Spiral Patterning of Au Nanoparticles on Au Nanorod Surface to Form Chiral AuNR@AuNP Helical Superstructures Templated by DNA Origami

Plasmonic motifs with precise surface recognition sites are crucial for assembling defined nanostructures with novel functionalities and properties. In this work, a unique and effective strategy is successfully developed to pattern DNA recognition sites in a helical arrangement around a gold nanorod (AuNR), and a new set of heterogeneous AuNR@AuNP plasmonic helices is fabricated by attaching complementary‐DNA‐modified gold nanoparticles (AuNPs) to the predesigned sites on the AuNR surface. AuNR is first assembled to one side of a bifacial rectangular DNA origami, where eight groups of capture strands are selectively patterned on the other side. The subsequently added link strands make the rectangular DNA origami roll up around the AuNR into a tubular shape, therefore giving birth to a chiral patterning of DNA recognition sites on the surface of AuNR. Following the hybridization with the AuNPs capped with the complementary strands to the capture strands on the DNA origami, left‐handed and right‐handed AuNR@AuNP helical superstructures are precisely formed by tuning the pattern of the recognition sites on the AuNR surface. Our strategy of nanoparticle surface patterning innovatively realizes hierarchical self‐assembly of plasmonic superstructures with tunable chiroptical responses, and will certainly broaden the horizon of bottom‐up construction of other functional nanoarchitectures with growing complexity.     

DNA Polymer Brush Patterning through Photocontrollable Surface‐Initiated DNA Hybridization Chain Reaction

The fabrication of DNA polymer brushes with spatial resolution onto a solid surface is a crucial step for biochip research and related applications, cell‐free gene expression study, and even artificial cell fabrication. Here, for the first time, a DNA polymer brush patterning method is reported based on the photoactivation of an ortho‐nitrobenzyl linker‐embedded DNA hairpin structure and a subsequent surface‐initiated DNA hybridization chain reaction (HCR). Inert DNA hairpins are exposed to ultraviolet light irradiation to generate DNA duplexes with two active sticky ends (toeholds) in a programmable manner. These activated DNA duplexes can initiate DNA HCR to generate multifunctional patterned DNA polymer brushes with complex geometrical shapes. Different multifunctional DNA polymer brush patterns can be fabricated on certain areas of the same solid surface using this method. Moreover, the patterned DNA brush surface can be used to capture target molecules in a desired manner.     

Biochips for Cell Biology by Combined Dip‐Pen Nanolithography and DNA‐Directed Protein Immobilization

A general methodology for patterning of multiple protein ligands with lateral dimensions below those of single cells is described. It employs dip pen nanolithography (DPN) patterning of DNA oligonucleotides which are then used as capture strands for DNA‐directed immobilization (DDI) of oligonucleotide‐tagged proteins. This study reports the development and optimization of PEG‐based liquid ink, used as carrier for the immobilization of alkylamino‐labeled DNA oligomers on chemically activated glass surfaces. The resulting DNA arrays have typical spot sizes of 4–5 μm with a pitch of 12 μm micrometer. It is demonstrated that the arrays can be further functionalized with covalent DNA‐streptavidin (DNA‐STV) conjugates bearing ligands recognized by cells. To this end, biotinylated epidermal growth factor (EGF) is coupled to the DNA‐STV conjugates, the resulting constructs are hybridized with the DNA arrays and the resulting surfaces used for the culturing of MCF‐7 (human breast adenocarcinoma) cells. Owing to the lateral diffusion of transmembrane proteins in the cell's plasma membrane, specific recruitment and concentration of EGF receptor can be induced specifically at the sites where the ligands are bound on the solid substrate. This is a clear demonstration that this method is suitable for precise functional manipulations of subcellular areas within living cells.     

Capture and Culturing of Living Cells on Microstructured DNA Substrates

A modular system for the DNA‐directed immobilization of antibodies was applied to capture living cells on microstructured DNA surfaces. It is demonstrated in two different set‐ups, static incubation and hydrodynamic flow, that this approach is well suited for specific capture and selection of cells from culture medium. The adhered cells show intact morphology and they can be cultivated to grow to dense monolayers, restricted to the lateral dimensions of DNA spots on the surface. Owing to the modularity of surface biofunctionalization, the system can readily be configured to serve as a matrix for adhesion and growth of different cells, as demonstrated by specific binding of human embryonic kidney cells (HEK293) and Hodgkin lymphoma L540cy cells onto patches bearing appropriate recognition moieties inside a microfluidic channel. We therefore anticipate that the systems described here should be useful for fundamental research in cell biology or applications in biomedical diagnostics, drug screening, and nanobiotechnology.     

