A universal colorimetry for nucleic acids and aptamer-specific ligands detection based on DNA hybridization amplification

Electroactive polymer tag modified nanosensors for enhanced intracellular ATP detection

ATP plays a crucial role in cell energy supply, so the quantification of intracellular ATP levels is particularly important for understanding many physio-pathological processes. The intracellular quantification of this non-electroactive molecule can be realized using aptamer-modified nanoelectrodes, but is hindered by the limited quantity of modification and electroactive tags on the nanosized electrodes. Herein, we developed a simple but effective electrochemical signal amplification strategy for intracellular ATP detection, which replaces the regular ATP aptamer-linked ferrocene monomer with a polymer, thus greatly magnifying the amounts of electrochemical reporters linked to one chain of the aptamer and enhancing the signals. This ferrocene polymer-ATP aptamer was further immobilized onto Au nanowire electrodes (SiC@C@Au NWEs) to achieve accurate quantification of intracellular ATP in single cells, presenting high electrochemical signal output and high specificity. This work not only provides a powerful tool for quantifying intracellular ATP but also offers a simple and versatile strategy for electrochemical signal amplification in the detection of broader non-electroactive molecules involved in different kinds of intracellular physiological processes.

Advances in Point-of-Care Testing of microRNAs Based on Portable Instruments and Visual Detection

MicroRNAs (miRNAs) are a class of small noncoding RNAs that are approximately 22 nt in length and regulate gene expression post-transcriptionally. miRNAs play a vital role in both physiological and pathological processes and are regarded as promising biomarkers for cancer, cardiovascular diseases, neurodegenerative diseases, and so on. Accurate detection of miRNA expression level in clinical samples is important for miRNA-guided diagnostics. However, the common miRNA detection approaches like RNA sequencing, qRT-PCR, and miRNA microarray are performed in a professional laboratory with complex intermediate steps and are time-consuming and costly, challenging the miRNA-guided diagnostics. Hence, sensitive, highly specific, rapid, and easy-to-use detection of miRNAs is crucial for clinical diagnosis based on miRNAs. With the advantages of being specific, sensitive, efficient, cost-saving, and easy to operate, point-of-care testing (POCT) has been widely used in the detection of miRNAs. For the first time, we mainly focus on summarizing the research progress in POCT of miRNAs based on portable instruments and visual readout methods. As widely available pocket-size portable instruments and visual detection play important roles in POCT, we provide an all-sided discussion of the principles of these methods and their main limitations and challenges, in order to provide a guide for the development of more accurate, specific, and sensitive POCT methods for miRNA detection.

Electrochemical aptamer biosensor for DNA detection based on label-free aptamers

Electrochemical aptasensor has been broadly advanced for nucleic acid detection. However, it is a long-term goal to design an aptasensor with high specificity, flexibility, and simplicity. In this work, we develop a strategy of triblock DNA probe, which consists of two DNA probes at both ends and ployA fragments in the middle as probe-polyA-probe. PolyA fragment has high affinity to the surface of gold electrode, so it can be assembled on the electrode surface via polyA instead of traditional Au-S bonds. When the target DNA is simultaneously hybridized with the two capture probes, the hybridization stability can be improved due to the strong base stacking effect. [Ru(NH₃)₆]³⁺, as signal probe, can be electrostatically adsorbed on the negatively charged DNA skeleton. A wide linear range (10 pM-10 μM) is obtained with a detection limit of 2.9 pM. Our electrochemical aptasensor has good repeatability, stability, and specificity. More importantly, the electrochemical sensor can successfully detect DNA in human serum samples, which proves its practical value and extensive applicability in complex environment.

Applications of hybridization chain reaction optical detection incorporating nanomaterials: A review

The development of powerful, simple and cost-effective signal amplifiers has significant implications for biological research and analysis. Hybridization chain reaction (HCR) has attracted increasing attention because of its enzyme-free, simple, and efficient amplification. In the HCR process, an initiator probe triggered a pair of metastable hairpins through a cross-opening process to propagate a chain reaction of hybridization events, yielding a long-nicked double-stranded nucleic acid structure. To achieve more noticeable signal amplification, nanomaterials, including graphene oxide, quantum dots, gold, silver, magnetic, and other nanoparticles, were integrated with HCR. Various types of colorimetric, fluorescence, plasmonic analyses or chemiluminescence optical sensing strategies incorporating nanomaterials have been developed to analyze various targets, such as nucleic acids, small biomolecules, proteins, and metal ions. This review summarized the recent advances of HCR technology pairing diverse nanomaterials in optical detection and discussed their challenges.

