Pyrene-Stacked Nanostructures Constructed in the Recombinant Tobacco Mosaic Virus Rod Scaffold

The effect of pyrenes introduced into a tobacco mosaic virus (TMV) coat protein monomer on the formation and stability of the TMV assembly was investigated. The possible arrangement of the pyrenes in the inner cavity of the TMV rod was also estimated. The pyrene derivative was introduced to four specific amino acids in the cavity of the TMV rod structure. Rod-structure formation was examined by atomic force microscopy (AFM). Two pyrene-attached mutants (positions 99 and 100) assembled to increase the length of the rod structures by 2.5 microm at pH 5.5. The interaction of the pyrene moieties in the TMV cavity was investigated by steady-state and time-resolved spectroscopic analysis. Strong excimer emission with significantly short wavelength (465 nm) was observed from the two mutants mentioned above. Excitation and UV-visible spectra indicate that the pyrene moieties form pi-stacked structures in the TMV cavity. Details of the pyrene interaction were investigated by analyzing the fluorescence lifetime of the excimer. Results suggest that the pyrenes formed preassociated rigid structures with partially overlapped geometry in the restricted space of the TMV cavity. The pyrenes effectively stabilize the TMV rod through a pi-stacking interaction in a well-ordered way, and the single pyrene moiety introduced into the monomer affects the overall formation of the TMV rod structure.

Rational Design of DNA Nanoarchitectures

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.

Probing lectin and sperm with carbohydrate-modified quantum dots

We report the encapsulation of quantum dots with biologically important beta-N-acetylglucosamine (GlcNAc) in different ratios, together with studies of their specific/sensitive multivalent interactions with lectins and sperm by fluorimetry, transmission electron microscopy, dynamic light scattering microscopy, confocal imaging techniques, and flow cytometry. These GlcNAc-encapsulated quantum dots (QDGLNs) specifically bind to wheat germ agglutinin, and cause fluorescence quenching and aggregation. Further studies of QDGLNs and the mannose-encapsulated QDs (QDMANs) with sperm revealed site-specific interactions, in which QDGLNs bind to the head of the sperm, while QDMANs spread over the whole sperm body.

Nanomaterial-based amplified transduction of biomolecular interactions

This article reviews progress in the development of nanomaterials for amplified biosensing and discusses different nanomaterial-based bioamplification strategies. Signal amplification has attracted considerable attention for ultrasensitive detection of disease markers and biothreat agents. The emergence of nanotechnology is opening new horizons for highly sensitive bioaffinity and biocatalytic assays and for novel biosensor protocols that employ electronic, optical, or microgravimetric signal transduction. Nucleic acids and antibodies functionalized with metal or semiconductor nanoparticles have been employed as amplifying tags for the detection of DNA and proteins. The coupling of different nanomaterial-based amplification platforms and amplification processes dramatically enhances the intensity of the analytical signal and leads to ultrasensitive bioassays. The successful realization of the new nanoparticle-based signal amplification strategies requires proper attention to nonspecific adsorption issues. The implications of such nanoscale materials on amplified biodetection protocols and on the development of modern biosensors are discussed.

Metal Ion Coordination to Azole Nucleosides

To evaluate the possibility of introducing azole nucleosides as building blocks for metal-mediated base pairs in artificial oligonucleotides, imidazole nucleoside, 1,2,4-triazole nucleoside and tetrazole nucleoside have been synthesized and characterized. The X-ray crystal structures of p-toluoyl-protected 1,2,4-triazole and tetrazole nucleosides are reported. Contrary to the situation primarily found for deoxyribonucleosides, the sugar moieties adopt C3'-endo conformations. The acidity of the beta nucleosides increases with increasing number of nitrogen ring atoms, giving pKa values of 6.01 +/- 0.05, 1.32+/-0.05 and <-3, respectively. This decrease in basicity results in a decreasing ability to form 2:1 complexes with linearly coordinating metal ions such as Ag+ and Hg2+. In all cases, the Ag+ complexes are of higher stability than the corresponding Hg2+ complexes. Whereas imidazole nucleoside forms highly stable 2:1 complexes with both metal ions (estimated log beta2 values of >10), only Ag+ is able to reach this coordination pattern in the case of triazole nucleoside (log beta2 = 4.3 +/- 0.1). Tetrazole nucleoside does not form 2:1 complexes at all under the experimental conditions used. These data suggest that imidazole nucleoside, and to a lesser extent 1,2,4-triazole nucleoside, are likely candidates for successful incorporation as ligands in oligonucleotides based on metal-mediated base pairs. DFT calculations further corroborate this idea, providing model complexes for such base pairs with glycosidic bond distances (10.8-11.0 Angstroms) resembling those in idealized B-DNA (10.85 Angstroms).

