DNA nanomachines and nanostructures involving quadruplexes

DNA is an attractive component for molecular recognition, because of its self-assembly properties. Its three-dimensional structure can differ markedly from the classical double helix. For example, DNA or RNA strands carrying guanine or cytosine stretches associate into four-stranded structures called G-quadruplexes or i-DNA, respectively. Since 2002, several groups have described nanomachines that take advantage of this structural polymorphism. We first introduce the unusual structures that are involved in these devices (i.e., i-DNA and G-quadruplexes) and then describe the opening and closing steps that allow cycling. A quadruplex-duplex molecular machine is then presented in detail, together with the rules that govern its formation, its opening/closing kinetics and the various technical and physico-chemical parameters that play a role in the efficiency of this device. Finally, we review the few examples of nanostructures that involve quadruplexes.     

Functional nanomachines: Recent advances in synthetic molecular machinery

A mini-review: As the top-down approach for miniaturisation of technology reaches its inherent limitations, robust strategies to build nanoscale machinery components, which have the ability to convert an input energy into motion, from the molecular level up, become increasingly important. Nature is certainly the most proficient in the control of molecular level motion; nevertheless, many successes have been enjoyed in the pursuit of mimicking key aspects of nature’s molecular machines, including two state switches, ion pumps, unidirectional rotary motors and molecular robots that can move molecular cargo. This mini-review outlines of some of the most impressive recent examples towards this end.     

Artificial nanomachines based on interlocked molecular species: recent advances

The bottom-up construction and operation of nanoscale machines and motors, that is, supramolecular systems wherein the molecular components can be set in motion in a controlled manner for ultimately accomplishing a function, is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest. Research in the last decade has shown that species made of interlocked molecular components like rotaxanes, catenanes and related systems are most attractive candidates. In recent times, the evolution of the structural and functional design of such systems has led to the construction and operation of complex molecular machines that, in some cases, are able to do specific tasks. This tutorial review is intended to discuss the design principles for nanomachines based on interlocked molecules, and to provide a timely overview on representative prototype systems.     

Cargo-towing synthetic nanomachines: towards active transport in microchip devices

This review article discusses the use of synthetic catalytic nano motors for cargo manipulations and for developing miniaturized lab-on-chip systems based on autonomous transport. The ability of using chemically-powered artificial nanomotors to capture, transport and release therapeutic payloads or nanostructured biomaterials represents one of the next major prospects for nanomotor development. The increased cargo-towing force of such self-propelled nanomotors, along with their precise motion control within microchannel networks, versatility and facile functionalization, pave the way to new integrated functional lab-on-a-chip powered by active transport and perform a series of tasks. Such use of cargo-towing artificial nanomotors has been inspired by on-chip kinesin molecular shuttles. Functionalized nano/microscale motors can thus be used to pick a selected nano/microscale chemical or biological payload target at the right place, transport and deliver them to a target location in a timely manner. Key challenges for using synthetic nanomachines for driving transport processes along microchannel networks are discussed, including loading and unloading of cargo and precise motion control, along with recent examples of related cargo manipulation processes and guided transport in lab-on-a-chip formats. The exciting research area of cargo-carrying catalytic man-made nanomachines is expected to grow rapidly, to lead to new lab-on-a-chip formats and to provide a wide range of future microchip opportunities.     

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.     

DNA tile based self-assembly: building complex nanoarchitectures.

DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.     

Single-molecule DNA logic nanomachines based on origami

<正>Nowadays, it is a truism that chemists, bioengineers and others must be schooled in cell and molecular biology, including knowledge of the cellular, elemental and molecular building blocks of living systems. Inspired by exquisite and efficient biomolecular machines in living cells, such as ATPases that catalyze the decomposition of ATP into ADP and free phosphate ion, researchers representing multiple dis-     

DNA-based machines

Nucleic acids include substantial information in their base sequence and their hybridization-complexation motifs. Recent research efforts attempt to utilize this biomolecular information to develop DNA nanostructures exhibiting machine-like functions. DNA nano-assemblies revealing tweezers, motor, and walker activities exemplify a few such machines. The DNA-based machines provide new components that act as sensitive sensors, transporters, or drug delivery systems.     

Synthesis and optical properties of three-dimensional porous core-shell nanoarchitectures

Three-dimensional porous core-shell nanostructures consisting of gold skeletons and silver shells were fabricated by controllable electroless plating. Optical properties of the 3D nanocomposite with a heterogeneous interface exhibit a significant shell-thickness dependence. The porous core-shell structure with an optimized shell thickness of approximately 3-5 nm exhibits a considerable improvement in surface-enhanced Raman scattering. This study has important implications in the functionalization of nanoporous metals by surface modification.     

DNA-based asymmetric catalysis: sequence-dependent rate acceleration and enantioselectivity

This study shows that the role of DNA in the DNA-based enantioselective Diels-Alder reaction of azachalcone with cyclopentadiene is not limited to that of a chiral scaffold. DNA in combination with the copper complex of 4,4'-dimethyl-2,2'-bipyridine (Cu-L1) gives rise to a rate acceleration of up to 2 orders of magnitude compared to Cu-L1 catalysis alone. Furthermore, both the enantioselectivity and the rate enhancement prove to be dependent on the DNA-sequence. These features are the main reasons for the efficient and enantioselective catalysis observed with salmon testes DNA/Cu-L1 in the Diels-Alder reaction. The fact that absolute levels of stereocontrol can be achieved with a simple and weak DNA-binding complex like Cu-L1 is a clear demonstration of the power of the supramolecular approach to hybrid catalysis.     