Direct Readout of Single Nucleobase Variations in an Oligonucleotide

Direct, low‐cost, label‐free, and enzyme‐free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild‐type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic‐acid‐based sensing and disease diagnosis.     

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.     

Biopebble Containers: DNA‐Directed Surface Assembly of Mesoporous Silica Nanoparticles for Cell Studies

The development of methods for colloidal self‐assembly on solid surfaces is important for many applications in biomedical sciences. Toward this goal, described is a versatile class of mesoporous silica nanoparticles (MSN) that contain on their surface various types of DNA molecules to enable their self‐assembly into micropatterned surface architectures useful for cell studies. Monodisperse dye‐doped MSN are synthesized by biphase stratification and functionalized with an aptamer oligonucleotide that serves as gatekeeper for the triggered release of encapsulated molecular cargo, such as fluorescent dye rhodamine B or the anticancer drug doxorubicin. One or two additional types of oligonucleotides are installed on the MSN surface to enable DNA‐directed immobilization on solid substrates bearing patterns of complementary capture oligonucleotides. It is demonstrated that this strategy can be used for efficient self‐assembly of microstructured surface architectures, which not only promote the adhesion and guidance of cells but also are capable of affecting the fate of adhered cells through triggered release of their cargo. It is believed that this approach is useful for diverse applications in tissue engineering and nanobio sciences.     

DNA‐Directed Assembly of Capture Tools for Constitutional Studies of Large Protein Complexes

Large supramolecular protein complexes, such as the molecular machinery involved in gene regulation, cell signaling, or cell division, are key in all fundamental processes of life. Detailed elucidation of structure and dynamics of such complexes can be achieved by reverse‐engineering parts of the complexes in order to probe their interactions with distinctive binding partners in vitro. The exploitation of DNA nanostructures to mimic partially assembled supramolecular protein complexes in which the presence and state of two or more proteins are decisive for binding of additional building blocks is reported here. To this end, four‐way DNA Holliday junction motifs bearing a fluorescein and a biotin tag, for tracking and affinity capture, respectively, are site‐specifically functionalized with centromeric protein (CENP) C and CENP‐T. The latter serves as baits for binding of the so‐called KMN component, thereby mimicking early stages of the assembly of kinetochores, structures that mediate and control the attachment of microtubules to chromosomes in the spindle apparatus. Results from pull‐down experiments are consistent with the hypothesis that CENP‐C and CENP‐T may bind cooperatively to the KMN network.     

Flow‐Through Microbial Capture by Antibody‐Coated Microsieves

A new flow‐through method for rapid capture and detection of microorganisms is developed using optically‐flat microengineered membranes. Selective and efficient capture of Salmonella is demonstrated with antibodies coated on membranes (microsieves) having a pore size much larger than the microorganism itself. The silicon‐nitride membranes are first photochemically coated with 1,2‐epoxy‐9‐decene yielding stable Si–C and N–C linkages. The resultant epoxide‐terminated microsieves are subsequently biofunctionalized with anti‐Salmonella antibodies. The capture efficiency of antibody‐coated microsieves with different pore sizes (2.0–5.0 μm) is studied with Salmonella enterica enterica serotype Typhimurium suspensions (10⁷ cfu mL^–1). The antibody‐coated microsieves capture 52% (2 μm microsieves), 30% (3.5 μm microsieves), and 12% (5 μm microsieves) of Salmonella from the suspension. The influence of flow rate (0.8–16 μL min^–1 mm^–2) on the capture efficiency of antibody‐coated 3.5 μm microsieves is investigated. The capture efficiency increases from ≈30% to ≈70% when the flow‐rate decreases from 16 to 0.8 μL min^–1 mm^–2. Antibody‐coated 3.5 μm microsieves can capture Salmonella rapidly and directly from fresh milk suspension (capture 35% at concentration of 80 cfu mL^–1). The use of antibody‐coated microsieves as microbial selective capture devices is thus shown to be highly promising for the direct capture of microorganisms.     

