Nanostructured luminescently labeled nucleic acids

Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron); (ii) the labeling of bulk nucleic acids (e.g. single‐stranded DNA, double‐stranded DNA) with nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver nanoclusters). This review surveys recent advances in these three different approaches to the generation of nanostructured luminescently labeled nucleic acids, and includes both direct and indirect labeling methods.     

Nanopore sensors: From hybrid to abiotic systems

This paper provides an overview of different nanostructured architectures utilised in electrochemical devices and their application in biosensing and bioelectronics. Emphasis is placed on the fabrication of nanostructured films based on a layer-by-layer (LBL) films approach. We discuss the theory and the mechanism of charge transfer in polyelectrolyte multilayer films (PEM), as well as between biomolecules and redox centres, for the development of more sensitive and selective biosensors. Further, this paper presents an overview of topics involving the interaction between nanostructured materials, including metallic nanoparticles and carbon materials, and their effects on the preservation of the activity of biological molecules immobilised on electrode surfaces. This paper also presents examples of biological molecules utilised in film fabrication, such as DNA, several kinds of proteins, and oligonucleotides, and of the role of molecular interaction in biosensing performance. Towards the utilisation of LBL films, examples of several architectures and different electrochemical approaches demonstrate the potential of nanostructured LBL films for several applications that include the diagnosis and monitoring of diseases. Our main aim in this review is to survey what can assist researchers by presenting various approaches currently used in the field of bioelectrochemistry utilising supramolecular architectures based on an LBL approach for application in electrochemical biosensing.     

Cationic silanes stabilize intermediates in DNA condensation.

In vitro condensation of DNA has been widely studied to gain insight into the mechanisms of DNA compaction in biological systems such as chromosomes and phage heads and has been used to produce nanostructured particles with novel material and functional properties. Here we report on the condensation of DNA in aqueous solutions by cationic silanes, which combine the condensing properties of polyamines with the cross-linking chemistry of silanes. DNA can be reversibly condensed into classical toroidal and rod-shaped structures with these agents. At low silane concentrations DNA forms a variety of looped structures with well-defined characteristics, including flower- and sausage-shaped forms. These structures suggest that at low silane concentrations a DNA-DNA contact in which the strands are at very large angles to each other is stabilized. Changes in these structures observed as a function of silane concentration suggest possible pathways for the formation of toroids and rods.     

Detection of point mutations in the HBV polymerase gene using a fluorescence intercalator in reverse micelles

We report a novel and simple method for mutation detection in DNA oligonucleotides using a double-stranded DNA specific dye (SYBR Green I) in nanostructured molecular assemblies, called reverse micelles. The intercalation of SYBR Green I into the duplex DNA exhibits fluorescent emission in a CTAB/isooctane reverse micellar system as well as in an aqueous solution. We found marked differences in the fluorescence intensity between perfectly matched and mismatched 52-mer synthetic oligonucleotides, which were designed to contain the YMDD motif of the hepatitis B virus (HBV) polymerase gene, in a reverse micellar solution. Using this method, we successfully detected a mutation in PCR-amplified oligonucleotides of the HBV polymerase gene in sera of four patients with chronic hepatitis B. This detection method does not require DNA immobilization, chemical modification of DNA, or any special apparatus; it only needs a normal fluorescence spectrophotometer, an inexpensive dye, and just 10 pmol of sample DNA.     

Sensitive detection of proteins using assembled cascade fluorescent DNA nanotags based on rolling circle amplification

A novel cascade fluorescence signal amplification strategy based on the rolling circle amplification (RCA)-aided assembly of fluorescent DNA nanotags as fluorescent labels and multiplex binding of the biotin-streptavidin system was proposed for detection of protein target at ultralow concentration. In the strategy, fluorescent DNA nanotags are prepared relying on intercalating dye arrays assembled on nanostructured DNA templates by intercalation between base pairs. The RCA product containing tandem-repeat sequences could serve as an excellent template for periodic assembly of fluorescent DNA nanotags, which were presented per protein recognition event to numerous fluorescent DNA nanotags for assay readout. Both the RCA and the multiplex binding system showed remarkable amplification efficiency, very little nonspecific adsorption, and low background signal. Using human IgG as a model protein, the designed strategy was successfully demonstrated for the ultrasensitive detection of protein target. The results revealed that the strategy exhibited a dynamic response to human IgG over a three-decade concentration range from 1.0 pM to 1.0 fM with a limit of detection as low as 0.9 fM. By comparison with the assay of multiple labeling antibodies with the dye/DNA conjugate, the limit of detection was improved by 4 orders. The designed signal amplification strategy would hold great promise as a powerful tool to be applied for the ultrasensitive detection of target protein in immunoassay.     

CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells

DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.     

Flexible glucose sensor using CVD-grown graphene-based field effect transistor

In this paper, a new concept to achieve improved probe-target recognition has been devised by introducing a novel class of DNA-functionalized three-dimensional (3D), stand-free, and nanostructured electrodes. The gold nanofibrous electrodes were created using MHZ ultrafast laser material processing in air at ambient conditions. The developed nanofibrous DNA biosensor was characterized by cyclic voltammetry with the use of ferrocyanide as an electrochemical redox indicator. Currently, electrochemical signal enhancement which is of great significance for improving the sensitivity in DNA detection remains a great challenge. Through, enhanced surface area-to-volume ratio and more efficient arrangement of probe molecules on nanofibrous electrodes, our newly developed electrode system overcomes some of the sensitivity challenges of the existing systems. This nanofiber-based system realizes femtomolar (fM) sensitivity toward complementary target DNA, and demonstrates a very wide dynamic range (from 1 fM to 1 nM).     

Nanomaterials in biological environment: a review of computer modelling studies

Nanotechnology is set to impact a vast range of fields, including computer science, materials technology, engineering/manufacturing and medicine. As nanotechnology grows so does exposure to nanostructured materials, thus investigation of the effects of nanomaterials on biological systems is paramount. Computational techniques can allow investigation of these systems at the nanoscale, providing insight into otherwise unexaminable properties, related to both the intentional and unintentional effects of nanomaterials. Herein, we review the current literature involving computational modelling of nanoparticles and biological systems. This literature has highlighted the common modes in which nanostructured materials interact with biological molecules such as membranes, peptides/proteins and DNA. Hydrophobic interactions are the most favoured, with π-stacking of the aromatic side-chains common when binding to a carbonaceous nanoparticle or surface. van der Waals forces are found to dominate in the insertion process of DNA molecules into carbon nanotubes. Generally, nanoparticles have been observed to disrupt the tertiary structure of proteins due to the curvature and atomic arrangement of the particle surface. Many hydrophobic nanoparticles are found to be able to transverse a lipid membrane, with some nanoparticles even causing mechanical damage to the membrane, thus potentially leading to cytotoxic effects. Current computational techniques have revealed how some nanoparticles interact with biological systems. However, further research is required to determine both useful applications and possible cytotoxic effects that nanoparticles may have on DNA, protein and membrane structure and function within biosystems.     

Surface Enhanced Raman Spectroscopy Detection of Biomolecules Using EBL Fabricated Nanostructured Substrates

Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules is reported. The entire sequence of relevant experimental steps is described, involving the fabrication of nanostructured substrates using electron beam lithography, immobilization of biomolecules on the substrates, and their characterization utilizing surface-enhanced Raman spectroscopy (SERS). Three different designs of nano-biological systems are employed, including protein A, glucose binding protein, and a dopamine binding DNA aptamer. In the latter two cases, the binding of respective ligands, D-glucose and dopamine, is also included. The three kinds of biomolecules are immobilized on nanostructured substrates by different methods, and the results of SERS imaging are reported. The capabilities of SERS to detect vibrational modes from surface-immobilized proteins, as well as to capture the protein-ligand and aptamer-ligand binding are demonstrated. The results also illustrate the influence of the surface nanostructure geometry, biomolecules immobilization strategy, Raman activity of the molecules and presence or absence of the ligand binding on the SERS spectra acquired.     

