Assembly of DNA nanostructures with branched tris-DNA

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

Organic Semiconductor-DNA Hybrid Assemblies

Organic semiconductors are photonic and electronic materials with high luminescence, quantum efficiency, color tunability, and size-dependent optoelectronic properties. The self-assembly of organic molecules enables the establishment of a fabrication technique for organic micro- and nano-architectures with well-defined shapes, tunable sizes, and defect-free structures. DNAs, a class of biomacromolecules, have recently been used as an engineering material capable of intricate nanoscale structuring while simultaneously storing biological genetic information. Here, the up-to-date research on hybrid materials made from organic semiconductors and DNAs is presented. The trends in photonic and electronic phenomena discovered in DNA-functionalized and DNA-driven organic semiconductor hybrids, comprising small molecules and polymers, are observed. Various hybrid forms of solutions, arrayed chips, nanowires, and crystalline particles are discussed, focusing on the role of DNA in the hybrids. Furthermore, the recent technical advances achieved in the integration of DNAs in light-emitting devices, transistors, waveguides, sensors, and biological assays are presented. DNAs not only serve as a recognizing element in organic-semiconductor-based sensors, but also as an active charge-control material in high-performance optoelectronic devices.

Eosin Y dye-based porous organic polymers for highly efficient heterogeneous photocatalytic dehydrogenative coupling reaction

Eosin Y dye has been successfully embedded into a nanoporous network EY-POPs through a bottom-up strategy. The polymers could be used as highly effective and reusable heterogeneous organo-photocatalyst for the dehydrogenative coupling reaction.

DNA-melamine hybrid molecules: from self-assembly to nanostructures

Single-stranded DNA-melamine hybrid molecular building blocks were synthesized using a phosphoramidation cross-coupling reaction with a zero linker approach. The self-assembly of the DNA-organic hybrid molecules was achieved by DNA hybridization. Following self-assembly, two distinct types of nanostructures in the form of linear chains and network arrays were observed. The morphology of the self-assembled nanostructures was found to depend on the number of DNA strands that were attached to a single melamine molecule.

Monomolecular sheets of propeller-shaped triethyl 4,4',4''-[benzene-1,3,5-triyltris(ethyne-2,1-diyl)]tribenzoate deuterochloroform monosolvate

The title compound, C39H30O6·CDCl3, has a chemical threefold axis and an approximately planar structure, with an ethoxycarbonyl substituent on each of the terminal benzenes oriented in the same direction, thus forming a propeller-shaped molecule. This molecule is of particular interest in the field of metal-organic frameworks (MOFs), where its hydrolyzed analogue forms MOF structures with high surface areas. The benzene ring which occupies the centre of the molecule forms π-π interactions to the equivalent benzene ring at a perpendicular distance of 3.32 (1) Å. Centrosymmetric dimers formed in this way are interconnected by intermolecular C-H···π interactions with a rather short H···CgA distance of 2.51 Å (CgA is the centroid of the central benzene ring). The molecules are arranged in regular parallel sheets. Within a sheet, molecules are interconnected via C-H···O interactions where all carbonyl O atoms participate in weak hydrogen bonds as hydrogen-bond acceptors. Neighbouring sheets are connected through the above-mentioned π-π and C-H···π interactions.

Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers: a computational-experimental study of the role of linkage direction in product distributions and stabilities

Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3'-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5'-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.

Syntheses of organic molecule-DNA hybrid structures

Investigation of robust and efficient pathways to build DNA-organic molecule hybrid structures is fundamentally important to realize controlled placement of single molecules for potential applications, such as single-molecule electronic devices. Herein, we report a systematic investigation of synthetic processes for preparing organic molecule-DNA building blocks and their subsequent elongation to generate precise micrometer-sized structures. Specifically, optimal cross-coupling routes were identified to enable chemical linkages between three different organic molecules, namely, polyethylene glycol (PEG), poly(p-phenylene ethynylene) (PPE), and benzenetricarboxylate, with single-stranded (ss) DNA. The resulting DNA-organic molecule hybrid building blocks were purified and characterized by both denaturing gel electrophoresis and electrospray ionization mass spectrometry (ESI-MS). The building blocks were subsequently elongated through both the DNA hybridization and ligation processes to prepare micrometer-sized double-stranded (ds) DNA-organic molecule hybrid structures. The described synthetic procedures should facilitate future syntheses of various hybrid DNA-based organic molecular structures.

Synthesis of DNA-organic molecule-DNA triblock oligomers using the amide coupling reaction and their enzymatic amplification

Precise electrical contact between single-molecule and electrodes is a first step to study single-molecule electronics and its application such as (bio)sensors and nanodevices. To realize a reliable electrical contact, we can use DNA as a template in the field of nanoelectronics because of its micrometer-scaled length with the thickness of nanometer-scale. In this paper, we studied the reactivity of the amide-coupling reaction to tether oligodeoxynucleotides (ODNs) to organic molecules and the elongation of the ODNs by the polymerase chain reaction (PCR) to synthesize 1.5 kbp dsDNA-organic molecule-1.5 kbp dsDNA (DOD) triblock architecture. The successful amide-coupling reactions were confirmed by electrospray ionization mass spectrometry (ESI-MS), and the triblock architectures were characterized by 1% agarose gel electrophoresis and atomic force microscope (AFM). Our result shows that this strategy is simple and makes it easy to construct DNA-organic molecule-DNA triblock architectures and potentially provides a platform to prepare and investigate single molecule electronics.