Nanoporous gold electrode as a platform for the construction of an electrochemical DNA hybridization biosensor

Uncertainties in synthetic DNA-based data storage

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.

A label-free electrochemical aptasensor for breast cancer cell detection based on a reduced graphene oxide-chitosan-gold nanoparticle composite

Regarding the cancer fatal consequences, early detection and progression monitoring are the most vital issues in patients' treatment and mortality reduction. Therefore, there is a great demand for fast, inexpensive, and selective detection methods. Herein, a graphene-based aptasensor was designed for sensitive human breast cancer cell detection. A reduced graphene oxide-chitosan-gold nanoparticles composite was used as a biocompatible substrate for the receptor stabilization. The significant function of the aptamer on this composite is due to the synergistic effects of the components in improving the properties of the composite, including increasing the electrical conductivity and effective surface area. After the aptasensor incubation in MCF-7 cancer cells, the cell membrane proteins interacted specifically with the three dimensional-structure of the AS1411 aptamer, resulting in the cell capture on the aptasensor. The aptasensor fabrication steps were investigated by cyclic voltammetry and electrochemical impedance spectroscopy. The higher cell concentrations concluded to the higher captured cells on the aptasensor which blocked the Ferro/Ferricyanide access to the sensor, causing increases in the charge transfer resistances. This aptasensor shows a linear relationship with the cell concentration logarithm, high selectivity, a wide linear range of 1 × 10¹-1 × 10⁶ cells/mL, and a low detection limit of 4 cells/mL.

Disposable electrodes from waste materials and renewable sources for (bio)electroanalytical applications

The numerous advantages of disposable and screen-printed electrodes (SPEs) particularly in terms of portability, sensibility, sensitivity and low-cost led to the massive application of these electroanalytical devices. To limit the electronic waste and recover precious materials, new recycling processes were developed together with alternative SPEs fabrication procedures based on renewable, biocompatible sources or waste materials, such as paper, agricultural byproducts or spent batteries. The increased interest in the use of eco-friendly materials for electronics has given rise to a new generation of highly performing green modifiers. From paper based electrodes to disposable electrodes obtained from CD/DVD, in the last decades considerable efforts were devoted to reuse and recycle in the field of electrochemistry. Here an overview of recycled and recyclable disposable electrodes, sustainable electrode modifiers and alternative fabrication processes is proposed aiming to provide meaningful examples to redesign the world of disposable electrodes.

Poly(azomethine-urethane) and zeolite-based composite: Fluorescent biosensor for DNA detection

In the present paper, a highly selective and sensitive fluorescent biosensor based on poly(azomethine-urethane) and zeolite for the determination of DNA molecules was developed. Zeolite was chosen to enhance with anionic or cationic functional groups in polymer matrix and interaction between polymer and DNA. Several parameters such as polymer concentration, pH and incubation time effect on the sensitivity of the fluorescent biosensor were optimized. Linear range was determined between 2.50 and 25.00 nmol/L DNA concentration and limit of detection (LOD) of the biosensor was calculated as 0.095 nmol/L under the optimal conditions. Interference study was also performed in the presence of different amino acids, cations and organic compounds. The results clearly indicated that the tested cations and compounds were not induced a significant fluorescence change and the proposed zeolite-based biosensor was shown a good selectivity for DNA.

Electrochemical Deposition of Nanomaterials for Electrochemical Sensing

The most commonly used methods to electrodeposit nanomaterials on conductive supports or to obtain electrosynthesis nanomaterials are described. Au, layered double hydroxides (LDHs), metal oxides, and polymers are the classes of compounds taken into account. The electrochemical approach for the synthesis allows one to obtain nanostructures with well-defined morphologies, even without the use of a template, and of variable sizes simply by controlling the experimental synthesis conditions. In fact, parameters such as current density, applied potential (constant, pulsed or ramp) and duration of the synthesis play a key role in determining the shape and size of the resulting nanostructures. This review aims to describe the most recent applications in the field of electrochemical sensors of the considered nanomaterials and special attention is devoted to the analytical figures of merit of the devices.

