Three-dimensional self-organization of supramolecular self-assembled porphyrin hollow hexagonal nanoprisms

A self-assembly technique assisted with surfactant is developed to fabricate one-dimensional (1D) nanostructure of zinc meso-tetra (4-pyridyl) porphyrin. The so-prepared nanostructure appears in a shape of hollow hexagonal nanoprism with uniform size. The length and aspect ratio of the nanoprisms is easily tunable by controlling the stoichiometric ratio of porphyrin over surfactant. The internal structure of the nanoprisms is well described by XRD. Furthermore, as a result of dispersivity and regular geometric shape, these nanoprisms can readily self-organize into an ordered, smectic three-dimensional (3D) architecture through simple evaporation of the solvent. The results should be significant in porphyrin crystallization and porphyrin application in optoelectronic device, catalysis, drug delivery, and molecular filtration.     

Ionic self-assembled organic nanobelts from the hexagonal phase complexes and their cyclodextrin inclusions

The supramolecular ionic self-assembly (ISA) strategy has been used to construct the long-range ordered hierarchical aggregates from the complexes of 1-adamantanamine hydrochloride (AdCl) and sodium bis(2-ethyl-1-hexyl)sulfosuccinate (AOT). The formed AOT-Ad complexes have been proved to possess a composition of equal molar ratio and a hexagonal columnar structure with Ad blocks as the core and AOT outside. More interestingly, the length, width, and thickness of the aggregates are on the order of milli-, micro-, and nanometer, respectively, and can thus be taken as one type of organic nanobelt. Such nanobelts are plastic and stable to resist breakage even bent to a circle, which makes them useful in the fields of novel nanomaterial fabrication. In addition, the ISA process of this aggregate can be tuned by including Ad blocks in beta-cyclodextrins to form a supramolecular complex, which is comparatively stable in the water and expected to self-assemble into some other ordered structures.     

Tensegrity: construction of rigid DNA triangles with flexible four-arm DNA junctions

A tensegrity strategy has been explored to construct a rigid geometrical structure (triangles) from flexible DNA four-arm junctions. The resulting DNA triangles could self-assemble into 1D and 2D arrays. This tensegrity strategy is expected to play an important role in the design of biomimetic nanomaterials.     

Assembly of DNA triangles mediated by perylene bisimide caps

Perylene bisimides (PBI) have been synthetically incorporated as caps onto a Y-shaped DNA triple strand. These PBI caps serve as "sticky" ends in the spontaneous assembly of larger DNA ensembles, linking the triangular DNA through stacking interactions. This, in turn, yields a hypsochromic shift in the absorption and a red shift in the fluorescence as characteristic optical readouts. This assembly occurs spontaneously without any enzymatic ligation process and without the use of overhanging DNA as sticky ends. Instead, dimerizations of the PBI chromophores in the assembly are controlled by the DNA as a structural scaffold. Thereby, the PBI-driven assembly is fully reversible. Due to the fact that PBI dimerization does not occur in the single strand, the aggregates can be destroyed by thermal dehybridization of the DNA scaffold and reassembled by reannealing of the DNA construct. In view of the fact that PBI forms stable radical anions, the presented DNA architectures are not only interesting optical biomaterials, but are also promising materials for molecular electronics with DNA.     

Multilayer DNA origami packed on hexagonal and hybrid lattices

"Scaffolded DNA origami" has been proven to be a powerful and efficient approach to construct two-dimensional or three-dimensional objects with great complexity. Multilayer DNA origami has been demonstrated with helices packing along either honeycomb-lattice geometry or square-lattice geometry. Here we report successful folding of multilayer DNA origami with helices arranged on a close-packed hexagonal lattice. This arrangement yields a higher density of helical packing and therefore higher resolution of spatial addressing than has been shown previously. We also demonstrate hybrid multilayer DNA origami with honeycomb-lattice, square-lattice, and hexagonal-lattice packing of helices all in one design. The availability of hexagonal close-packing of helices extends our ability to build complex structures using DNA nanotechnology.     

Hybridization of oligonucleotide by using DNA self-assembled monolayer

The interaction between DNA immobilized on surface and oligonucleotides at the interface is important in detection and diagnostic processes. However, it is difficult to immobilize DNA with maintaining its activity and to realize an efficient hybridization in previous methods. Here, to establish a novel DNA-functionalized surface, the DNA self-assembled monolayer (SAM) was constructed on a gold substrate using thiolated DNA composed of double-stranded (ds) and single-stranded (ss) portion. The DNA SAM was characterized by surface plasmon resonance (SPR), XPS. The hybridization of ss portion of DNA was attempted using the SAM, and in situ monitored by SPR. XPS measurement indicated that the thiolated DNA could form a stable monolayer on a gold substrate through sulfur–gold interaction. SPR measurement implied that the long axis of the DNA standing on the substrate. These results indicated formation of the DNA SAM on the substrate. Hybridization of target DNA containing a complementary sequence for the probe portion was observed by SPR. Moreover, one mismatch of oligonucleotide could be distinguished using the DNA SAM. The SPR result indicates that hybridization of target DNA and probe DNA on the DNA SAM occurs on the DNA SAM.     

