Ru(II) Tris(bipyridyl) Complexes with Six Oligonucleotide Arms as Precursors for the Generation of Supramolecular Assemblies

Encapsulation of luminescent homoleptic [Ru(dpp)3](2+)-type chromophores within an amphiphilic dendritic environment

A new series of homoleptic metallodendrimers has been synthesized through ruthenium-metal complexation by dendritically modified bathophenanthroline ligands. The presence of hydrophilic oligo(ethylene glycol) groups on the surface of the monodisperse metal complexes enabled the solubilization of all of the fractal species in a wide range of solvents, including water. The specific properties of all of these compounds have been systematically investigated by using photophysical techniques as a function of the generation number. Accordingly, the encapsulation of the highly luminescent [Ru(dpp)(3)](2+)-type (dpp=4,7-diphenyl-1,10-phenanthroline) core unit within a dendritic microenvironment creates a powerful means to shield the center from dioxygen quenching. This shielding effect, as exerted on the phosphorescent ruthenium-derived center, is reflected by enhanced emission intensities and extended excited-state lifetimes that are close to the highest values reported so far, even in an air-equilibrated aqueous medium. Interestingly, when inspecting the largest dendritic assembly, that is, the third-generation assembly, significant drops in emission quantum yields and lifetimes are observed. This anomalous behavior has been attributed to the folding of the branches towards the luminescent core.

Molecular-glue-triggered DNA assembly to form a robust and photoresponsive nano-network

A robust and photoresponsive DNA network has been designed and constructed from branched DNA and molecular glue. The molecular glue is photoswitchable and can specifically bind to G-G mismatched double-stranded DNA. The assembly process can be reversibly controlled by manipulating the wavelength of light. The approach is flexible, allowing tuning of the size, morphology as well as the cavity of the network by variation of the molar ratio and the isotropic/anisotropic character of the branched building blocks. The assembled architectures are versatile and heat tolerant. These properties should allow the use of the network in further applications.

Metal-complex/DNA conjugates: a versatile building block for DNA nanoarrays

The use of DNA networks as templates for forming nanoarrays of metallic centres shows an exciting potential to generate addressable nanostructures. Inorganic units can be photoactive, electroactive and/or can possess magnetic and catalytic properties and can adopt different spatial arrangements due to their varied coordination nature. All these properties influence both the structure and function of passive DNA scaffolds and provide DNA nanostructures as a new platform for new materials in emerging technologies, such as nanotechnology, biosensing or biocomputing.

Chemical approaches to DNA nanotechnology

Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials.

Two base pair duplexes suffice to build a novel material

Tetrahedral DNA hybrids with tetrakis(p-hydroxyphenyl)methane cores hybridize in a sequence-specific fashion at much higher temperatures than isolated linear duplexes. Dinucleotide DNA arms suffice to induce the formation of a solid at room temperature; this demonstrates the strength of multivalent binding. The graphic shows a view of a modeled assembly.

DNA-Metal Base Pairs

Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.

Assembly of DNA nanostructures with branched tris-DNA

Branched tris-DNA, in which two oligonucleotides of the same sequence and one other oligonucleotide of a different sequence are connected with a rigid central linker, was prepared chemically by using a DNA synthesizer. Two branched tris-DNA molecules with complementary DNA sequences form dimer and tetramer as well as linear and spherical oligomer complexes. The complex formation was studied by UV/thermal denaturation, enzyme digestion, gel electrophoresis, and AFM imaging.

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).

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).