Preparation, Modification, Characterization, and Biosensing Application of Nanoporous Gold Using Electrochemical Techniques

Nanoporous gold (np-Au), because of its high surface area-to-volume ratio, excellent conductivity, chemical inertness, physical stability, biocompatibility, easily tunable pores, and plasmonic properties, has attracted much interested in the field of nanotechnology. It has promising applications in the fields of catalysis, bio/chemical sensing, drug delivery, biomolecules separation and purification, fuel cell development, surface-chemistry-driven actuation, and supercapacitor design. Many chemical and electrochemical procedures are known for the preparation of np-Au. Recently, researchers are focusing on easier and controlled ways to tune the pores and ligaments size of np-Au for its use in different applications. Electrochemical methods have good control over fine-tuning pore and ligament sizes. The np-Au electrodes that are prepared using electrochemical techniques are robust and are easier to handle for their use in electrochemical biosensing. Here, we review different electrochemical strategies for the preparation, post-modification, and characterization of np-Au along with the synergistic use of both electrochemistry and np-Au for applications in biosensing.

Spin-coated Au-nanohole arrays engineered by nanosphere lithography for a Staphylococcus aureus 16S rRNA electrochemical sensor

The nanopatterning of gold nanoparticle (AuNP) arrays on an indium tin oxide (ITO) electrode using efficient and low-cost methods is described. This process used nanosphere lithography (NSL) encompassing the deposition of monolayered Polystyrene (PS) followed by a convective self-assembly drop coating protocol onto the ITO substrate that further acted as the mask after the AuNP assembly. The results showed that spin-coating allowed AuNPs to follow the contour and adhere to the PS nanospheres. The final products, after etching the PS, generated a highly ordered Au-nanohole array on an ITO substrate. The Au-nanohole arrays on the ITO electrode provided a greater surface area and successfully enhanced the peak current of electrochemical measurements by 82% compared with bare ITO and was used to detect Staphylococcus aureus 16S rRNA hybridization. In contrast to non-templated AuNP structures, the Au-nanohole arrays on the ITO electrode contributed to an optimum sensitivity improvement in DNA hybridization detection by 23%, along with an impressive limit of detection (LOD) of 10 pM. The high specificity of this distinguished structure was also achieved in the hybridization measurements of multi-analyte pathogens. These findings indicate that the combination of PS nanosphere lithography, followed by the spin-coating of AuNPs, leads to an inexpensive and simple engineering process that effectively generates uniform Au-nanohole arrays on ITO, which provides a greater surface area to optimize the electrochemical performance of the DNA biosensor.

A multistep photothermic-driven drug release system using wire-framed Au nanobundles

Here, wire-framed Au nanobundles (WNBs), which consist of randomly oriented and mutually connected Au wires to form a bundle shape, are synthesized. In contrast to conventional nanoparticles (spheres, rods, cubes, and stars), which exhibit nanostructure only on the surface, cross-sectional view image shows that WNBs have nanostructures in a whole volume. By using this specific property of WNBs, an externally controllable multistep photothermic-driven drug release (PDR) system is demonstrated for in vivo cancer treatment. In contrast to conventional nanoparticles that encapsulate a drug on their surface, WNBs preserve the drug payload in the overall inner volume, providing a drug loading capacity sufficient for cancer therapy. An improved in vivo therapeutic efficacy of PDR therapy is also demonstrated by delivering sufficient amount of drugs to the target tumor region.

Highly sensitive electrochemical detection of DNA hybridisation by coupling the chemical reduction of a redox label to the electrode reaction of a solution phase mediator

We have described a highly sensitive method for detecting DNA hybridisation using a redox-labeled stem loop probe. The redox labels were poly(styrene-co-acrylic) (PSA) spheres of 454 nm diameter, modified by methylene blue (MB) deposited alternatively with poly(sodium 4-styrene sulphonate) (PSS) in a layer-by-layer process. Each PSA sphere carried approx. 3.7 × 10(5) molecules of MB, as determined optically. DIG-tagged stem loop probes were immobilised on screen printed electrodes bearing anti-DIG antibodies. Binding with the target enabled straightening of the stem loop, which made attachment to the MB-coated PSA spheres possible. For measuring the current from the direct reduction of MB by differential pulse voltammetry, a 30 mer DNA target common to 70 strains of Escherichia coli was calibrated across the range 1.0 fM to 100 pM (gradient = 3.2 × 10(-8) A (log fM)(-1), r(2) = 0.95, n = 60), with an LOD of ∼58 fM. By using Fe(CN)6(3-/4-) as a solution phase mediator for the MB reduction, we were able to lower the LOD to ∼39 aM (gradient = 5.95 × 10(-8) A (log aM)(-1), r(2) = 0.96, n = 30), which corresponds to the detection of 0.76 ag (∼50 molecules) in the 2 μL analyte sample. We hypothesise that the lowering of the LOD was due to the fact that not all the MB labels were able to contact the electrode surface.

