DNA Biosensor Based on Carbon Paste Electrodes Modified by Polymer Multilayer

An electrochemical DNA biosensor was developed by DNA immobilization at the electrode surface and its electrochemical behavior was studied in relation with different materials added in the paste. The aim was to study new materials for the development of new electrode surfaces, to be applied in the study of DNA – drug interactions. New electrochemical sensing materials using polymer multilayers were reported for the adsorption of DNA. These materials were prepared by mixing a polymer ion exchanger and graphite powder. The mixture was then used to render the modified carbon paste electrode (CPE), on the surface of which the dsDNA was adsorbed and studied by differential pulse voltammetry (DP voltammetry). The signal of guanine oxidation peak of DNA was followed. This modified biosensor was applied for the study of the interaction between DNA and the known intercalators Ethidium Bromide (EB) and Acridine Orange (AO). The established biosensor exhibited an improvement of its sensitivity and repeatability compared with the conventional CPE DNA biosensor.     

Transient DNA‐Based Nanostructures Controlled by Redox Inputs

Synthetic DNA has emerged as a powerful self‐assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self‐assembly of DNA‐based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life‐like properties. So far, dissipative control has been achieved using DNA‐recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long‐term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non‐enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide‐bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.     

Metal-complex/DNA conjugates: a versatile building block for DNA nanoarrays

The use of DNA networks as templates for forming nanoarrays of metallic centres shows an exciting potential to generate addressable nanostructures. Inorganic units can be photoactive, electroactive and/or can possess magnetic and catalytic properties and can adopt different spatial arrangements due to their varied coordination nature. All these properties influence both the structure and function of passive DNA scaffolds and provide DNA nanostructures as a new platform for new materials in emerging technologies, such as nanotechnology, biosensing or biocomputing.     

Engineering Multifunctional DNA Hybrid Nanospheres through Coordination‐Driven Self‐Assembly

Developing simple and general approaches for the synthesis of nanometer‐sized DNA materials with specific morphologies and functionalities is important for various applications. Herein, a novel approach for the synthesis of a new set of DNA‐based nanoarchitectures through coordination‐driven self‐assembly of Fe^II ions and DNA molecules is reported. By fine‐tuning the assembly, Fe–DNA nanospheres of precise sizes and controlled compositions can be produced. The hybrid nanoparticles can be tailored for delivery of functional DNA to cells in vitro and in vivo with enhanced biological function. This highlights the potential of metal ion coordination as a tool for directing the assembly of DNA architectures, which conceptualizes a new pathway to expand the repertoire of DNA‐based nanomaterials. This methodology will advance both the fields of DNA nanobiotechnology and metal–ligand coordination chemistry.     

Transient DNA-Based Nanostructures Controlled by Redox Inputs

Synthetic DNA has emerged as a powerful self-assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self-assembly of DNA-based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life-like properties. So far, dissipative control has been achieved using DNA-recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long-term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non-enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide-bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.     

Selective, controllable, and reversible aggregation of polystyrene latex microspheres via DNA hybridization

The directed three-dimensional self-assembly of microstructures and nanostructures through the selective hybridization of DNA is the focus of great interest toward the fabrication of new materials. Single-stranded DNA is covalently attached to polystyrene latex microspheres. Single-stranded DNA can function as a sequence-selective Velcro by only bonding to another strand of DNA that has a complementary sequence. The attachment of the DNA increases the charge stabilization of the microspheres and allows controllable aggregation of microspheres by hybridization of complementary DNA sequences. In a mixture of microspheres derivatized with different sequences of DNA, microspheres with complementary DNA form aggregates, while microspheres with noncomplementary sequences remain suspended. The process is reversible by heating, with a characteristic "aggregate dissociation temperature" that is predictably dependent on salt concentration, and the evolution of aggregate dissociation with temperature is observed with optical microscopy.     