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

DNA tube structures controlled by a four-way-branched DNA connector

A novel method for preparation of DNA tubes using the DNA tile system with assistance of a four-way branched DNA-porphyrin connector is described. The detailed DNA tube structures were characterized by atomic force microscopy (AFM).

Studies on 2D hybrid films of half surfactant-covered Au nanoparticles at the air/water interface

A hybrid monolayer film of Au nanoparticles, half-covered with dioctadecyldimethylammonium chloride (DODAC), was prepared at the air/water interface and characterized using transmission electron microscopy (TEM), a quartz-crystal microbalance, and infrared spectra measurements. TEM images of the hybrid film showed that the distribution of Au nanoparticles depends on the surface density of DODAC and reaction time. IR spectral data provided evidence for a surface-enhanced effect of the Au nanoparticles. The wavenumber of CH(2)-stretch vibrations of DODAC in the infrared external reflection spectra revealed that the DODAC molecules were adsorbed onto the Au nanoparticles in a close-packed crystalline state for any surface density of DODAC, which is different from the usual behavior of Langmuir monolayers.

Preparative Manipulation of Gold Nanoparticles by Reversible Binding to a Polymeric Solid Support

A preparative scheme is presented for controlled modification of gold nanoparticles (NPs) by using reversible binding to a polymeric solid support through boronic acid chemistry. Octanethiol-capped Au NPs were bound to a boronic acid functionalized resin by custom-synthesized bifunctional linker molecules. The NPs were chemically released from the resin to the solution, with one (or a few) linker molecules embedded in their capping layer. This was confirmed by rebinding the linker-derivatized NPs to a boronic resin, exploiting the reversibility of the boronic acid/diol chemistry. The same scheme was employed to demonstrate a new method for affinity separation of NPs by means of a solid-phase reaction. The use of boronic acid provides versatility and chemical reversibility, while the polymeric solid support affords the separation and preparative aspects. The method presented here may be useful in various facets of NP handling, manipulation, and separation.

An OsII-Bisbipyridine-4-Picolinic Acid Complex Mediates the Biocatalytic Growth of Au Nanoparticles: Optical Detection of Glucose and Acetylcholine Esterase Inhibition

The complex Os(II)-bisbipyridine-4-picolinic acid, [Os(bpy)(2)PyCO(2)H](2+) (1), mediates the biocatalyzed growth of Au nanoparticles, Au NPs, and enables the spectroscopic assay of biocatalyzed transformations and enzyme inhibition by following the Au NP plasmon absorbance. In one system, [Os(bpy)(2)PyCO(2)H](2+) mediates the biocatalyzed oxidation of glucose and the growth of Au NPs in the presence of glucose oxidase, GOx, AuCl(4) (-), citrate and Au NP seeds. The mechanism of the Au NPs growth involves the oxidation of the [Os(bpy)(2)PyCO(2)H](2+) complex by AuCl(4) (-) to form [Os(bpy)(2)PyCO(2)H](3+) and Au(I). The [Os(bpy)(2)PyCO(2)H](3+) complex mediates the GOx biocatalyzed oxidation of glucose and the regeneration of the mediator 1. Citrate reduces Au(I) and enlarges the Au seeds by the catalytic deposition of gold on the Au NP seeds. In the second system, the enzyme acetylcholine esterase, AChE, is assayed by the catalytic growth of the Au NPs. The hydrolysis of acetylcholine (2) by AChE to choline is followed by the [Os(bpy)(2)PyCO(2)H](3+) mediated oxidation of choline to betaine and the concomitant growth of the Au NPs. The mediated growth of the Au NPs is inhibited by 1,5-bis(4-allyldimethylammonium-phenyl)pentane-3-one dibromide (3). A competitive inhibition process was demonstrated (K(M)=0.13 mM, K(I)=2.6 microM) by following the growth of the Au NPs.

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.