Enzyme-catalysed assembly of DNA hydrogel

DNA is a remarkable polymer that can be manipulated by a large number of molecular tools including enzymes. A variety of geometric objects, periodic arrays and nanoscale devices have been constructed. Previously we synthesized dendrimer-like DNA and DNA nanobarcodes from branched DNA via ligases. Here we report the construction of a hydrogel entirely from branched DNA that are three-dimensional and can be crosslinked in nature. These DNA hydrogels were biocompatible, biodegradable, inexpensive to fabricate and easily moulded into desired shapes and sizes. The distinct difference of the DNA hydrogel to other bio-inspired hydrogels (including peptide-based, alginate-based and DNA (linear)-polyacrylamide hydrogels) is that the crosslinking is realized via efficient, ligase-mediated reactions. The advantage is that the gelling processes are achieved under physiological conditions and the encapsulations are accomplished in situ-drugs including proteins and even live mammalian cells can be encapsulated in the liquid phase eliminating the drug-loading step and also avoiding denaturing conditions. Fine tuning of these hydrogels is easily accomplished by adjusting the initial concentrations and types of branched DNA monomers, thus allowing the hydrogels to be tailored for specific applications such as controlled drug delivery, tissue engineering, 3D cell culture, cell transplant therapy and other biomedical applications.     

Nanoscale programmable sequence-specific patterning of DNA scaffolds using RecA protein

Molecular self-assembly inherent to many biological molecules, in conjunction with suitable molecular scaffolds to facilitate programmable positioning of nanoscale objects, offers a promising approach for the integration of functional nanoscale complexes into macroscopic host devices. Here, we report the use of the protein RecA as a means of highly efficient programmable patterning of double-stranded (ds)DNA molecules with molecular-scale precision at specific locations along the DNA strand. RecA proteins form nucleoprotein filaments with single-stranded (ss)DNA molecules, which are chosen to be of sequence homologous to the desired binding region on the dsDNA scaffold. We show that the patterning yield can be in excess of 85% and we demonstrate that concurrent patterning of multiple locations on the same dsDNA scaffold can be achieved with separation between the assembled nucleoprotein filaments of less than 4?nm. This is an important prerequisite for this programmable and flexible DNA scaffold patterning technique to be employed in molecular-?and nanoscale assembly applications.     

Carbon nanotubes as electrodes for dielectrophoresis of DNA

Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field gradients for trapping nanoscale objects, e.g., single molecules. We compare the efficiency and other characteristics of dielectrophoresis between carbon nanotube electrodes and lithographically fabricated metallic electrodes, in the case of trapping nanoscale DNA molecules. The results are analyzed using finite element method simulations and reveal information about the frequency-dependent polarizability of DNA.     

Fabrication of Flexible Metal‐Nanoparticle Films Using Graphene Oxide Sheets as Substrates

Graphene‐based sheets that possess a unique nanostructure and a variety of fascinating properties are appealing as promising nanoscale building blocks of new composites. Herein, graphene oxide sheets are used as the nanoscale substrates for the formation of silver‐nanoparticle films. These silver‐nanoparticle films assembled on graphene oxide sheets are flexible and can form stable suspensions in aqueous solutions. They can also be easily processed, forming macroscopic films with high reflectivity. Raman signals of graphene oxide in such hybrid films are increased by the attached silver nanoparticles, displaying surface‐enhanced Raman scattering activity. The degree of enhancement can be adjusted by varying the quantity of silver nanoparticles on the graphene oxide sheets.     

A statistical study on nanoparticle movements in a microfluidic channel

Microfluidic channels have received much attention because they can be used to control and transport nanoscale objects such as nanoparticles, nanowires, carbon nanotubes, DNA and cells. However, so far, practical channels have not been easy to design because they require very expensive fabrication and sensitive experiments. Numerical approaches can be alternatives or supplementary measures to predict the performance of new channels because they efficiently explain nanoscale multi-physics phenomena and successfully solve nanowire alignment and cell adhesion problems. In this paper, a newly updated immersed finite element method that accounts for collision force and Brownian motion as well as fluid-solid interaction is proposed, and is applied to simulate nanoparticle movements in a microfluidic channel. As part of the simulation, Brownian motion effects in a single nanoparticle focusing lens system are examined under different temperature conditions, and the resulting transport efficiencies are discussed. Furthermore, nanoparticle movements in a double focusing lens system are predicted to show the enhancement of focusing efficiency.     

