DNA point mutation detection based on DNA ligase reaction and nano-Au amplification: a piezoelectric approach

Electrochemiluminescent bioassay based on Ru@Zr-BTC-MOFs nanoparticles for determination of let-7a miRNA using the hybridization chain reaction

Carboxyl-rich tris(4,4'-dicarboxylic acid-2,2'-bipyridyl) ruthenium(II) ([Ru(dcbpy)3]2+) and 1,3,5-phenyl tricarboxylic acid (H3BTC) were used as the organic ligand to synthesize the metal-organic frameworks by a simple one-pot hydrothermal method with ZrCl4 as metal ion source. Subsequently, the excellent electrochemiluminescence (ECL) luminophore (denoted as Ru@Zr-BTC-MOFs) was obtained. The Ru@Zr-BTC-MOFs displayed outstanding ECL properties, and a sensitive ECL bioassay based on Ru@Zr-BTC-MOFs was designed for the detection of let-7a microRNA (miRNA) using hybrid chain reaction (HCR). Under the optimal experimental conditions, the proposed bioassay exhibited a good linear relationship in the range from 50.0 fM to 5.00 × 102 pM with a detection limit of 3.71 fM. Besides, the proposed sensor exhibited satisfactory performance in real samples. The recovery was 91 ~ 108%, and the relative standard deviation was less than 5.6%. It might have potential clinical applications for detecting miRNA in biomedical research and clinical diagnosis. The schematic diagram of the preparation of Ru@Zr-BTC-MOFs (a) and ECL sensor for detecting let -7a (b).

Nanostructures for Biosensing, with a Brief Overview on Cancer Detection, IoT, and the Role of Machine Learning in Smart Biosensors

Biosensors are essential tools which have been traditionally used to monitor environmental pollution and detect the presence of toxic elements and biohazardous bacteria or virus in organic matter and biomolecules for clinical diagnostics. In the last couple of decades, the scientific community has witnessed their widespread application in the fields of military, health care, industrial process control, environmental monitoring, food-quality control, and microbiology. Biosensor technology has greatly evolved from in vitro studies based on the biosensing ability of organic beings to the highly sophisticated world of nanofabrication-enabled miniaturized biosensors. The incorporation of nanotechnology in the vast field of biosensing has led to the development of novel sensors and sensing mechanisms, as well as an increase in the sensitivity and performance of the existing biosensors. Additionally, the nanoscale dimension further assists the development of sensors for rapid and simple detection in vivo as well as the ability to probe single biomolecules and obtain critical information for their detection and analysis. However, the major drawbacks of this include, but are not limited to, potential toxicities associated with the unavoidable release of nanoparticles into the environment, miniaturization-induced unreliability, lack of automation, and difficulty of integrating the nanostructured-based biosensors, as well as unreliable transduction signals from these devices. Although the field of biosensors is vast, we intend to explore various nanotechnology-enabled biosensors as part of this review article and provide a brief description of their fundamental working principles and potential applications. The article aims to provide the reader a holistic overview of different nanostructures which have been used for biosensing purposes along with some specific applications in the field of cancer detection and the Internet of things (IoT), as well as a brief overview of machine-learning-based biosensing.

Label-Free Detection of DNA Mutations by Nanopore Analysis

Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion. The method was rapid and highly sensitive with a detection limit of 4.8 nM in a 10 min electrical recording. Furthermore, the nanopore assay could differentiate among perfect match, one mismatch, and two mismatches. In addition, simulated serum samples were successfully analyzed. Our developed nanopore-based DNA mutation detection strategy should find useful application in genetic diagnosis.

Overview of Piezoelectric Biosensors, Immunosensors and DNA Sensors and Their Applications

Piezoelectric biosensors are a group of analytical devices working on a principle of affinity interaction recording. A piezoelectric platform or piezoelectric crystal is a sensor part working on the principle of oscillations change due to a mass bound on the piezoelectric crystal surface. In this review, biosensors having their surface modified with an antibody or antigen, with a molecularly imprinted polymer, with genetic information like single stranded DNA, and biosensors with bound receptors of organic of biochemical origin, are presented and discussed. The mentioned recognition parts are frequently combined with use of nanoparticles and applications in this way are also introduced. An overview of the current literature is given and the methods presented are commented upon.