DNA-conjugated polymers for self-assembled DNA chip fabrication.

We developed two DNA-conjugated polymers, one based on polyallylamine and the other on polyacrylic acid, for use in DNA chips. A 30-mer single-stranded DNA probe and thioctic acid were covalently attached to polyallylamine as sidechains. The same single-stranded DNA and 3-(pyridyldithio)propionyl hydrazide were covalently attached to polyacrylic acid as sidechains. Both DNA-conjugated polymers could be specifically immobilized onto a gold sensor substrate by a self-assembly technique. The interactions between fully matched DNA and each DNA-conjugated polymer were investigated by surface plasmon resonance. A gold surface modified with either DNA-conjugated polymer recognized fully matched DNA much better than unmatched DNA. The hybridization selectivity and efficiency of DNA-conjugated polyallylamine was optimized by adjusting the pH so as to reduce the effects of cationic polymer sidechains. The hybridization selectivity and efficiency of DNA-conjugated polymers were higher than those of a conventional immobilized thiol-based DNA. The coating of DNA-conjugated polymers reduced nonspecific adsorption of DNA by the gold substrate. DNA-conjugated polyacrylic acid was more selective toward fully matched DNA than was DNA-conjugated polyallylamine. Therefore, DNA-conjugated polymers show promise for application in novel DNA chips.     

Expression of chirality in columnar hexagonal phases or DNA and nucleosomes

It is surprising to see how eukaryotic chromosomes or sperm nuclei are highly condensed chromatin materials and how they can sometimes present spectacular helical morphologies. We may suspect that these helical shapes originate from the chiral properties of DNA and other components of chromatin. Dense solutions of DNA and nucleosomes can be prepared in vitro to reproduce some of the characteristics of chromatin. They form multiple ordered phases, either mesophases or 3D crystals, that can be useful to analyze precisely how chiral structures can emerge, or not, from interactions between these constitutive elements. We address the question of the competition between twist and hexagonal packing in dense states of DNA, nucleosomes, chromatin and chromosomes. From the microscopic analysis of many examples, we show how the twist arising from the chirality of the objects can be diluted in the phase and/or expelled along twist walls. These walls are either parallel or normal to the direction of the columns. In the first case, we determine that the twist axis lies parallel to one θ₂ direction of the hexagonal network. Helical shapes of chromosomes and bundles of DNA and chromatin may also be consequences of this competition, as illustrated here.     

Trianionic organoborate triangles

The rigid, angular ligand 3,3,3',3'-tetramethyl-1,1'spirobisindane-5,5',6,6'-tetrol, LH4, in the form of its tetra-anion, L(4-), affords crystalline compounds containing the triangular macrocyclic boron derivative [B3L3](3-) with the counter cations, triethylammonium, imidazolium, tetraethylammonium, and protonated dabco (dabco = 1,4-diazabicyclo[2,2,2]octane). Within a triangular unit all three chiral L(4-) ligands have the same hand although the crystal does contain a racemic mixture of macrocycles. In all four compounds, one out of the three counter-cations per macrocycle is bound inside the macrocycle.     

Chromatographic selectivity triangles

2010 marked the 50th anniversary of the use of selectivity triangles to characterize chromatographic phases. Such plots ultimately identify and quantify the blend of intermolecular interactions that occur between solutes and solvents/phases. The first chromatographic triangle was proposed by Brown and applied to GC stationary phases. Snyder then developed the influential solvent selectivity triangle (SST) based on the gas-liquid partition data of Rohrschneider. The SST was combined with simplex experimental designs to optimize RPLC separations. Subsequent criticisms of the work revolved around the inaccurate predictions that resulted from the SST. These inaccuracies ultimately relate to the inability of the SST to account for the effects of water on the interaction ability of organic solvents. Other criticisms focused on the selection of the three probe solutes (ethanol, dioxane, and nitromethane) that were used to define the apices of the SST. Here, the concerns include the lack of explicit consideration of dispersion interactions and the fact that the three probes do not represent any single intermolecular interaction but rather reflect a blend of intermolecular interactions. The SST approach was modified for NPLC by redefining the triangle apices to reflect the localization, general adsorption, and basicity of NPLC mobile phase modifiers. Because water is generally absent in NPLC, the triangle approach leads to better predictions for NPLC than for RPLC. In subsequent modifications of selectivity triangles, Fu and Khaledi have created a micellar selectivity triangle (MST) based on linear solvation energy relationships (LSERs) and Zhang and Carr have used the Dolan-Snyder hydrophobic subtraction model to create RPLC column selectivity triangles. We end this review by highlighting more recent methods for comparing selectivities and by discussing a new 3D visualization tool for classifying chromatographic systems as having similar or different fundamental energetics of retention and hence having similar or different selectivities.     