Nanopore Biosensors: Monitoring of an ATP‐Binding Aptamer and its Conformational Changes Using an α‐Hemolysin Nanopore (Small 1/2011)

An aptamer is a specific oligonucleotide sequence that spontaneously forms a secondary structure capable of selectively binding an analyte. An aptamer’s conformation is the key to specific binding of a target molecule, even in the case of very closely related targets. Nanopores are a sensitive tool for the single‐molecule analysis of DNA, peptides, and proteins transporting through the pore. Herein, a single α‐hemolysin natural nanopore is utilized to sense the conformational changes of an adenosine 5’‐triphosphate (ATP)‐binding aptamer (ABA). The known DNA sequence of the ABA is used as a model to develop real‐time monitoring of molecular conformational changes that occur by binding targets. The native, folded ABA structure has a nanopore unfolding time of 4.17 ms, compared with 0.29 ms for the ABA:ATP complex. A complementary 14‐mer strand, which binds the ABA sequence in the key nucleic acids responsible for folding, forms linear duplex DNA, resulting in a nanopore transit time of 0.50 ms and a higher capture probability than that of the folded ABA oligomer. Competition assays between the ABA:ATP and ABA:reporter complexes are carried out, and the results suggest that the ABA:ATP complex is formed preferentially. The nanopore allows for the detection of an ABA in its folded, ATP‐bound, and linear conformations.     

Microfabricated linear hydrogel microarray for single-nucleotide polymorphism detection

A platform is developed for rapid, multiplexed detection of single-nucleotide polymorphisms using gels copolymerized with oligonucleotide capture probes in a linear microchannel array. DNA samples are analyzed by electrophoresis through the linear array of gels, each containing 20-40 μM of a unique oligonucleotide capture probe. Electrophoresis of target DNA through the capture sites and the high concentration of capture probes within the gels enables significantly shorter incubation times than standard surface DNA microarrays. These factors also result in a significant concentration of target within the gels, enabling precise analysis of as little as 0.6 femtomoles of DNA target. Differential melting of perfectly matched and mismatched targets from capture probes as a function of electric field and temperature enables rapid, unambiguous identification of single-nucleotide polymorphisms.     

Design of Hierarchical Beads for Efficient Label‐Free Cell Capture

Defined hierarchical materials promise cell analysis and call for application‐driven design in practical use. The further issue is to develop advanced materials and devices for efficient label‐free cell capture with minimum instrumentation. Herein, the design of hierarchical beads is reported for efficient label‐free cell capture. Silica nanoparticles (size of ≈15 nm) are coated onto silica spheres (size of ≈200 nm) to achieve nanoscale surface roughness, and then the rough silica spheres are combined with microbeads (≈150–1000 µm in diameter) to assemble hierarchical structures. These hierarchical beads are built via electrostatic interaction, covalent bonding, and nanoparticle adherence. Further, after functionalization by hyaluronic acid (HA), the hierarchical beads display desirable surface hydrophilicity, biocompatibility, and chemical/structural stability. Due to the controlled surface topology and chemistry, HA‐functionalized hierarchical beads afford high cell capture efficiency up to 98.7% in a facile label‐free manner. This work guides the development of label‐free cell capture techniques and contributes to the construction of smart interfaces in bio‐systems.     

Improving the Sensitivity of Fluorescence‐Based Immunoassays by Photobleaching the Autofluorescence of Magnetic Beads

In fluorescence‐based assays, usually a target molecule is captured using a probe conjugated to a capture surface, and then detected using a second fluorescently labeled probe. One of the most common capture surfaces is a magnetic bead. However, magnetic beads exhibit strong autofluorescence, which often overlaps with the emission of the reporter fluorescent dyes and limits the analytical performance of the assay. Here, several widely used magnetic beads are photobleached and their autofluorescence is reduced to 1% of the initial value. Their autofluorescence properties, including their photobleaching decay rates and autofluorescence spectra pre‐ and post‐photobleaching, and the stability of the photobleaching over a period of two months are analyzed. The photobleached beads are stable over time and their surface functionality is retained. In a high‐sensitivity LX‐200 system using photobleached magnetic beads, human interleukin‐8 is detected with a threefold improvement in detection limit and signal‐to‐noise ratio over results achievable with nonbleached beads. Since many contemporary immunoassays rely on magnetic beads as capture surfaces, prebleaching the beads may significantly improve the analytical performance of these assays. Moreover, nonmagnetic beads with low autofluorescence are also successfully photobleached, suggesting that photobleaching can be applied to various capture surfaces used in fluorescence‐based assays.     

