives with carboxylic acid-functionalized discotic mesogens did not result in the formation of hydrogen-bonded complexes.     

Self-assembly of conjugated polymers for anisotropic nanostructures

As their potential applications in various electronic devices increase, the preparation of anisotropic conjugated polymer nanostructures are highly desirable. This paper presents a review of the literature and our recent results on the self-assembly of one-, two- and three-dimensional anisotropic nanostructures using conjugated polymers as building blocks, including the formation of one-dimensional (1D) nanofibers and nanotubes, two-dimensional (2D) nanoribbons and nanosheets, and three-dimensional (3D) superstructures. The mechanisms guiding the formation of various nanostructures are analyzed by a cooperative effect of - stacking interaction and other noncovalent interactions.     

Growth and characterization of highly branched nanostructures of magnetic nanoparticles

Magnetite nanoparticles of Fe(3)O(4) have been found to grow into large highly branched nanostructures including nanochains and highly branched nanotrees in the solid state through a postannealing process. By varying the preparation conditions such as annealing time and temperature, the nanostructures could be easily manipulated. Changing the starting concentration of the magnetic nanoparticle solution also caused significant changes of the nanoarchitectures. When the magnetic nanoparticle concentration is low, the nanoparticles formed straight rods mainly with an average diameter of 80 nm and a length of several microns. With increasing concentration of the nanoparticles, treelike structures began to form. With further increase of the concentration, well-ordered nanostructures with the appearance of snowflakes were generated. The driving force for the formation of the highly ordered nanostructures includes interaction between the nanoparticles and interaction through surface-capping molecules. This experiment demonstrates that novel nanostructures can be generated by self-assembly of magnetic nanoparticles under the solid state.     

Multicomponent assembly of boron-based dendritic nanostructures

A new synthetic strategy for the construction of boron-based macrocycles and dendrimers is described. Condensation of aryl- and alkylboronic acids with 3,4-dihydroxypyridine is shown to give pentameric macrocycles in which five boronate esters are connected by dative B-N bonds. Three macrocycles have been characterized crystallographically. The boron atoms of these assemblies represent chiral centers, and the assembly process is highly diastereoselective. Attachment of amino or aldehyde groups in the meta position of the arylboronic acid building blocks does not interfere with macrocyclization. This allows performing multicomponent assembly reactions between functionalized boronic acids, dihydroxypyridine ligands, and amines or aldehydes, respectively. Reaction of 3,5-diformylphenylboronic acid, 3,4-dihydroxypyridine, and a primary amine R-NH2 (R=Ph, Bn) gives dendritic nanostructures having a pentameric macrocyclic core and 10 amine-derived R groups in their periphery. Combination of 3,5-diformylphenylboronic acid with 2,3-dihydroxypyridine and the dendron 3,5-(benzyloxy)benzylamine, on the other hand, results in formation of a dendrimer with a tetrameric macrocyclic core and eight dendrons in its periphery.     

Kinetics-driven growth of orthogonally branched single-crystalline magnesium oxide nanostructures

Orthogonally branched single-crystalline magnesium oxide nanostructures were synthesized through a simple chemical vapor transport and condensation process in a flowing Ar/O(2) atmosphere. Other morphologies, such as cubes and nanowires, can also be obtained under different controlled conditions. The formation of different types of nanostructures can be tuned by modifying oxygen partial pressure during the synthesis. All the nanostructures are cubic single-crystalline enclosed by low-index {100} facets. Growth mechanisms for the nanostructures are discussed in detail: different supersaturation ratios, relatively high substrate temperatures, and surface defects in certain crystallographic planes cooperatively take important effects on determining the product morphologies. Structural defect-related blue light emission of the three types of MgO nanostructures was investigated. The MgO nanostructures with abundant morphologies may find applications in various nanodevices, and the kinetics-driven methodology might be exploited to synthesize similar nanostructures of other functional oxide materials.     