Biomimetic helical rosette nanotubes and nanocrystalline hydroxyapatite coatings on titanium for improving orthopedic implants

Natural bone consists of hard nanostructured hydroxyapatite (HA) in a nanostructured protein-based soft hydrogel template (ie, mostly collagen). For this reason, nanostructured HA has been an intriguing coating material on traditionally used titanium for improving orthopedic applications. In addition, helical rosette nanotubes (HRNs), newly developed materials which form through the self-assembly process of DNA base pair building blocks in body solutions, are soft nanotubes with a helical architecture that mimics natural collagen. Thus, the objective of this in vitro study was for the first time to combine the promising attributes of HRNs and nanocrystalline HA on titanium and assess osteoblast (bone-forming cell) functions. Different sizes of nanocrystalline HA were synthesized in this study through a wet chemical precipitation process following either hydrothermal treatment or sintering. Transmission electron microscopy images showed that HRNs aligned with nanocrystalline HA, which indicates a high affinity between both components. Some of the nanocrystalline HA formed dense coatings with HRNs on titanium. More importantly, results demonstrated enhanced osteoblast adhesion on the HRN/nanocrystalline HA-coated titanium compared with conventional uncoated titanium. Among all the HRN/nanocrystalline HA coatings tested, osteoblast adhesion was the greatest when HA nanometer particle size was the smallest. In this manner, this study demonstrated for the first time that biomimetic HRN/nanocrystalline HA coatings on titanium were cytocompatible for osteoblasts and, thus, should be further studied for improving orthopedic implants.     

Increased endothelial and vascular smooth muscle cell adhesion on nanostructured titanium and CoCrMo

In the body, vascular cells continuously interact with tissues that possess nanostructured surface features due to the presence of proteins (such as collagen and elastin) embedded in the vascular wall. Despite this fact, vascular stents intended to restore blood flow do not have nanoscale surface features but rather are smooth at the nanoscale. As the first step towards creating the next generation of vascular stent materials, the objective of this in vitro study was to investigate vascular cell (specifically, endothelial, and vascular smooth muscle cell) adhesion on nanostructured compared with conventional commercially pure (cp) Ti and CoCrMo. Nanostructured cp Ti and CoCrMo compacts were created by separately utilizing either constituent cp Ti or CoCrMo nanoparticles as opposed to conventional micron-sized particles. Results of this study showed for the first time increased endothelial and vascular smooth muscle cell adhesion on nanostructured compared with conventional cp Ti and CoCrMo after 4 hours' adhesion. Moreover, compared with their respective conventional counterparts, the ratio of endothelial to vascular smooth muscle cells increased on nanostructured cp Ti and CoCrMo. In addition, endothelial and vascular smooth muscle cells had a better spread morphology on the nanostructured metals compared with conventional metals. Overall, vascular cell adhesion was better on CoCrMo than on cp Ti. Results of surface characterization studies demonstrated similar chemistry but significantly greater root-mean-square (rms) surface roughness as measured by atomic force microscopy (AFM) for nanostructured compared with respective conventional metals. For these reasons, results from the present in vitro study provided evidence that vascular stents composed of nanometer compared with micron-sized metal particles (specifically, either cp Ti or CoCrMo) may invoke cellular responses promising for improved vascular stent applications.     

Electrophoretic fabrication of chitosan-zirconium-oxide nanobiocomposite platform for nucleic acid detection

The present work describes electrophoretic fabrication of nanostructured chitosan-zirconium-oxide composite (CHIT-NanoZrO(2)) film (180 nm) onto indium-tin-oxide (ITO)-coated glass plate. This nanobiocomposite film has been explored as immobilization platform for probe DNA specific to M. Tuberculosis as model biomolecule to investigate its sensing characteristics. It is revealed that pH-responsive behavior of CHIT and its cationic skeleton is responsible for the movement of CHIT-NanoZrO(2) colloids toward cathode during electrophoretic deposition. The FT-IR, SEM, TEM, and EDX techniques have been employed for the structural, morphological, and composition analysis of the fabricated electrodes. The morphological studies clearly reveal uniform inter-linking and dispersion of hexagonal nanograins of ZrO(2) (30-50 nm) into the chitosan matrix, resulting in homogeneous nanobiocomposite formation. Electrochemical response measurements of DNA/CHIT-NanoZrO(2)/ITO bioelectrode, carried out using cyclic voltammetry and differential pulse voltammetry, reveal that this bioelectrode can specifically detect complementary target DNA up to 0.00078 μM with sensitivity of 6.38 × 10(-6) AμM(-1).     