DNA meets synthetic polymers--highly versatile hybrid materials

The combination of synthetic polymers and DNA has provided biologists, chemists and materials scientists with a fascinating new hybrid material. The challenges in preparing these molecular chimeras were overcome by different synthetic strategies that rely on coupling the nucleic acid moiety and the organic polymer in solution or on solid supports. The morphologies and functions of the bioorganic block copolymers can be controlled by the nature of the synthetic polymer segment as well as by the sequence composition and length of the DNA. Recent developments have expanded the scope and applications of these hybrid materials in a number of different areas including biology and medicine, as well as bio- and nanotechnology. Their usage ranges from gene delivery through to DNA detection to programmable nano-containers for DNA-templated organic reactions.     

Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores

Branched oligonucleotides with "CG zippers" as DNA arms assemble into materials from micromolar solutions. Their synthesis has been complicated by low yields in solid-phase syntheses. Here we present a solution-phase synthesis based on phosphoramidites of dimers and phenolic cores that produces six-arm or four-arm hybrids in up to 61% yield. On the level of hybrids, only the final product has to be purified by precipitation or chromatography. A total of five different hybrids were prepared via the solution-phase route, including new hybrid (TCG)(4)TTPA with a tetrakis(triazolylphenyl)adamantane core and trimer DNA arms. The new method is more readily scaled up than solid-phase syntheses, uses no more than 4 equiv of phosphoramidite per phenolic alcohol, and provides routine access to novel materials that assemble via predictable base-pairing interactions.     

The resurgence of Coulter counting for analyzing nanoscale objects

This review discusses recent advances in the science and technology of Coulter counting. The Coulter counting principle has been used to determine the size, concentration, and in favorable cases the surface charge, of nanometer-scale colloidal particles, viruses, DNA and other polymers, and metal ions. A resurgence of interest in the field of COulter counting is occurring because of the advent of new technologies that permit fabrication of membranes containing single, robust, and chemically well-defined channels having smaller and more uniform sizes than could be prepared in the past. These channels are prepared from biological materials, such as self-assembling membrane proteins, and from synthetic materials such as polymers, carbon nanotubes, and silicon-based inorganic materials. In addition to particle characterization, there have been a few recent examples of using Coulter counters to study chemical processes, such as the dehybridization of DNA.     

Novel enzyme/DNA/inorganic nanomaterials: a new generation of biocatalysts

The design, synthesis and properties of a new class of enzyme/DNA/inorganic nanobiomaterials are described here. DNA has been used to stabilize the enzymes intercalated in the galleries of the inorganic solid, alpha-Zr(iv) phosphate (alpha-Zr(HPO(4))(2).H(2)O, abbreviated as alpha-ZrP). Interestingly, the presence of DNA improved the activity and stability of the bound enzymes. Key studies leading to the current strategy are presented initially, and these are followed by more recent developments. Several enzymes and proteins, including horseradish peroxidase, lysozyme, glucose oxidase, chymotrypsin, bovine serum albumin, cytochrome c, met-hemoglobin and met-myoglobin are successfully intercalated in the galleries of alpha-ZrP, under benign ambient conditions (aqueous buffered solutions, at room temperature and neutral pH). These novel materials are characterized by XRD, SEM and TEM as well as by biochemical, calorimetric and spectroscopic methods. Spectroscopic studies (circular dichroism, CD), for example, indicated that co-intercalation of DNA improved the retention of bound enzyme structure. The activity was enhanced markedly (five-fold) when DNA is co-intercalated, when compared to the activity in the absence of DNA. Addition of DNA to the sample, after enzyme intercalation, did not make any improvements. Our hypothesis is that enzyme-DNA supramolecular complex binds to the solid and the unfavorable interactions between the enzyme and the solid are minimized. These novel nanobiocomposite materials provide a simple method for packaging DNA and aid in engineering more effective synthetic materials for gene/RNA-delivery and drug delivery applications.     