Labeling-free fluorescent detection of DNA hybridization through FRET from pyrene excimer to DNA intercalator SYBR green I

A novel labeling-free fluorescence complex probe has been developed for DNA hybridization detection based on fluorescence resonance energy transfer (FRET) mechanism from pyrene excimer of pyrene-functionalized poly [2-(N, N-dimethylamino) ethyl methacrylate] (PFP) to SYBR Green I (SG, a specific intercalator of double-stranded DNA) in a cost-effective, rapid and simple manner. The complex probe consists of the positively charged PFP, SG and negatively charged single-stranded DNA (ssDNA). Upon adding a complementary strand to the complex probe solution, double-stranded DNA (dsDNA) was formed, followed by the intercalation of SG into dsDNA. The pyrene excimer emission was overlapped with the absorption of SG very well and the electrostatic interactions between PFP and dsDNA kept them in close proximity, enabling efficient FRET from pyrene excimer to SG. The fluorescence of SG in the duplex DNA resulting from FRET can be successfully applied to detect DNA hybridization with high sensitivity for a very low detection limit of 10nM and excellent selectivity for detection of single base pair mismatch.

Porous Gold Films-A Short Review on Recent Progress

Porous gold films have attracted increasing interest over the last ten years due to the unique properties of high specific surface area and electrical conductivity combined with chemical stability and ability to alter the surface chemistry. Several methods have been developed to synthesize porous gold films such as de-alloying, templating, electrochemical, and self-assembling. These porous gold films are used in diverse fields, for example, as electrochemical and Raman sensors or for chemical catalysis. Here, we provide a short review on the progress of porous gold films over the past ten years, including the synthesis and applications of such films.

Flower-like ZnO nanostructure based electrochemical DNA biosensor for bacterial meningitis detection

Zinc oxide (ZnO) nanostructures possessing flower-like morphology have been synthesised onto platinized silicon substrate by simple and economical hydrothermal method. The interaction of physically immobilized single stranded thiolated DNA (ss th-DNA) probe of N. meningitides onto the nanostructured ZnO (ZNF) matrix surface have been investigated using cyclic voltammetry (CV) and electrochemical impeadance spectroscopy (EIS). The electrochemical sensing response behaviour of the DNA bioelectrode (ss th-DNA/ZNF/Pt/Si) has been studied by both differential pulse voltammetric (DPV) as well as impedimetric techniques. The fabricated DNA biosensor can quantify wide range of the complementary target ss th-DNA in the range 5-240 ng μl(-1) with good linearity (R=0.98), high sensitivity (168.64 μA ng(-1) μl cm(-2)) and low detection limit of about 5 ng μl(-1). Results emphasise that the fabricated flower-like ZnO nanostructures offer a useful platform for the immobilization of DNA molecules and could be exploited for efficient detection of complementary target single stranded DNA corresponding to N. meningitides.

Dual amplification of single nucleotide polymorphism detection using graphene oxide and nanoporous gold electrode platform

In the present manuscript, a strategy to prompt the sensitivity of a biosensor based on the dual amplification of signal by applying a nanoporous gold electrode (NPGE) as a support platform and soluble graphene oxide (GO) as an indicator has been developed.