Nano and micro architectures for self-propelled motors

Self-propelled micromotors are emerging as important tools that help us understand the fundamentals of motion at the microscale and the nanoscale. Development of the motors for various biomedical and environmental applications is being pursued. Multiple fabrication methods can be used to construct the geometries of different sizes of motors. Here, we present an overview of appropriate methods of fabrication according to both size and shape requirements and the concept of guiding the catalytic motors within the confines of wall. Micromotors have also been incorporated with biological systems for a new type of fabrication method for bioinspired hybrid motors using three-dimensional (3D) printing technology. The 3D printed hybrid and bioinspired motors can be propelled by using ultrasound or live cells, offering a more biocompatible approach when compared to traditional catalytic motors.     

Tuning the conductance of a molecular switch

The ability to control the conductance of single molecules will have a major impact in nanoscale electronics. Azobenzene, a molecule that changes conformation as a result of a trans/cis transition when exposed to radiation, could form the basis of a light-driven molecular switch. It is therefore crucial to clarify the electrical transport characteristics of this molecule. Here, we investigate, theoretically, charge transport in a system in which a single azobenzene molecule is attached to two carbon nanotubes. In clear contrast to gold electrodes, the nanotubes can act as true nanoscale electrodes and we show that the low-energy conduction properties of the junction may be dramatically modified by changing the topology of the contacts between the nanotubes and the molecules, and/or the chirality of the nanotubes (that is, zigzag or armchair). We propose experiments to demonstrate controlled electrical switching with nanotube electrodes.     

Nano and micro architectures for self-propelled motors

Abstract

Self-propelled micromotors are emerging as important tools that help us understand the fundamentals of motion at the microscale and the nanoscale. Development of the motors for various biomedical and environmental applications is being pursued. Multiple fabrication methods can be used to construct the geometries of different sizes of motors. Here, we present an overview of appropriate methods of fabrication according to both size and shape requirements and the concept of guiding the catalytic motors within the confines of wall. Micromotors have also been incorporated with biological systems for a new type of fabrication method for bioinspired hybrid motors using three-dimensional (3D) printing technology. The 3D printed hybrid and bioinspired motors can be propelled by using ultrasound or live cells, offering a more biocompatible approach when compared to traditional catalytic motors.     

Novel bioinorganic nanostructures based on mesolamellar intercalation or single-molecule wrapping of DNA using organoclay building blocks

Nanosheets or nanoclusters of aminopropyl-functionalized magnesium phyllosilicate (AMP) were prepared in water by exfoliation and used as structural building blocks for the preparation of DNA-based hybrid nanostructures in the form of ordered mesolamellar nanocomposites or highly elongated nanowires, respectively. The former consisted of alternating layers of single sheets of AMP interspaced with intercalated monolayers of intact double-stranded DNA molecules of relatively short length ( approximately 700 base pairs) that were accessible to small molecules such as ethidium bromide. In contrast, the nanowires comprised isolated micrometer-long molecules of lambda-DNA or plasmid DNA that were sheathed in an ultrathin organoclay layer and which were either protected from or remained accessible to endonuclease-mediated clipping depending on the extent of biomolecule wrapping. Both types of hybrid nanostructures showed a marked increase in the DNA melting (denaturation) temperature, indicating significant thermal stabilization of the confined biomolecules. Our results suggest that nanoscale building blocks derived from organically modified inorganic clays could be useful agents for enhancing the chemical, thermal, and mechanical stability of isolated molecules or ensembles of DNA. Such constructs should have increased potential as functional components in bionanotechnology and nonviral gene transfection.     

Magnetic field mediated nanowire alignment in liquids for nanocomposite synthesis

The motion of magnetic nanowires can be manipulated by a magnetic field in liquids so that their distribution, alignment and orientation can be effectively controlled. The small dimensions of nanoscale entities result in an extremely low Reynolds number, and a steady state Stokes flow approximation was adopted to analyze the nanowire motion under the influences of applied field. The effects of fluid viscosity and external field on the motion of different sized nanowires were investigated. Polydimethylsiloxane composites with nickel nanowires as reinforcing fillers were synthesized as a demonstration of the effectiveness of magnetic alignment. Anisotropic magnetic properties and mechanical strengthening effects were explored.     

Direct observation of stepwise movement of a synthetic molecular transporter

Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor and fuel, all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold, and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor. Real-time atomic force microscopy allows direct observation of individual steps of a single motor, revealing mechanistic details of its operation. This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.     

