DNA nanodevices

The molecular recognition properties of DNA molecules combined with the distinct mechanical properties of single and double strands of DNA can be utilized for the construction of nanodevices, which can perform ever more tasks with possible applications ranging from nanoconstruction to intelligent drug delivery. With the help of DNA it is possible to construct machinelike devices that are capable of rotational motion, pulling and stretching, or even unidirectional motion. It is possible to devise autonomous nanodevices, to grab and release molecules, and also to perform simple information-processing tasks.     

Conductivity of a single DNA duplex bridging a carbon nanotube gap

We describe a general method to integrate DNA strands between single-walled carbon nanotube electrodes and to measure their electrical properties. We modified DNA sequences with amines on either the 5' terminus or both the 3' and 5' termini and coupled these to the single-walled carbon nanotube electrodes through amide linkages, enabling the electrical properties of complementary and mismatched strands to be measured. Well-matched duplex DNA in the gap between the electrodes exhibits a resistance on the order of 1 M(Omega). A single GT or CA mismatch in a DNA 15-mer increases the resistance of the duplex approximately 300-fold relative to a well-matched one. Certain DNA sequences oriented within this gap are substrates for Alu I, a blunt end restriction enzyme. This enzyme cuts the DNA and eliminates the conductive path, supporting the supposition that the DNA is in its native conformation when bridging the ends of the single-walled carbon nanotubes.     

Controllable nanoreactor confined to atomic force microscopy tips and its application in low copy DNA ligation

Less molecules reaction, especially at the single molecule level, plays an important role in biochemical or chemical research. It is also significant to achieve low copy or single molecule DNA ligation during the whole genome project. In this paper, a new type of nanoreactor was constructed around atomic force microscopy (AFM) tips under certain humidity, where DNA molecules can be limited to a special space through water meniscus, so the probability of molecules collision was increased and the efficiency of DNA ligation was greatly enhanced. Combined with the nanomanipulation based on AFM, controllable nanoreactor may provide a new tool to single molecule reaction. Low copy DNA ligation was successfully achieved by this method. Results showed the number of DNA molecules involved in the nanoreactor can not be more than sixty. This method will found a base for the ultimate realization of single-molecule DNA ligation.     

Effect of hydration on electrical conductivity of DNA duplex: Green’s function study combined with DFT

The electrical conductivity of DNA duplex is affected by many factors such as DNA base sequence, hydration of DNA duplex, connecting configuration between DNA duplex and electrodes, thermal fluctuation of DNA duplex structure. We here investigate the electrical conducting properties of DNA duplexes sandwiched between Au electrodes by molecular simulations using nonequilibrium Green’s function method coupled with density functional theory. The results reveal the dependence of electrical conductivity on DNA base sequence as well as hydration, which are in qualitative agreement with experiment. The present results indicate the important role played by hydrating water molecules in the electrical conductivity through DNA duplexes.     

The relevance of nonlinear stacking interactions in simple models of double-stranded DNA.

Single molecule DNA experiments provide interesting data that allow a better understanding of the mechanical interactions between the strands and the nucleotides of this molecule. In some sense, these experiments complement the classical ones about DNA thermal denaturation. It is well known that the original Peyrard-Bishop (PB) model by means of a harmonic stacking potential and a nonlinear substrate potential has been able to predict the existence of a critical temperature of full denaturation of the molecule. In the present paper, driven by the findings of single molecule experiments, we substitute the original harmonic intra-strand stacking potential with a Duffing type potential. By elementary and analytical arguments, we show that with this choice it is possible to obtain a sharp transition in the classical domain wall solution of the PB model and the compactification of the classical solitary wave solutions of other models for the dynamics of DNA. We discuss why these solutions may improve our knowledge of the DNA dynamics in several directions.     