DNA-based phosphane ligands

In order to expand the repertoire of DNA sequences specifically interacting with transition metals, we report here the first examples of DNA sequences carrying mono- and bidentate phosphane ligands as well as P,N-ligands. Aminoalkyl-modified oligonucleotides have been reacted at predetermined internal sites with carboxylate derivatives of pyrphos, BINAP and phosphinooxazoline (PHOX) 2 b-d. Carbodiimide coupling in the presence of N-hydroxysuccinimide provided the DNA-ligand conjugates in 38-78 % yield. Phosphane-containing oligonucleotides and their phosphane sulfide analogues were characterized by mass spectrometry (MALDI-TOF and FT-ICR-ESI) and their stability after purification and isolation was systematically investigated. While DNA-appended pyrphos ligand was quickly oxidized, BINAP and PHOX conjugates showed high stabilities, making them useful precursors for incorporation of transition metals into DNA.     

DNA分子器件*

DNA不仅是一种重要的生物遗传物质,而且可以在生命科学以外的领域,尤其是在信息科学、材料科学中发挥重要作用.作为重要的部件,DNA分子器件的研究引起了科学家们的注意.本文对DNA分子器件的发展以及DNA分子器件的实现和应用前景及不足进行了较详尽的评述.     

Hierarchical assembly of diphenylalanine into dendritic nanoarchitectures

Highly ordered, multi-dimensional dendritic nanoarchitectures were created via self-assembly of diphenylalanine from an acidic buffer solution. The self-similarity of dendritic structures was characterized by examining their fractal dimensions with the box-counting method. The fractal dimension was determined to be 1.7, which demonstrates the fractal dimension of structures generated by diffusion limited aggregation on a two-dimensional substrate surface. By confining the dendritic assembly of diphenylalanine within PDMS microchannels, the self-similar dendritic growth could be hierarchically directed to create linearly assembled nanoarchitectures. Our approach offers a novel pathway for creating and directing hierarchical nanoarchitecture from biomolecular assembly.     

Controlled self-assembly of amphiphilic oligopeptides into shape-specific nanoarchitectures

Here, we report a novel, programmable, molecular self-assembling system to fabricate shape-specific, three-dimensional nanoarchitectures. Three types of simple 16-mer peptides consisting of hydrophobic Leu and hydrophilic Lys, LKL16, KLK16, and LK16, were prepared as building blocks for nanofabrications. A detailed analysis of the conformation and self-assembling mechanism was performed by using circular dichroism (CD), FTIR spectroscopy, and atomic force microscopy (AFM). A wide variety of self-assembled nanoarchitectures, such as beta-sheet-plates, beta-sheet-fibers, alpha-helix-particles, and alpha-helix-plates, could be fabricated by tuning the peptide sequence, reaction time, and solution pH. The ability to control the self-assembled nanostructures should provide a simple and/or essential insight into the mechanism of peptide aggregation, including amyloid formation, and it should be useful for the design of novel bio-related nanomaterials.     

Silver-colloid-nucleated cytochrome c superstructures encapsulated in silica nanoarchitectures

We recently discovered that self-organized superstructures of the heme protein cytochrome c (cyt. c) are nucleated in buffer by gold nanoparticles. The protein molecules within the superstructure survive both silica sol-gel encapsulation and drying from supercritical carbon dioxide to form air-filled biocomposite aerogels that exhibit gas-phase binding activity for nitric oxide. In this investigation, we report that viable proteins are present in biocomposite aerogels when the nucleating metal nanoparticle is silver rather than gold. Silver colloids were synthesized via reduction of an aqueous solution of Ag+ using either citrate or borohydride reductants. As determined by transmission electron microscopy and UV-visible absorption spectroscopy, the silver nanoparticles vary in size and shape depending on the synthetic route, which affects the fraction of cyt. c that survives the processing necessary to form a biocomposite aerogel. Silver colloids synthesized via the citrate preparation are polydisperse, with sizes ranging from 1 to 100 nm, and lead to low cyt. c viability in the dried bioaerogels (approximately 15%). Protein superstructures nucleated at approximately 10-nm Ag colloids prepared via the borohydride route, including citrate stabilization of the borohydride-reduced metal, retain significant protein viability within the bioaerogels (approximately 45%).     

Self-assembly of flowerlike AlOOH boehmite 3D nanoarchitectures

In this work, a hydrothermal route using an ethanol-water solution to progressively synthesize a sequence of flowerlike three-dimensional gamma-AlOOH boehmite nanostructures without employing templates or matrixes for self-assembly is presented. The flowerlike boehmite nanoarchitectures exhibit three hierarchies of self-organization, i.e., single-crystalline nanorods, nanostrips, and bundles, which are characterized by scanning and transmission electron microscopy. The sequence of products obtained after different processing times indicates a self-assembly mechanism. The hydrogen bonding on the surface of nanorods or nanostrips possibly plays a key role, as identified by FTIR spectra of the products after they had been heated to 1000 degrees C. The specific surface area and pore-size distribution of the obtained product as determined by gas-sorption measurements show that the boehmite nanoarchitectures exhibit high BET surface area and porosity properties.     

Engineering DNA-based functional materials

While DNA is a genetic material, it is also an inherently polymeric material made from repeating units called nucleotides. Although DNA's biological functions have been studied for decades, the polymeric features of DNA have not been extensively exploited until recently. In this tutorial review, we focus on two aspects of using DNA as a polymeric material: (1) the engineering methods, and (2) the potential real-world applications. More specifically, various strategies for constructing DNA-based building blocks and materials are introduced based on DNA topologies, which include linear, branched/dendritic, and networked. Different applications in nanotechnology, medicine, and biotechnology are further reviewed.