Real-time electrochemical monitoring of adenosine triphosphate in the picomolar to micromolar range using graphene-modified electrodes

We report on a competitive electrochemical detection system that is free of wash steps and enables the real-time monitoring of adenosine triphosphate (ATP) in a quantitative manner over a five-log concentration range. The system utilizes a recognition surface based on ATP aptamer (ATPA) capture probes prebound to electroactive flavin adenine dinucleotide (FAD) molecules, and a signaling surface utilizing graphene (Gr) and gold nanoparticle (AuNP) modified carbon paste electrode (Gr-AuNP-CPE) that is optimized to enhance electron-transfer kinetics and signal sensitivity. Binding of ATP to ATPA at the recognition surface causes the release of an equivalent concentration of FAD that can be quantitatively monitored in real time at the signaling surface, thereby enabling a wide linear working range (1.14 × 10(-10) to 3.0 × 10(-5) M), a low detection limit (2.01 × 10(-11) M using graphene and AuNP modified glassy carbon), and fast target binding kinetics (steady-state signal within 12 min at detection limit). Unlike assays based on capture probe-immobilized electrodes, this double-surface competitive assay offers the ability to speed up target binding kinetics by increasing the capture probe concentration, with no limitations due to intermolecular Coulombic interactions and nonspecific binding. We utilize the real-time monitoring capability to compute kinetic parameters for target binding and to make quantitative distinctions on degree of base-pair mismatch through monitoring target binding kinetics over a wide concentration range. On the basis of the simplicity of the assay chemistry and the quantitative detection of ATP within fruit and serum media, as demonstrated by comparison of ATP levels against those determined using a standard high-performance liquid chromatography (HPLC)-UV absorbance method, we envision a versatile detection platform for applications requiring real-time monitoring over a wide target concentration range.

Nanostructured rough gold electrodes as platforms to enhance the sensitivity of electrochemical genosensors

An electrochemical DNA genosensor constructed by using rough gold as electrode support is reported in this work. The electrode surface nanopatterning was accomplished by repetitive square-wave perturbing potential (RSWPP). A synthetic 25-mer DNA capture probe, modified at the 5' end with a hexaalkylthiol, able to hybridize with a specific sequence of lacZ gene from the Enterobacteriaceae bacterial family was assembled to the rough gold surface. A 25 bases synthetic sequence fully complementary to the thiolated DNA capture probe and a 326 bases fragment of lacZ containing a fully matched sequence with the capture probe, which was amplified by a specific asymmetric polymerase chain reaction (aPCR), were employed as target sequences. The hybridization event was electrochemically monitored by using two different indicators, hexaammineruthenium (III) chloride showing an electrostatic DNA binding mode, and pentaamineruthenium-[3-(2-phenanthren-9-yl-vinyl)-pyridine] (in brief RuL) which binds to double stranded DNA (dsDNA) following an intercalative mechanism. After optimization of the different variables involved in the hybridization and detection reactions, detection limits of 5.30 pg μL(-1) and 10 pg μL(-1) were obtained for the 25-mer synthetic target DNA and the aPCR amplicon, respectively. A RSD value of 6% was obtained for measurements carried out with 3 different genosensors prepared in the same manner.

DNA hairpins as temperature switches, thermometers and ionic detectors

Temperature is of major importance in most branches of science and technology as well as in everyday life, and with the miniaturization of electronic devices and the increasing ability to make research into small-scale systems, a specific need for very small thermostats and thermometers has been created. Here we describe how DNA molecules can be used as nanoscale sensors to meet these requirements. We illustrate how the hybridization kinetics between bases in DNA molecules combined with conformational changes of the DNA backbone can be exploited in the construction of simple but versatile temperature switches and thermometers, which can be built into electronic systems. DNA based sensors are at the same time applicable as ion detectors to monitor the chemical environment of a specific system.

Nanoporous Gold Electrodes and Their Applications in Analytical Chemistry

Nanoporous gold prepared by dealloying Au:Ag alloys has recently become an attractive material in the field of analytical chemistry. This conductive material has an open, 3D porous framework consisting of nanosized pores and ligaments with surface areas that are 10s to 100s of times larger than planar gold of an equivalent geometric area. The high surface area coupled with an open pore network makes nanoporous gold an ideal support for the development of chemical sensors. Important attributes include conductivity, high surface area, ease of preparation and modification, tunable pore size, and a bicontinuous open pore network. In this paper, the fabrication, characterization, and applications of nanoporous gold in chemical sensing are reviewed specifically as they relate to the development of immunosensors, enzyme-based biosensors, DNA sensors, Raman sensors, and small molecule sensors.