Investigation of radiation damage to microcapsules in environmental SEM

Abstract

The radiation damage to a specimen in the chamber of electron microscopes has been studied extensively in the past few years. However, for the specific case of specimens with a core/shell structure, such as microcapsules and biological cells, there has been little experimentation devoted to understanding how the radiation may affect their mechanical properties. In the present work, single melamine formaldehyde (MF) microcapsules were imaged using an environmental electron microscope (ESEM) under both dry and wet modes under conditions of different accelerating voltages. The changes in the morphology (shape) were monitored as a function of radiation time. In addition, a newly developed ESEM based nanomanipulation technique was used to measure how the force imposed on single MF microcapsules for a given deformation changed with radiation time, in order to identify a time window within which the radiation damage to the microcapsules may be negligible in order to be able to study the mechanical properties of the particles. Based on the findings, the nanomanipulation technique was applied to measure the force versus displacement for compressing single microcapsules to rupture, including determination of their rupture mode.     

PX DNA triangle oligomerized using a novel three-domain motif

Structural DNA nanotechnology is directed at building objects, lattices, and arrays from cohesive interactions between DNA molecules. The predominant means of doing this takes advantage of the information inherent in Watson-Crick base pairing in duplex formation and in sticky-ended cohesion. Nevertheless, other forms of nucleic acid cohesion are also known, particularly paranemic edge-sharing interactions (PX). Here we report the formation of a triangular species that has four strands per edge, held together by PX interactions. We demonstrate by nondenaturing gel electrophoresis and by atomic force microscopy (AFM) that we can combine a partial triangle with other strands to form a four-stranded molecule that is robust. By combining them with a new mixed-fusion type of three-domain molecule, we demonstrate by AFM that these triangles can be self-assembled into a linear array.     

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.     

Automatic Drift Compensation Using Phase Correlation Method for Nanomanipulation

Nanomanipulation and nanofabrication with an atomic force microscope (AFM) or other scanning probe microscope (SPM) are a precursor for nanomanufacturing. It is still a challenging task to accomplish nanomanipulation automatically. In ambient conditions without stringent environmental controls, the task of nanomanipulation requires extensive human intervention to compensate for the spatial uncertainties of the SPM. Among these uncertainties, the thermal drift, which affects spatial resolution, is especially hard to solve because it tends to increase with time, and cannot be compensated simultaneously by feedback from the instrument. In this paper, a novel automatic compensation scheme is introduced to measure and estimate the drift one-step ahead. The scheme can be subsequently utilized to compensate for the thermal drift so that a real-time controller for nanomanipulation can be designed, as if the drift did not exist. Experimental results show that the proposed compensation scheme can predict drift with a small error, and therefore, can be embedded in the controller for manipulation tasks.     

Natural fiber-reinforced thermoplastic starch composites obtained by melt processing

Thermoplastic starch (TPS) from industrial non-modified corn starch was obtained and reinforced with natural strands. The influence of the reinforcement on physical–chemical properties of the composites obtained by melt processing has been analyzed. For this purpose, composites reinforced with different amounts of either sisal or hemp strands have been prepared and evaluated in terms of crystallinity, water sorption, thermal and mechanical properties. The results showed that the incorporation of sisal or hemp strands caused an increase in the glass transition temperature (T_g) of the TPS as determined by DMTA. The reinforcement also increased the stiffness of the material, as reflected in both the storage modulus and the Young’s modulus. Intrinsic mechanical properties of the reinforcing fibers showed a lower effect on the final mechanical properties of the materials than their homogeneity and distribution within the matrix. Additionally, the addition of a natural latex plasticizer to the composite decreased the water absorption kinetics without affecting significantly the thermal and mechanical properties of the material.     

A microfluidic system for large DNA molecule arrays

Single molecule approaches offer the promise of large, exquisitely miniature ensembles for the generation of equally large data sets. Although microfluidic devices have previously been designed to manipulate single DNA molecules, many of the functionalities they embody are not applicable to very large DNA molecules, normally extracted from cells. Importantly, such microfluidic devices must work within an integrated system to enable high-throughput biological or biochemical analysis-a key measure of any device aimed at the chemical/biological interface and required if large data sets are to be created for subsequent analysis. The challenge here was to design an integrated microfluidic device to control the deposition or elongation of large DNA molecules (up to millimeters in length), which would serve as a general platform for biological/biochemical analysis to function within an integrated system that included massively parallel data collection and analysis. The approach we took was to use replica molding to construct silastic devices to consistently deposit oriented, elongated DNA molecules onto charged surfaces, creating massive single molecule arrays, which we analyzed for both physical and biochemical insights within an integrated environment that created large data sets. The overall efficacy of this approach was demonstrated by the restriction enzyme mapping and identification of single human genomic DNA molecules.     