Synthesis of Peptide Hormones using Recombinant DNA Techniques

Recombination of genetic material enables the creation of new bacterial strains which can synthesize specific proteins in large amounts. Such bacteria permit the production of previously inaccessible proteins. They can therefore be used as starting materials for the production of drugs which will open up new paths for therapy. Several proteins produced by bacteria after DNA recombination are presently undergoing clinical trials while others are already being produced on a large scale. Thus, in the area of recombinant DNA techniques the transition from the research laboratory to industrial exploitation has occurred much faster than was anticipated several years ago. The methods, possibilities and problems encountered in the synthesis of peptide hormones by bacteria after DNA recombination are outlined, using insulin, somatostatin, and growth hormone as examples. Great emphasis is placed on the molecular biological aspects of this approach.     

Self-assembled free-floating nanomaterials from sequence-defined polymers

Sequence-defined polymers can be programmed to self-assemble into precise nanostructures for applications in biosensing, drug delivery, optics, and molecular computation. Inspired by the natural self-assembly processes present in biological protein and DNA systems, sets of molecular design rules have emerged across materials classes as instructions to build a variety of tunable structures. This review highlights recent advances in self-assembled sequence-defined and sequence-specific polymers across peptides, peptoids, DNA, and non-biological synthetic materials, with a focus on synthesis, assembly processes and overall structure. Specifically, these self-assembled structures are free-floating, as such constructs can potentially serve as a platform for the aforementioned applications. Emphasis is placed on the molecular design of polymers that self-assemble into zero-dimensional, one-dimensional, two-dimensional, or three-dimensional nanostructures. With the development of automated syntheses and increasing control over self-assembly, future work may focus on emerging classes of compatible hybrid materials with exciting directions toward new architectures and applications.     

Supramolecular DNA assembly

The powerful self-assembly features of DNA make it a unique template to finely organize and control matter on the nanometre scale. While DNA alone offers a high degree of fidelity in its self-assembly, a new area of research termed 'supramolecular DNA assembly' has recently emerged. This field combines DNA building blocks with synthetic organic, inorganic and polymeric structures. It thus brings together the toolbox of supramolecular chemistry with the predictable and programmable nature of DNA. The result of this molecular partnership is a variety of hybrid architectures, that expand DNA assembly beyond the boundaries of Watson-Crick base pairing into new structural and functional properties. In this tutorial review we outline this emerging field of study, and describe recent research aiming to synergistically combine the properties inherent to DNA with those of a number of supramolecular scaffolds. This ultimately creates structures with numerous potential applications in materials science, catalysis and medicine.     

Programmed co-assembly of DNA-peptide hybrid microdroplets by phase separation

Biopolymers, including DNA and peptides have been used as excellent self-assembling building blocks for programmable single-component or hybrid materials, due to their controlled molecular interactions.However, combining two assembling principles of DNA-based programmability and peptide-based specific molecular interactions for hybrid structures to microscale has not yet been achieved. In this study,we describe a hybrid microsystem that emerges from the co-assembly of DNA origami structure and s...     

Biological soft materials

With one or two exceptions, biological materials are "soft", meaning that they combine viscous and elastic elements. This mechanical behavior results from self-assembled supramolecular structures that are stabilized by noncovalent interactions. It is an ongoing and profound challenge to understand the self-organization of biological materials. In many cases, concepts can be imported from soft-matter physics and chemistry, which have traditionally focused on materials such as colloids, polymers, surfactants, and liquid crystals. Using these ideas, it is possible to gain a new perspective on phenomena as diverse as DNA condensation, protein and peptide fibrillization, lipid partitioning in rafts, vesicle fusion and budding, and others, as discussed in this selective review of recent highlights from the literature.     