Confined Synthesis of 2D Nanostructured Materials toward Electrocatalysis

2D nanostructured materials have shown great application prospects in energy conversion, owing to their unique structural features and fascinating physicochemical properties. Developing efficient approaches for the synthesis of well‐defined 2D nanostructured materials with controllable composition and morphology is critical. The emerging concept, confined synthesis, has been regarded as a promising strategy to design and synthesize novel 2D nanostructured materials. This review mainly summarizes the recent advances in confined synthesis of 2D nanostructured materials by using layered materials as host matrices (also denoted as “nanoreactors”). By virtue of the space‐ and surface‐confinement effects of these layered hosts, various well‐organized 2D nanostructured materials, including 2D metals, 2D metal compounds, 2D carbon materials, 2D polymers, 2D metal‐organic frameworks (MOFs) and covalent‐organic frameworks (COFs), as well as 2D carbon nitrides are successfully synthesized. The wide employment of these 2D materials in electrocatalytic applications (e.g., electrochemical oxygen/hydrogen evolution reactions, small molecule oxidation, and oxygen reduction reaction) is presented and discussed. In the final section, challenges and prospects in 2D confined synthesis from the viewpoint of designing new materials and exploring practical applications are commented, which would push this fast‐evolving field a step further toward greater success in both fundamental studies and ultimate industrialization.     

Chitosan encapsulated quantum dots platform for leukemia detection

We report results of the studies relating to electrophoretic deposition of nanostructured composite of chitosan (CS)-cadmium-telluride quantum dots (CdTe-QDs) onto indium-tin-oxide coated glass substrate. The high resolution transmission electron microscopic studies of the nanocomposite reveal molecular level coating of the CdTe-QDs with CS molecules in the colloidal dispersion medium. This novel composite platform has been explored to fabricate an electrochemical DNA biosensor for detection of chronic myelogenous leukemia (CML) by immobilizing amine terminated oligonucleotide probe sequence containing 22 base pairs, identified from BCR-ABL fusion gene. The results of differential pulse voltammetry reveal that this nucleic acid sensor can detect as low as 2.56 pM concentration of complementary target DNA with a response time of 60s. Further, the response characteristics show that this fabricated bioelectrode has a shelf life of about 6 weeks and can be used for about 5-6 times. The results of experiments conducted using clinical patient samples reveal that this sensor can be used to distinguish CML positive and the negative control samples.     

Biogenic nanoparticles: copper, copper oxides, copper sulphides, complex copper nanostructures and their applications

Copper nanoparticles have been the focus of intensive study due to their potential applications in diverse fields including biomedicine, electronics, and optics. Copper-based nanostructured materials have been used in conductive films, lubrification, nanofluids, catalysis, and also as potent antimicrobial agent. The biogenic synthesis of metallic nanostructured nanoparticles is considered to be a green and eco-friendly technology since neither harmful chemicals nor high temperatures are involved in the process. The present review discusses the synthesis of copper nanostructured nanoparticles by bacteria, fungi, and plant extracts, showing that biogenic synthesis is an economically feasible, simple and non-polluting process. Applications for biogenic copper nanoparticles are also discussed.     

Negatively charged self-assembling DNA/poloxamine nanospheres for in vivo gene transfer

Over the past decade, numerous nonviral cationic vectors have been synthesized. They share a high density of positive charges and efficiency for gene transfer in vitro. However, their positively charged surface causes instability in body fluids and cytotoxicity, thereby limiting their efficacy in vivo. Therefore, there is a need for developing alternative molecular structures. We have examined tetrabranched amphiphilic block copolymers consisting of four polyethyleneoxide/polypropyleneoxide blocks centered on an ethylenediamine moiety. Cryo-electron microscopy, ethidium bromide fluorescence and light and X-ray scattering experiments performed on vector-DNA complexes showed that the dense core of the nanosphere consisted of condensed DNA interacting with poloxamine molecules through electrostatic, hydrogen bonding and hydrophobic interactions, with DNA molecules also being exposed at the surface. The supramolecular organization of block copolymer/DNA nanospheres induced the formation of negatively charged particles. These particles were stable in a solution that had a physiological ionic composition and were resistant to decomplexation by heparin. The new nanostructured material, the structure of which clearly contrasted with that of lipoplexes and polyplexes, efficiently transferred reporter and therapeutic genes in skeletal and heart muscle in vivo. Negatively charged supramolecular assemblies hold promise as therapeutic gene carriers for skeletal and heart muscle-related diseases and expression of therapeutic proteins for local or systemic uses.     