HolT Hunter: Software for identifying and characterizing low‐strain DNA holliday triangles

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models. © 2012 Wiley Periodicals, Inc.     

Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold

Assembly of gold nanoparticles (AuNP) into designer architectures with reliablity is important for nanophotonics and nanoelectronics applications. Toward this goal we present a new strategy to prepare AuNPs monofunctionalized with lipoic acid modified DNA oligos. This strategy offers increased bonding strength between DNA oligos and AuNP surface. These conjugates are further selectively mixed with other DNA strands and assembled into fixed sized DNA nanostructures carring a discrete number of AuNPs at desired positions. Atomic force microscopy imaging reveals a dramatically improved yield of the AuNPs on DNA tile structure compared to the ensembles using monothiolate AuNP-DNA conjugates.     

Self-assembly of hexagonal DNA two-dimensional (2D) arrays

A three-point-star DNA motif has been designed and constructed, which can self-assemble into hexagonal two-dimensional lattices. The resulting lattices are up to 1 mm.     

Fullerenes as tilings of surfaces

If a fullerene is defined as a finite trivalent graph made up solely of pentagons and hexagons, embedding in only four surfaces is possible: the sphere, torus, Klein bottle, and projective (elliptic) plane. The usual spherical fullerenes have 12 pentagons; elliptic fullerenes, 6; and toroidal and Klein-bottle fullerenes, none. Klein-bottle and elliptic fullerenes are the antipodal quotients of centrosymmetric toroidal and spherical fullerenes, respectively. Extensions to infinite systems (plane fullerenes, cylindrical fullerenes, and space fullerenes) are indicated. Eigenvalue spectra of all four classes of finite fullerenes, are reviewed. Leapfrog fullerenes have equal numbers of positive and negative eigenvalues, with 0, 0, 2, or 4 eigenvalues zero for spherical, elliptic, Klein-bottle, and toroidal cases, respectively.     

Electrochemistry using self-assembled DNA monolayers on highly oriented pyrolytic graphite

Duplex DNA functionalized with pyrene has been utilized to fabricate DNA-modified electrodes on highly oriented pyrolytic graphite (HOPG). Films have been characterized using AFM and radioactive labeling as well as electrochemically. The data obtained are consistent with a close-packed structure in the film with helices oriented in a nearly upright orientation, as seen earlier with the fabrication of thiol-tethered duplexes on gold. Also as on gold, we observe the reduction of DNA-bound intercalators in a DNA-mediated reaction. The reduction of the intercalator is attenuated in the presence of the single-base mismatches, CA and GT, independent of the sequence composition of the oligonucleotide. This sensitivity to single-base mismatches is enhanced when methylene blue reduction is coupled in an electrocatalytic cycle with ferricyanide. The extended potential range afforded by the HOPG surface has allowed us also to investigate the electrochemistry of previously inaccessible metallointercalators, Ru(bpy)2dppz2+ and Os(phen)2dppz2+, at the DNA-modified HOPG surface. These results support the application of DNA-modified HOPG as a convenient and reproducible surface for electrochemical DNA sensors using DNA-mediated charge transport.     

Nanomechanics of the formation of DNA self-assembled monolayers and hybridization on microcantilevers

Biomolecular interactions over the surface of a microcantilever can produce its bending motion via changes of the surface stress, which is referred to nanomechanical response. Here, we have studied the interaction forces responsible for the bending motion during the formation of a self-assembled monolayer of thiolated 27-mer single-stranded DNA on the gold-coated side of a microcantilever and during the subsequent hybridization with the complementary nucleic acid. The immobilization of the single-stranded DNA probe gives a mean surface stress of 25 mN/m and a mean bending of 23 nm for microcantilevers with a length and thickness of about 200 microm and 0.8 microm, respectively. The hybridization with the complementary sequence could not be inferred from the nanomechanical response. The nanomechanical response was compared with data from well-established techniques such as surface plasmon resonance and radiolabeling, to determine the surface coverage and study the intermolecular forces between neighboring DNA molecules anchored to the microcantilever surface. From both techniques, an immobilization surface density of 3 x 10(12) molecules/cm(2) and a hybridization efficiency of 40% were determined. More importantly, label-free hybridization was clearly detected in the same conditions with a conventional sensor based on surface plasmon resonance. The results imply that the nanomechanical signal during the immobilization process arises mainly from the covalent attachment to the gold surface, and the interchain interactions between neighboring DNA molecules are weak, producing an undetectable surface stress. We conclude that detection of nucleic acid hybridization with nanomechanical sensors requires reference cantilevers to remove nonspecific signals, more sensitive microcantilever geometries, and immobilization chemistries specially addressed to enhance the surface stress variations.