Discontinuous Nanoporous Membranes Reduce Non‐Specific Fouling for Immunoaffinity Cell Capture

The microfluidic isolation of target cells using adhesion‐based surface capture has been widely explored for biology and medicine. However, high‐throughput processing can be challenging due to interfacial limitations such as transport, reaction, and non‐specific fouling. Here, it is shown that antibody‐functionalized capture surfaces with discontinuous permeability enable efficient target cell capture at high flow rates by decreasing fouling. Experimental characterization and theoretical modeling reveal that “wall effects” affect cell–surface interactions and promote excess surface accumulation. These issues are partially circumvented by reducing the transport and deposition of cells near the channel walls. Optimized microfluidic devices can be operated at higher cell concentrations with significant improvements in throughput.     

Magneto‐Controllable Capture and Release of Cancer Cells by Using a Micropillar Device Decorated with Graphite Oxide‐Coated Magnetic Nanoparticles

Aiming to highly efficient capture and analysis of circulating tumor cells, a micropillar device decorated with graphite oxide‐coated magnetic nanoparticles is developed for magneto‐controllable capture and release of cancer cells. Graphite oxide‐coated, Fe₃O₄ magnetic nanoparticles (MNPs) are synthesized by solution mixing and functionalized with a specific antibody, following by the immobilization of such modified MNPs on our designed micropillar device. For the proof‐of‐concept study, a HCT116 colorectal cancer cell line is employed to exam the capture efficiency. Under magnetic field manipulation, the high density packing of antibody‐modified MNPs on the micropillars increases the local concentration of antibody, as well as the topographic interactions between cancer cells and micropillar surfaces. The flow rate and the micropillar geometry are optimized by studying their effects on capture efficiency. Then, a different number of HCT116 cells spiked in two kinds of cell suspension are investigated, yielding capture efficiency >70% in culture medium and >40% in blood sample, respectively. Moreover, the captured HCT116 cells are able to be released from the micropillars with a saturated efficiency of 92.9% upon the removal of applied magnetic field and it is found that 78% of the released cancer cells are viable, making them suitable for subsequent biological analysis.     

SMART RHESINs—Superparamagnetic Magnetite Architecture Made of Phenolic Resin Hollow Spheres Coated with Eu(III) Containing Silica Nanoparticles for Future Quantitative Magnetic Particle Imaging Applications

Magnetic particle imaging (MPI) is a powerful and rapidly growing tomographic imaging technique that allows for the non-invasive visualization of superparamagnetic nanoparticles (NPs) in living matter. Despite its potential for a wide range of applications, the intrinsic quantitative nature of MPI has not been fully exploited in biological environments. In this study, a novel NP architecture that overcomes this limitation by maintaining a virtually unchanged effective relaxation (Brownian plus Néel) even when immobilized is presented. This superparamagnetic magnetite architecture made of phenolic resin hollow spheres coated with Eu(III) containing silica nanoparticles (SMART RHESINs) was synthesized and studied. Magnetic particle spectroscopy (MPS) measurements confirm their suitability for potential MPI applications. Photobleaching studies show an unexpected photodynamic due to the fluorescence emission peak of the europium ion in combination with the phenol formaldehyde resin (PFR). Cell metabolic activity and proliferation behavior are not affected. Colocalization experiments reveal the distinct accumulation of SMART RHESINs near the Golgi apparatus. Overall, SMART RHESINs show superparamagnetic behavior and special luminescent properties without acute cytotoxicity, making them suitable for bimodal imaging probes for medical use like cancer diagnosis and treatment. SMART RHESINs have the potential to enable quantitative MPS and MPI measurements both in mobile and immobilized environments.     

A Hierarchical 3D Nanostructured Microfluidic Device for Sensitive Detection of Pathogenic Bacteria