Alginate modified nanostructured calcium carbonate with enhanced delivery efficiency for gene and drug delivery

To improve the performance of nanostructured calcium carbonate in gene delivery, a hydrophilic polysaccharide, alginate, was added to calcium carbonate co-precipitation systems to form alginate/CaCO(3)/DNA nanoparticles. The size and ζ-potential of the nanoparticles were measured by a zetasizer. Due to the existence of alginate chains which retarded the growth of calcium carbonate based co-precipitates, the alginate/CaCO(3)/DNA nanoparticles exhibited a decreased size and enhanced stability in the aqueous solution. To evaluate the gene and drug co-delivery ability, doxorubicin hydrochloride (DOX), a water-soluble anticancer drug, was loaded in the nanoparticles to form alginate/CaCO(3)/DNA/DOX nanoparticles. The in vitro gene transfections mediated by different nanoparticles in 293 T cells and HeLa cells were carried out, using pGL3-Luc as a reporter plasmid. With an appropriate amount of alginate, the gene transfection efficiency of alginate modified nanoparticles could be significantly enhanced as compared with the nanoparticles without alginate modification for the gene delivery systems, as well as the gene and drug co-delivery systems. The study on in vitro cell inhibition effects showed that the cell viability decreased with increasing DOX amount loaded in alginate/CaCO(3)/DNA/DOX nanoparticles. The alginate modification is a useful strategy to improve the calcium carbonate co-precipitation technique for the preparation of gene and drug delivery systems, and the nanoparticles prepared in this study have promising applications in gene and drug delivery.     

Negatively charged self-assembling DNA/poloxamine nanospheres for in vivo gene transfer

Over the past decade, numerous nonviral cationic vectors have been synthesized. They share a high density of positive charges and efficiency for gene transfer in vitro. However, their positively charged surface causes instability in body fluids and cytotoxicity, thereby limiting their efficacy in vivo. Therefore, there is a need for developing alternative molecular structures. We have examined tetrabranched amphiphilic block copolymers consisting of four polyethyleneoxide/polypropyleneoxide blocks centered on an ethylenediamine moiety. Cryo-electron microscopy, ethidium bromide fluorescence and light and X-ray scattering experiments performed on vector–DNA complexes showed that the dense core of the nanosphere consisted of condensed DNA interacting with poloxamine molecules through electrostatic, hydrogen bonding and hydrophobic interactions, with DNA molecules also being exposed at the surface. The supramolecular organization of block copolymer/DNA nanospheres induced the formation of negatively charged particles. These particles were stable in a solution that had a physiological ionic composition and were resistant to decomplexation by heparin. The new nanostructured material, the structure of which clearly contrasted with that of lipoplexes and polyplexes, efficiently transferred reporter and therapeutic genes in skeletal and heart muscle in vivo. Negatively charged supramolecular assemblies hold promise as therapeutic gene carriers for skeletal and heart muscle-related diseases and expression of therapeutic proteins for local or systemic uses.     

Novel materials for bone and cartilage regeneration

Materials that enhance bone and cartilage regeneration promise to be valuable in both research and clinical applications. Both natural and synthetic polymers can be used to create scaffolds that support cells and incorporate cues which guide tissue repair. Recently, electrospinning, peptide self-assembly and biomineralisation have been employed to fabricate nanostructured scaffolds that better mimic the complex extracellular environment found within tissues, in vivo. The incorporation of peptide motifs recognised by cell receptors and the use of recombinant DNA technology have enabled the creation of scaffolds with new levels of biofunctionality. Advances in materials design will enhance our ability to create highly tailored cellular environments for bone and cartilage regeneration.     

Preparation of Nanostructured Film Arrays for Transmission Localized Surface Plasmon Sensing

This article presents a concise review of preparation methods for transparent nanostructured films, with an emphasis on their current applications in transmission-localized surface plasmon resonance (T-LSPR) sensing. One of the first methods used for the fabrication of transparent nanostructured metal films is a direct vacuum evaporation of thin gold films. Self-induced formations of small gold islands result in transparent nanostructured gold arrays. The most well-established method is a nanosphere lithography developed by Van Duyne. Nanotriangular island arrays with controlled size and optical properties can be fabricated by this protocol. A different nanolithography method known as focused ion beam milling is reported and used for the fabrication of nanohole arrays. Simple assembly of solution-phase synthesized nanoparticles has also been utilized for the preparation of nanoparticle arrays capable of T-LSPR sensing. Lastly, this article also describes a new preparation strategy, in which self-assembly/thermolysis of nanoparticle multilayers is employed to obtain transparent nanoisland architectures on glass substrates.