Generalized theory for nanoscale voltammetric measurements of heterogeneous electron-transfer kinetics at macroscopic substrates by scanning electrochemical microscopy

Here we report on a generalized theory for scanning electrochemical microscopy to enable the voltammetric investigation of a heterogeneous electron-transfer (ET) reaction with arbitrary reversibility and mechanism at the macroscopic substrate. In this theory, we consider comprehensive nanoscale experimental conditions where a tip is positioned at a nanometer distance from a substrate to detect the reactant or product of a substrate reaction at any potential in the feedback or substrate generation/tip collection mode, respectively. Finite element simulation with the Marcus-Hush-Chidsey formalism predicts that a substrate reaction under the nanoscale mass transport conditions can deviate from classical Butler-Volmer behavior to enable the precise determination of the standard ET rate constant and reorganization energy for a redox couple from the resulting tip current-substrate potential voltammogram as obtained at quasi-steady state. Simulated voltammograms are generalized in the form of analytical equations to allow for reliable kinetic analysis without the prior knowledge of the rate law. Our theory also predicts that a limiting tip current can be controlled kinetically to be smaller than the diffusion-limited current when a relatively inert electrode material is investigated under the nanoscale voltammetric conditions.     

Isothermal Hybridization Kinetics of DNA Assembly of Two‐Dimensional DNA Origami

The Watson–Crick base‐pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA‐based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room‐temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple‐scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.     

Multi-walled carbon nanotubes and metallic nanoparticles and their application in biomedicine

Interdisciplinary research has become a matter of paramount importance for novel applications of nanomaterials in biology and medicine. As such, many disciplines-physics, chemistry, microbiology, cell biology, and material science-all contribute to the design, synthesis and fabrication of functional and biocompatible devices at the nanometer scale. Since the most areas of cell biology and biomedicine deal with functional entities such as DNA and proteins, mimicry of these structures and function in the nanosize range offers exciting opportunities for the development of biosensors, biochips, and bioplatforms. In this report we highlight the potential benefits and challenges that arise in the manufacture of biocompatible nanoparticles and nano-networks that can be coupled with biological objects. Among the challenges facing us are those concerned with making the necessary advances in enabling affordability, innovation, and quality of manufactured nanodevices for rapid progress in the emerging field of bio-nanotechnology. The convergence of nanotechnology and biomedicine makes nanoscale research highly promising for new discoveries that can cost-effectively accelerate progress in moving from basic research to practical prototypes and products.     

N2‐Plasma‐Assisted One‐Step Alignment and Patterning of Graphene Oxide on a SiO2/Si Substrate Via the Langmuir–Blodgett Technique

Precise control of the placement and patterning of graphene on various substrates has tremendous impact in many fields, such as nanoscale electronics, multifunctional optoelectronic devices, and molecular sensing. A one‐step facile technique involving N₂‐plasma promotes surface modification and enhances the surface wettability of the substrate. The technique is employed to create partially hydrophilic surfaces on SiO₂/Si substrate with the aid of various templates, enabling the selective deposition, alignment, and formation of patterns comprising monolayer graphene oxide (GO) sheets; it successfully uses the Langmuir–Blodgett (LB) deposition technique over a large area without the need of any sophisticated equipment. Various characterization techniques are carried out in order to understand the possible mechanism behind the pinning of the GO on the partially treated areas. It is a relatively easy and swift process that can reliably accomplish specific surface modification with high bonding strength between GO and the substrate. This technique allows the creation of patterns with controllable dimensions. For example, the thickness of the GO sheets can be controlled; this is particularly important in creating arrays and devices at wafer‐scale. Being simple yet effective and inexpensive, this technique holds tremendous potential that can be exploited for numerous applications in the field of bio‐nanoelectronics.     

Synthetic Self‐Assembled Materials in Biological Environments

Synthetic self‐assembly has long been recognized as an excellent approach for the formation of ordered structures on the nanoscale. Although the development of synthetic self‐assembling materials has often been inspired by principles observed in nature (e.g., the assembly of lipids, DNA, proteins), until recently the self‐assembly of synthetic molecules has mainly been investigated ex vivo. The past few years however, have witnessed the emergence of a research field in which synthetic, self‐assembling systems are used that are capable of operating as bioactive materials in biological environments. Here, this up‐and‐coming field, which has the potential of becoming a key area in chemical biology and medicine, is reviewed. Two main categories of applications of self‐assembly in biological environments are identified and discussed, namely therapeutic and imaging agents. Within these categories key concepts, such as triggers and molecular constraints for in vitro/in vivo self‐assembly and the mode of interaction between the assemblies and the biological materials will be discussed.     