Efficient capture and rapid detection of pathogenic bacteria from body fluids lead to early diagnostics of bacterial infections and significantly enhance the survival rate. We propose a universal nano/microfluidic device integrated with a 3D nanostructured detection platform for sensitive and quantifiable detection of pathogenic bacteria. Surface characterization of the nanostructured detection platform confirms a uniform distribution of hierarchical 3D nano‐/microisland (NMI) structures with spatial orientation and nanorough protrusions. The hierarchical 3D NMI is the unique characteristic of the integrated device, which enables enhanced capture and quantifiable detection of bacteria via both a probe‐free and immunoaffinity detection method. As a proof of principle, we demonstrate probe‐free capture of pathogenic Escherichia coli (E. coli) and immunocapture of methicillin‐resistant‐Staphylococcus aureus (MRSA). Our device demonstrates a linear range between 50 and 10⁴ CFU mL^?1, with average efficiency of 93% and 85% for probe‐free detection of E. coli and immunoaffinity detection of MRSA, respectively. It is successfully demonstrated that the spatial orientation of 3D NMIs contributes in quantifiable detection of fluorescently labeled bacteria, while the nanorough protrusions contribute in probe‐free capture of bacteria. The ease of fabrication, integration, and implementation can inspire future point‐of‐care devices based on nanomaterial interfaces for sensitive and high‐throughput optical detection.     

Electrochemical biosensor for detection of BCR/ABL fusion gene using locked nucleic acids on 4-aminobenzenesulfonic acid-modified glassy carbon electrode

In this study, an electrochemical DNA biosensor was developed for detection of the breakpoint cluster region gene and the cellular abl (BCR/ABL) fusion gene in chronic myelogenous leukemia by using 18-mer locked, nucleic acid-modified, single-stranded DNA as the capture probe. The capture probe was covalently attached on the sulfonic-terminated aminobenzenesulfonic acid monolayer-modified glassy carbon electrode through the free amines of DNA bases based on the acyl chloride cross-linking reaction. The covalently immobilized capture probe could selectively hybridize with its target DNA to form double-stranded DNA (dsDNA) on the LNA/4-ABSA/GCE surface. Differential pulse voltammetry was used to monitor the hybridization reaction on the capture probe electrode. The decrease of the peak current of methylene blue, an electroactive indicator, was observed upon hybridization of the probe with the target DNA. The results indicated that, in pH 7.0 Tris-HCl buffer solution, the peak current was linear with the concentration of complementary strand in the range of 1.0 x 10 (-12)1.1 x 10 (-11) M with a detection limit of 9.4 x 10 (-13) M. This new method demonstrates its excellent specificity for single-base mismatch and complementary dsDNA after hybridization, and this probe has been used for assay of PCR real sample with satisfactory results.     

Bacterial DNA sample preparation from whole blood using surface-modified Si pillar arrays

A novel bacterial DNA sample preparation device for molecular diagnostics has been developed. On the basis of optimized conditions for bacterial adhesion, surface-modified silicon pillar arrays for bacterial cell capture were fabricated, and their ability to capture bacterial cells was demonstrated. The capture efficiency for bacterial cells such as Escherichia coli, Staphylococcus epidermidis, and Streptococcus mutans in buffer solution was over 75% with a flow rate of 400 microL/min. Moreover, the proposed method captured E. coli cells present in 50% whole blood effectively. The captured cells from whole blood were then in- situ lyzed on the surface of the microchip, and the eluted DNA was successfully amplified by qPCR. These results demonstrate that the full process of pathogen capture to DNA isolation from whole blood could be automated in a single microchip.     

Enzyme-amplified electrochemical detection of DNA using electrocatalysis of ferrocenyl-tethered dendrimer

We have developed a sandwich-type enzyme-linked DNA sensor as a new electrochemical method to detect DNA hybridization. A partially ferrocenyl-tethered poly(amidoamine) dendrimer (Fc-D) was used as an electrocatalyst to enhance the electronic signals of DNA detection as well as a building block to immobilize capture probes. Fc-D was immobilized on a carboxylic acid-terminated self-assembled monolayer (SAM) by covalent coupling of unreacted amine in Fc-D to the acid. Thiolated capture probe was attached to the remaining amine groups of Fc-D on the SAM via a bifunctional linker. The target DNA was hybridized with the capture probe, and an extension in the DNA of the target was then hybridized with a biotinylated detection probe. Avidin-conjugated alkaline phosphatase was bound to the detection probe and allowed to generate the electroactive label, p-aminophenol, from p-aminophenyl phosphate enzymatically. p-Aminophenol diffuses into the Fc-D layer and is then electrocatalytically oxidized by the electronic mediation of the immobilized Fc-D, which leads to a great enhancement in signal. Consequently, the amount of hybridized target can be estimated using the intensity of electrocatalytic current. This DNA sensor exhibits a detection limit of 20 fmol. Our method was also successfully applied to the sequence-selective discrimination between perfectly matched and single-base mismatched target oligonucleotides.