Terahertz spectroscopy for the isothermal detection of bacterial DNA by magnetic bead-based rolling circle amplification

A terahertz biosensor based on rolling circle amplification was developed for the isothermal detection of bacterial DNA.

A biosensor for the detection of single base mismatches in microRNA

Graphene oxide quenches fluorescence corresponding to only a mismatched target due to selective denaturing of the thermo-unstable duplex composed of probe peptide nucleic acid and single base mismatched target RNA and thus, the fluorescence signal only from perfectly matched target RNA is measured.

Biomedical applications of gold nanomaterials: opportunities and challenges

In the past few years, there has been an unprecedented development of gold nanomaterials (AuNMs) for potential clinical applications. Owing to their advantageous physical, chemical, and biological properties, AuNMs have attracted great attention in the nanomedicine arena for applications in biological sensing, biomedical imaging, drug delivery, and photothermal therapy. Their tunable size, shape, and surface characteristics coupled with excellent biocompatibility render them ideal candidates for translation from bench-top to bedside. This review summarizes the recent research on the applications of AuNM with a focus on biomedical diagnostics and therapeutics. The bio-interaction of these NM with cells and their in vivo responses are presented. After reviewing these potential applications, future challenges and prospects are discussed and the suitability of how AuNMs are used as effective tools in clinical medicine is assessed.

Safety issues and new rapid detection methods in traditional Chinese medicinal materials

The safety of traditional Chinese medicine (TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the 'bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.

Lab in a tube: a fast-assembled colorimetric sensor for highly sensitive detection of oligonucleotides based on a hybridization chain reaction

Upon adding T_HBV, the self-assembly of T_HBV with H₁ allows the rest of the DNA sequence of H₁ to accelerate H₁–H₂ complex formation. The G-quadruplex at the end of the H₁–H₂ complex could catalyze TMB into a colored product.

Towards high-performance, low-cost quartz sensors with high-density, well-separated, vertically aligned ZnO nanowires by low-temperature, seed-less, single-step, double-sided growth

Resonant sensors with nanostructured surfaces have long been considered as an emergent platform for high-sensitivity transduction because of the potentially very large sensing areas. Nevertheless, until now only complex, time-consuming, expensive and sub-optimal fabrication procedures have been described; in fact, especially with reference to in-liquid applications, very few devices have been reported. Here, we first demonstrate that, by immersing standard, ultra-low-cost quartz resonators with un-polished silver electrodes in a conventional zinc nitrate/HMTA equimolar nutrient solution, the gentle contamination from the metallic package allows direct growth on the electrodes of arrays of high-density (up to 10 μm⁻²) and well-separated (no fusion at the roots) ZnO nanowires without any seed layer or thermal annealing. The combination of high-density and good separation is ideal for increasing the sensing area; moreover, this uniquely simple, single-step process is suitable for conventional, ultra-low-cost and high-frequency quartzes, and results in devices that are already packaged and ready to use. As an additional advantage, the process parameters can be effectively optimized by measuring the quartz admittance before and after growth. As a preliminary test, we show that the sensitivity to the liquid properties of high-frequency (i.e. high sensitivity) quartzes can be further increased by nearly one order of magnitude and thus show the highest ever reported frequency shifts of an admittance resonance in response to immersion in both ethanol and water.

Detection of metal ions (Cu2+, Hg2+) and cocaine by using ligation DNAzyme machinery

The Cu(2+)-dependent ligation DNAzyme is implemented as a biocatalyst for the colorimetric or chemiluminescence detection of Cu(2+) ions, Hg(2+) ions, or cocaine. These sensing platforms are based on the structural tailoring of the sequence of the Cu(2+)-dependent ligation DNAzyme for specific analytes. The tethering of a subunit of the hemin/G-quadruplex DNAzyme to the ligation DNAzyme sequence, and the incorporation of an imidazole-functionalized nucleic-acid sequence, which acts as a co-substrate for the ligation DNAzyme that is tethered to the complementary hemin/G-quadruplex subunit. In the presence of different analytes, Cu(2+) ions, Hg(2+) ions, or cocaine, the pretailored Cu(2+)-dependent ligation DNAzyme sequence stimulates the respective ligation process by combining the imidazole-functionalized co-substrate with the ligation DNAzyme sequence. These reactions lead to the self-assembly of stable hemin/G-quadruplex DNAzyme nanostructures that enable the colorimetric analysis of the substrate through the DNAzyme-catalyzed oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS(2-), by H(2)O(2) into the colored product ABTS(·-), or the chemiluminescence detection of the substrate through the DNAzyme-catalyzed oxidation of luminol by H(2)O(2). The detection limits for the sensing of Cu(2+) ions, Hg(2+) ions, and cocaine correspond to 1 nM, 10 nM and 2.5 μM, respectively. These different sensing platforms also reveal impressive selectivities.

Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction

Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.

Determination of surface concentrations of individual molecule-layers used in nanoscale biosensors by in situ ATR-FTIR spectroscopy

For the development of nanowire sensors for chemical and medical detection purposes, the optimal functionalization of the surface is a mandatory component. Quantitative ATR-FTIR spectroscopy was used in situ to investigate the step-by-step layer formation of typical functionalization protocols and to determine the respective molecule surface concentrations. BSA, anti-TNF-α and anti-PSA antibodies were bound via 3-(trimethoxy)butylsilyl aldehyde linkers to silicon-oxide surfaces in order to investigate surface functionalization of nanowires. Maximum determined surface concentrations were 7.17 × 10(-13) mol cm(-2) for BSA, 1.7 × 10(-13) mol cm(-2) for anti-TNF-α antibody, 6.1 × 10(-13) mol cm(-2) for anti-PSA antibody, 3.88 × 10(-13) mol cm(-2) for TNF-α and 7.0 × 10(-13) mol cm(-2) for PSA. Furthermore we performed antibody-antigen binding experiments and determined the specific binding ratios. The maximum possible ratio of 2 was obtained at bulk concentrations of the antigen in the μg ml(-1) range for TNF-α and PSA.

Biosensors - classification, characterization and new trends

Biosensors represent promising analytical tools applicable in areas such as clinical diagnosis, food industry, environment monitoring and in other fields, where rapid and reliable analyses are needed. Some biosensors were successfully implemented in the commercial sphere, but majority needs to be improved in order to overcome some imperfections. This review covers the basic types, principles, constructions and use of biosensors as well as new trends used for their fabrication.

Noble metal nanoparticles for biosensing applications

In the last decade the use of nanomaterials has been having a great impact in biosensing. In particular, the unique properties of noble metal nanoparticles have allowed for the development of new biosensing platforms with enhanced capabilities in the specific detection of bioanalytes. Noble metal nanoparticles show unique physicochemical properties (such as ease of functionalization via simple chemistry and high surface-to-volume ratios) that allied with their unique spectral and optical properties have prompted the development of a plethora of biosensing platforms. Additionally, they also provide an additional or enhanced layer of application for commonly used techniques, such as fluorescence, infrared and Raman spectroscopy. Herein we review the use of noble metal nanoparticles for biosensing strategies—from synthesis and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics laboratory.

High-sensitive electrochemical detection of point mutation based on polymerization-induced enzymatic amplification

Here a highly sensitive electrochemical method is described for the detection of point mutation in DNA. Polymerization extension reaction is applied to specifically initiate enzymatic electrochemical amplification to improve the sensitivity and enhance the performance of point mutation detection. In this work, 5'-thiolated DNA probe sequences complementary to the wild target DNA are assembled on the gold electrode. In the presence of wild target DNA, the probe is extended by DNA polymerase over the free segment of target as the template. After washing with NaOH solution, the target DNA is removed while the elongated probe sequence remains on the sensing surface. Via hybridizing to the designed biotin-labeled detection probe, the extended sequence is capable of capturing detection probe. After introducing streptavidin-conjugated alkaline phosphatase (SA-ALP), the specific binding between streptavidin and biotin mediates a catalytic reaction of ascorbic acid 2-phosphate (AA-P) substrate to produce a reducing agent ascorbic acid (AA). Then the silver ions in solution are reduced by AA, leading to the deposition of silver metal onto the electrode surface. The amount of deposited silver which is determined by the amount of wild target can be quantified by the linear sweep voltammetry (LSV). The present approach proved to be capable of detecting the wild target DNA down to a detection limit of 1.0×10(-14) M in a wide target concentration range and identifying -28 site (A to G) of the β-thalassemia gene, demonstrating that this scheme offers a highly sensitive and specific approach for point mutation detection.