Ion channels from linear and branched bola-amphiphiles

The synthesis and characterization of the ion channel activity of three new bola-amphiphiles is described. These compounds are conceptually derived from a previously reported bis-cyclophane bola-amphiphile through opening of the cyclophanes to acyclic structures and were found to readily form ion channels in planar bilayer membranes as assessed by bilayer clamp single-channel analysis. All three compounds behaved very similarly: the dominant channels formed by all three are Ohmic with specific conductance of 10 +/- 1 pS (NaCl electrolyte) and 39 +/- 1 pS (CsCl electrolyte). Single-ion permeability ratios, determined from dissymmetric electrolyte experiments, showed the selectivity P(Cs(+)) > P(Na(+)) > P(Cl(-)). Less frequently, lower conductance channels were also observed to act independently of the dominant channels. The lifetimes of the dominant channels range from 70 to 280 ms for the three compounds with some very long-lived openings (20-40 s) observed for two of the three. The lower conductance states have shorter lifetimes. This study demonstrates that bis-macrocyclic compounds are not essential for channel formation by bola-amphiphiles, and opens a new class of channel-forming compounds for structure-activity optimization.     

Capillary zone electrophoresis of linear and branched oligosaccharides

The electrophoretic behavior of derivatized linear and branched oligosaccharides from various sources was examined in capillary zone electrophoresis with polyether-coated fused-silica capillaries. Two UV-absorbing (also fluorescent) derivatizing agents (2-amino-pyridine and 6-aminoquinoline) were utilized for the electrophoresis and sensitive dtection of neutral oligosaccharides, e.g., N-acetylchitooligosaccharides, high-mannose glycans and xyloglucan oligosaccharides. The oligosaccharides labelled with 6-aminoquinoline yielded eight times higher signal than those tagged with 2-aminopyridine. Plots of logarithmic electrophoretic mobilities of labelled N-acetylchitooligosaccharides with 6-aminoquinoline or 2-aminopyridine versus the number of sugar residues in the homologous series yielded straight lines in the size range studied, the slopes of which were independent of the tagging functions. The slopes of these lines are referred to as the N-acetylglucosaminyl group mobility decrement. The oligosaccharides were better resolved in the presence of tetrabutylammonium bromide in the running electrolyte. Furthermore, the electrophoretic mobilities of branched oligosaccharides were indexed with respect to linear homooligosaccharides, an approach that may prove valuable in correlating and predicting the mobilities of complex oligosaccharides.     

Modular assembly of metal-organic supercontainers incorporating sulfonylcalixarenes

A new strategy for the design of container molecules is presented. Sulfonylcalix[4]arenes, which are synthetic macrocyclic containers, are used as building blocks that are combined with various metal ions and tricarboxylate ligands to construct metal-organic "supercontainers" (MOSCs). These MOSCs possess both endo and exo cavities and thus mimic the structure of viruses. The synthesis of MOSCs is highly modular, robust, and predictable. The unique features of MOSCs are expected to provide exciting new opportunities for the exploration of their functional applications.     

Effective interaction parameter between branched and linear polystyrene

Values of the effective interaction parameter (χ) between regular, long‐branched polystyrene chains and their linear analogues were measured with small‐angle neutron scattering for several star‐branched chains and one comb‐type polymer. The contribution to this interaction due to architecture alone increases monotonically with star functionality for the set of polymers studied here. The interaction appears to be less sensitive to variations in arm size than would be expected from fluctuation theory predictions by G. H. Fredrickson, A. Liu, and F. S. Bates (Macromolecules 1994, 27, 2503) for a purely entropic interaction due to architecture. The change in χ with the volume fraction of the star in the blend is in agreement with the theory, however. The magnitudes of the interaction in the star/linear blends are small enough that bulk phase separation is unlikely, whereas that in the comb/linear blend is about 20 times higher for the same number of arms. Thus, bulk phase separation can be readily expected for comb/linear blends at commercially relevant values of molecular weights. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2549–2561, 2001