Electrochemical sensing of DNA hybridization based on duplex-specific charge compensation

A nonlabeling voltammetric detection method for DNA hybridization has been developed, in which [Fe(CN)(6)](3-) in solution can readily approach an electrode surface covered with a charge-compensated DNA duplex layer and thus provides a strong redox-sensing current. Charge compensation for negative charges on the DNA backbone has been specifically accomplished on DNA duplexes by discouraging nonspecific binding of positively charged intercalating molecules with single strands. A pretreatment of DNA-modified electrodes with sodium dodecyl sulfate before the intercalator binding process is essential in preventing the nonspecific binding. Since ferricyanide, the only electrochemically active species, is present in the voltammetric solution, the detection signal can be amplified by increasing its concentration. Combination of the duplex-specific charge compensation with the signal amplification has achieved a remarkable signal difference: in 30 mM [Fe(CN)(6)](3-), the area ratio between cyclic voltammograms of the hybridized and unhybridized electrodes is approximately 200 when 3,6-diaminoacridine is used as the intercalator. High sensitivity of the method has been demonstrated by detecting 10 fM (100 zmol in amount) of a target probe DNA.     

Engineering the pH‐Responsive Catalytic Behavior of AuNPs by DNA

Noble metal nanoparticles have attracted much interest in the heterogeneous catalysis. Particularly, efficient manipulation of the responsive catalytic properties of the metal nanoparticles is an interesting topic. In this work, a simple and efficient strategy is developed to regulate the pH‐responsive catalytic activities of glucose oxidase (GOx)‐mimicking gold nanoparticles (AuNPs). Four DNA strands (regulating strands) that differ slightly in sequences are used to interact non‐covalently with citrate‐capped AuNPs, resulting in markedly distinct pH‐dependent catalytic behavior of AuNPs. This is ascribed to the characteristic pH‐induced conformational change of the DNA strands that leads to the different adsorption capability to the NPs surface, as demonstrated by pH‐CD profiles of the respective DNA molecules. The pH‐dependent catalysis of AuNPs is also encoded with structural information of the double‐stranded DNA (including regulating strands and their complementary strands) that has conformation resistant or responsive to pH change. As a result, the catalysis can be programmed into an AND gate, a XNOR gate or a NOT gate, using pH and complementary strand as the inputs, the nanoparticle activity as the output and the regulating strands as the programs. This work can be expanded by engineering the catalytic behavior of noble metal nanoparticles to respond smartly to a variety of environmental stimuli, such as metal ions or light wavelengths. These results may provide insight into understanding ligand‐regulated nanometallic catalysis.     

Self‐Assembly of Microparticles by Supramolecular Homopolymerization of One Component DNA Molecule

DNA is a superb molecule for self‐assembly of nanostructures. Often many DNA strands are required for the assembly of one DNA nanostructure. For lowering the cost of synthesizing DNA strands and facilitating the assembly process, it is highly desirable to use a minimal number of unique strands for potential technological applications. Herein, a strategy is reported to assemble a series of DNA microparticles (DNAµPs) from one component DNA strand. As a demonstration of the application of the resulting DNAµPs, the design and assembled DNAµPs are modified to carry additional single‐stranded tails on their surfaces. The modified DNAµPs can either capture other nucleic acids or display CpG motifs to stimulate immune responses.     

A Supra‐photoswitch Involving Sandwiched DNA Base Pairs and Azobenzenes for Light‐Driven Nanostructures and Nanodevices

A supra‐photoswitch is designed for complete ON/OFF switching of DNA hybridization by light irradiation for the purpose of using DNA as a material for building nanostructures. Azobenzenes, attached to D ‐threoninols that function as scaffolds, are introduced into each DNA strand after every two natural nucleotides (in the form (NNX)n where N and X represent the natural nucleotide and the azobenzene moiety, respectively). Hybridization of these two modified strands forms a supra‐photoswitch consisting of alternating natural base pairs and azobenzene moieties. In this newly designed sequence, each base pair is sandwiched between two azobenzene moieties and all the azobenzene moieties are separated by base pairs. When the duplex is irradiated by visible light, the azobenzene moieties take the trans form and this duplex is surprisingly stable compared to the corresponding native duplex composed of only natural oligonucleotides. On the other hand, when the azobenzene moieties are isomerized to the cis form by UV light irradiation, the duplex is completely dissociated. Based on this design, a DNA hairpin structure is synthesized that should be closed by visible light irradiation and opened by UV light irradiation at the level of a single molecule. Indeed, perfect ON/OFF photoregulation is attained. This is a promising strategy for the design of supra‐photoswitches such as photoresponsive sticky ends on DNA nanodevices and other nanostructures.     