Sol–Gel‐Derived Biohybrid Materials Incorporating Long‐Chain DNA Aptamers

Sol–gel‐derived bio/inorganic hybrid materials have been examined for diverse applications, including biosensing, affinity chromatography and drug discovery. However, such materials have mostly been restricted to the interaction between entrapped biorecognition elements and small molecules, owing to the requirement for nanometer‐scale mesopores in the matrix to retain entrapped biorecognition elements. Herein, we report on a new class of macroporous bio/inorganic hybrids, engineered through a high‐throughput materials screening approach, that entrap micron‐sized concatemeric DNA aptamers. We demonstrate that the entrapment of these long‐chain DNA aptamers allows their retention within the macropores of the silica material, so that aptamers can interact with high molecular weight targets such as proteins. Our approach overcomes the major limitation of previous sol–gel‐derived biohybrid materials by enabling molecular recognition for targets beyond small molecules.     

DNA adsorbed on graphene and graphene oxide: Fundamental interactions,desorption and applications

Interfacing DNA oligonucleotides with graphene-based materials, especially graphene oxide, has produced many new sensors and devices. Since graphene oxide is an excellent fluorescence quencher, fluorescently labeled DNAs (probes) are nearly fully quenched upon adsorption. Addition of the complementary DNA results in probe desorption and fluorescence enhancement. Aside from its analytical applications, this system provides a fascinating topic for biointerface science. DNA can be adsorbed by graphene oxide via π–π stacking and hydrogen bonding, while it must overcome electrostatic repulsion at the same time. The mechanism of DNA-induced probe desorption has also been a topic of extensive discussion. In this article, DNA adsorption and desorption reactions and interactions with graphene oxide and related materials (e.g. graphene) are reviewed based on the current understandings. A few representative applications based on these processes are also described briefly.     

DNA origami: a quantum leap for self-assembly of complex structures

The spatially controlled positioning of functional materials by self-assembly is one of the fundamental visions of nanotechnology. Major steps towards this goal have been achieved using DNA as a programmable building block. This tutorial review will focus on one of the most promising methods: DNA origami. The basic design principles, organization of a variety of functional materials and recent implementation of DNA robotics are discussed together with future challenges and opportunities.     

DNA-templated assembly and electropolymerization of aniline on gold surface

Biomolecule template gives new opportunities for the fabrication of novel materials with special features. Here we report a route to the formation of DNA–polyaniline (PAn) complex, using immobilized DNA as a template. A gold electrode was first modified with monolayer of 2-aminoethanethiol by self-assembly. Thereafter, by simply immersing the gold electrode into DNA solution, DNA molecules can be attached onto the gold surface, followed by the DNA-templated assembly and electropolymerization of protonated aniline. The electrostatic interactions between DNA and aniline can keep the aniline monomers aligning along the DNA strands. Investigations by surface plasmon resonance (SPR), electrochemistry and reflection–absorption UV/Vis–Near IR spectroscopy substantially convince that PAn can be electrochemically grown around DNA template on gold surface. This work may be provides fundamental aspects for building PAn nanowires with DNA as template on solid surface if DNA molecules can be individually separated and stretched.     

Nanomaterial‐based Sensors for the Study of DNA Interaction with Drugs

The interaction of drugs with DNA has been searched thoroughly giving rise to an endless number of findings of undoubted importance, such as a prompt alert to harmful substances, ability to explain most of the biological mechanisms, or provision of important clues in targeted development of novel chemotherapeutics. The existence of some drugs that induce oxidative damage is an increasing point of concern as they can cause cellular death, aging, and are closely related to the development of many diseases. Because of a direct correlation between the response, strength/ nature of the interaction and the pharmaceutical action of DNA‐targeted drugs, the electrochemical analysis is based on the signals of DNA before and after the interaction with the DNA‐targeted drug. Nowadays, nanoscale materials are used extensively for offering fascinating characteristics that can be used in designing new strategies for drug‐DNA interaction detection. This work presents a review of nanomaterials (NMs) for the study of drug‐nucleic acid interaction. We summarize types of drug‐DNA interactions, electroanalytical techniques for evidencing these interactions and quantification of drug and/or DNA monitoring.