Quantum measurement and orientation tracking of fluorescent nanodiamonds inside living cells

Fluorescent particles are routinely used to probe biological processes. The quantum properties of single spins within fluorescent particles have been explored in the field of nanoscale magnetometry, but not yet in biological environments. Here, we demonstrate optically detected magnetic resonance of individual fluorescent nanodiamond nitrogen-vacancy centres inside living human HeLa cells, and measure their location, orientation, spin levels and spin coherence times with nanoscale precision. Quantum coherence was measured through Rabi and spin-echo sequences over long (>10 h) periods, and orientation was tracked with effective 1° angular precision over acquisition times of 89 ms. The quantum spin levels served as fingerprints, allowing individual centres with identical fluorescence to be identified and tracked simultaneously. Furthermore, monitoring decoherence rates in response to changes in the local environment may provide new information about intracellular processes. The experiments reported here demonstrate the viability of controlled single spin probes for nanomagnetometry in biological systems, opening up a host of new possibilities for quantum-based imaging in the life sciences.     

A local optical probe for measuring motion and stress in a nanoelectromechanical system

Nanoelectromechanical systems can be operated as ultrasensitive mass sensors and ultrahigh-frequency resonators, and can also be used to explore fundamental physical phenomena such as nonlinear damping and quantum effects in macroscopic objects. Various dissipation mechanisms are known to limit the mechanical quality factors of nanoelectromechanical systems and to induce aging due to material degradation, so there is a need for methods that can probe the motion of these systems, and the stresses within them, at the nanoscale. Here, we report a non-invasive local optical probe for the quantitative measurement of motion and stress within a nanoelectromechanical system, based on Fizeau interferometry and Raman spectroscopy. The system consists of a multilayer graphene resonator that is clamped to a gold film on an oxidized silicon surface. The resonator and the surface both act as mirrors and therefore define an optical cavity. Fizeau interferometry provides a calibrated measurement of the motion of the resonator, while Raman spectroscopy can probe the strain within the system and allows a purely spectral detection of mechanical resonance at the nanoscale.     

Macroscopic carbon nanotube assemblies: preparation, properties, and potential applications

As classical 1D nanoscale structures, carbon nanotubes (CNTs) possess remarkable mechanical, electrical, thermal, and optical properties. In the past several years, considerable attention has been paid to the use of CNTs as building blocks for novel high-performance materials. In this way, the production of macroscopic architectures based on assembled CNTs with controlled orientation and configurations is an important step towards their application. So far, various forms of macroscale CNT assemblies have been produced, such as 1D CNT fibers, 2D CNT films/sheets, and 3D aligned CNT arrays or foams. These macroarchitectures, depending on the manner in which they are assembled, display a variety of fascinating features that cannot be achieved using conventional materials. This review provides an overview of various macroscopic CNT assemblies, with a focus on their preparation and mechanical properties as well as their potential applications in practical fields.     

Wetting‐Controlled Localized Placement of Surface Functionalities within Nanopores

In the context of sensing and transport control, nanopores play an essential role. Designing multifunctional nanopores and placing multiple surface functionalities with nanoscale precision remains challenging. Interface effects together with a combination of different materials are used to obtain local multifunctionalization of nanoscale pores within a model pore system prepared by colloidal templating. Silica inverse colloidal monolayers are first functionalized with a gold layer to create a hybrid porous architecture with two distinct gold nanostructures on the top surface as well as at the pore bottom. Using orthogonal silane‐ and thiol‐based chemistry together with a control of the wetting state allows individual addressing of the different locations within each pore resulting in nanoscale localized functional placement of three different functional units. Ring‐opening metathesis polymerization is used for inner silica‐pore wall functionalization. The hydrophobized pores create a Cassie–Baxter wetting state with aqueous solutions of thiols, which enables an exclusive functionalization of the outer gold structures. In a third step, an ethanolic solution able to wet the pores is used to self‐assemble a thiol‐containing initiator at the pore bottom. Subsequent controlled radical polymerization provides functionalization of the pore bottom. It is demonstrated that the combination of orthogonal surface chemistry and controlled wetting states can be used for the localized functionalization of porous materials.