Direct mechanical measurements reveal the material properties of three-dimensional DNA origami

The application of three-dimensional DNA origami objects as rigid mechanical mediators or force sensing elements requires detailed knowledge about their complex mechanical properties. Using magnetic tweezers, we directly measure the bending and torsional rigidities of four- and six-helix bundles assembled by this technique. Compared to duplex DNA, we find the bending rigidities to be greatly increased while the torsional rigidities are only moderately augmented. We present a mechanical model explicitly including the crossovers between the individual helices in the origami structure that reproduces the experimentally observed behavior. Our results provide an important basis for the future application of 3D DNA origami in nanomechanics.     

Variability of the mechanical properties of bone, and its evolutionary consequences

The relative variabilities (coefficient of variation (CV)) of 10 different mechanical properties of compact bone were determined from 2166 measurements. All measures of variability were made on a minimum of four specimens from any bone. Three pre-yield properties had a CV of about 12%. Six post-yield properties had CVs varying from 24 to 46%. Pre-yield properties increase as a function of mineral content, whereas post-yield properties decrease. These differences give insight into mechanical phenomena occurring at different stages during loading. Furthermore, the fact that some properties are more tightly determined than others has implications for the optimum values set by natural selection. This assertion is made more rigorous using a simple mathematical model for the evolutionarily optimal allocation in a trade-off where one property is imprecisely determined. It is argued that in general the optimum will be biased in favour of the more tightly determined properties than would be the case if all properties had the same CV.     

Mechanical Peeling of Free‐Standing Single‐Walled Carbon‐Nanotube Bundles

An in situ electron microscopy study is presented of adhesion interactions between single‐walled carbon nanotubes (SWNTs) by mechanically peeling thin free‐standing SWNT bundles using in situ nanomanipulation techniques inside a high‐resolution scanning electron microscope. The in situ measurements clearly reveal the process of delaminating one SWNT bundle from its originally bound SWNT bundle in a controlled‐displacement manner and capture the deformation curvature of the delaminated SWNT bundle during the peeling process. A theoretical model based on nonlinear elastica theory is employed to interpret the measured deformation curvatures of the SWNTs and to quantitatively evaluate the peeling force and the adhesion strength between bundled SWNTs. The estimated adhesion energy per unit length for each pair of neighboring tubes in the peeling interface based on our peeling experiments agrees reasonably well with the theoretical value. This in situ peeling technique provides a potential new method for separating bundled SWNTs without compromising their material properties. The combined peeling experiments and modeling presented in this paper will be very useful to the study of the adhesion interactions between SWNTs and their nonlinear mechanical behaviors in the large‐displacement regime.     

Detection of Single DNA Molecule Hybridization on a Surface by Atomic Force Microscopy

Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single‐stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine‐tuning of the composition of the hybridization buffer. Single‐molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single‐molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.     

A DNA duplex with extremely enhanced thermal stability based on controlled immobilization on gold nanoparticles

The effect of DNA loadings on the thermal stability of DNA duplex immobilized on gold nanoparticles has been investigated. The modestly loaded duplexes on the gold nanoparticles showed enhanced thermal stability, as compared to that of the free duplex (without gold nanoparticles). However, the highly loaded duplex showed stability similar to that of free duplex. The stability could be controlled over a wide temperature range simply by varying the salt concentration (over 50 degrees C). Additionally, the gold nanoparticles with modestly loaded oligonucleotides could be used as nanoprobes for effective and fast strand exchange reactions, based on the increased thermal stability of the immobilized duplex. These results indicate that the interaction between the duplex and the nanoparticle surface plays an important role in determining the stability of the duplex.