Using nanoparticles to push the limits of detection

The size-dependent chemical and physical properties of nanoparticles inspire the design of unique assays and the use of new detection schemes while also offering the opportunity to vastly improve the results achieved when using traditional signal transduction methods. Herein, the most commonly exploited nanoparticle amplification schemes are organized and reviewed on the basis of the detection methods used to monitor the nanoparticle property of interest. The topics covered include the improved signal photostability and brightness of semiconductor quantum dots, the increased extinction coefficient of noble metal nanoparticles, the advantages of having a magnetic label on individual target molecules to facilitate separation, the multiplexing that is enabled with 'barcoded' nanoparticles, and the greatly amplified signals that can be achieved on the basis of conductivity changes, generated current, or simply by adding a 'massive' nanoparticle onto a small molecule target. Common approaches emerge among different nanoparticle materials and detection schemes, and it is also clear that there is still significant opportunity to use nanoparticles in as-yet-unimagined ways to further improve assay and sensor limits of detection.

Recent development of nano-materials used in DNA biosensors

As knowledge of the structure and function of nucleic acid molecules has increased, sequence-specific DNA detection has gained increased importance. DNA biosensors based on nucleic acid hybridization have been actively developed because of their specificity, speed, portability, and low cost. Recently, there has been considerable interest in using nano-materials for DNA biosensors. Because of their high surface-to-volume ratios and excellent biological compatibilities, nano-materials could be used to increase the amount of DNA immobilization; moreover, DNA bound to nano-materials can maintain its biological activity. Alternatively, signal amplification by labeling a targeted analyte with nano-materials has also been reported for DNA biosensors in many papers. This review summarizes the applications of various nano-materials for DNA biosensors during past five years. We found that nano-materials of small sizes were advantageous as substrates for DNA attachment or as labels for signal amplification; and use of two or more types of nano-materials in the biosensors could improve their overall quality and to overcome the deficiencies of the individual nano-components. Most current DNA biosensors require the use of polymerase chain reaction (PCR) in their protocols. However, further development of nano-materials with smaller size and/or with improved biological and chemical properties would substantially enhance the accuracy, selectivity and sensitivity of DNA biosensors. Thus, DNA biosensors without PCR amplification may become a reality in the foreseeable future.

Detection and haplotype differentiation of Southeast Asian alpha-thalassemia using polymerase chain reaction and a piezoelectric biosensor immobilized with a single oligonucleotide probe

DNA-based diagnosis of alpha-thalassemias routinely relies on polymerase chain reaction (PCR) and gel electrophoresis. Here, we developed a new procedure for the detection and haplotype differentiation of Southeast Asian (SEA) alpha-thalassemia using a 3-primer system for PCR coupling with a DNA-based piezoelectric biosensor. PCR products amplified from genomic DNA were differentiated directly by using a quartz crystal microbalance immobilized with a single oligonucleotide probe. The frequency changes after hybridization of the PCR products amplified from a representative sample of normal alpha-globin, SEA alpha-thalassemia heterozygote, and homozygote were 206+/-11, 256+/-5, and 307+/-3 Hz, respectively. The fabricated biosensor was evaluated through an examination of 18 blind specimens. It could accurately discriminate between normal and SEA alpha-thalassemic samples, which suggests that this biosensor system is a promising alternative technique to detect SEA alpha-thalassemia because of its specificity and less hazardous exposure as compared with conventional methods.

Quartz crystal microbalance immunosensor for the detection of antibodies to double-stranded DNA

We report the development of a novel quartz crystal microbalance immunosensor with the simultaneous measurement of resonance frequency and motional resistance for the detection of antibodies to double-stranded DNA (dsDNA). The immobilization of poly(L-lysine) and subsequent complexation with DNA resulted in formation of a sensitive dsDNA-containing nanofilm on the surface of a gold electrode. Atomic force microscopy has been applied for the characterization of a poly(L-lysine)-DNA film. After the blocking with bovine serum albumin, the immunosensor in flow-injection mode was used to detect the antibodies to dsDNA in purified protein solutions of antibodies to dsDNA and to single-stranded DNA, monoclonal human immunoglobulin G, DNase I and in blood serum of patients with bronchial asthma and systemic lupus erythematosus. Experimental results indicate high sensitivity and selectivity of the immunosensor.