Visual assay of Escherichia coli O157:H7 based on an isothermal strand displacement and hybrid chain reaction amplification strategy

Here, we describe a simple, sensitive, and enzyme-free method for visual point-of-care detection of 16S rRNA of Escherichia coli O157:H7 based on an isothermal strand displacement-hybrid chain reaction (ISD-HCR) and lateral flow strip (LFS). In this study, the secondary structure of 16S rRNA of E. coli O157:H7 was unwound by two helper oligonucleotides to expose the single-strand-specific nucleic acid sequence. The free specific sequence promoted the toehold-mediated strand displacement reaction to output a large number of FITC-labeled single-stranded DNA probes (capture probe [CP]). The 3'-end sequence of the reporter probe propagated a chain reaction of hybridization events between the two hairpin probes modified with biotin to form long nicked DNA polymers with multiple biotins (RP-HCR complexes); the free CP and RP-HCR complexes then form CP/RP-HCR complexes. The biotin-labeled double-stranded DNA CP/RP-HCR polymers then introduced numerous streptavidin (SA)-labeled gold nanoparticles (AuNPs) on the LFS. The accumulation of AuNPs produced a characteristic red band, which enabled visual detection of changes in the signal of 16S rRNA of E. coli O157:H7. The current approach could detect E. coli O157:H7 at concentrations as low as 10² CFU mL^-1 without instrumentation. This approach thus provides a simple, sensitive, and low-cost tool for point-of-care detection of pathogenic bacteria, especially in resource-limited countries.

Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA

Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses.

Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.

An amine-functionalized metal-organic framework and triple-helix molecular beacons as a sensing platform for miRNA ratiometric detection

Herein, a metal-organic framework (UiO-66-NH₂) with two functions (intrinsic fluorescence and fluorescence quenching ability) is designed to establish a ratiometric fluorescent platform for high-performance miRNA detection. The use of a fluorescent organic ligand endows the MOF material with a strong intrinsic fluorescence at 440 nm. In the presence of target miRNA, the fluorescence signal of the FAM is restored with the triple helix molecular beacons bind to the target. Using the I_FAM/I_MOF signal as the output, the prepared ratiometric probe was able to eliminate disturbance caused by the sensing environment. Under the optimal reaction conditions, including buffer pH of 7.4, temperature of 37 °C, and response time of 1 h, the best detection results can be obtained. The ratiometric fluorescence probe presented showed good sensitivity and selectivity for detecting miRNA-203 and the limit of detection was 400 pM with a wide linear range from 1 nM to 160 nM. In addition, this method was applied to diluted human serum and cell lysates, and good detection effect was realized.

Naked-eye based point-of-care detection of E.coli O157: H7 by a signal-amplified microfluidic aptasensor

Fast and sensitive detection of E.coli O157: H7 is significantly essential for clinical management as well as for transmission prevention during disease outbreaks. Though many types of detection strategies have been implemented for measuring E.coli O157: H7, most of them still rely on complex instruments or tedious/laborious setups, which restrict their applications in resource-limited scenarios. Herein, we introduce an eye-based microfluidic aptasensor (EA-Sensor) for fast detection of E.coli O157: H7 without the assist of any instruments. We demonstrate the perfect coupling of aptamer sensing, hybridization chain reaction (HCR)-amplification and a distance-based visualized readout to quantitatively determine the pathogen concentration. We first used gel-electrophoresis assay to evaluate the system and the results proved that E.coli O157: H7 was well recognized by the aptamer and HCR could increase the signal by about 100 folds. In addition, the Aptamer specificity and signal-amplification ability were verified on the EA-Sensor for sensing E.coli O157: H7 by naked eyes. Furthermore, we demonstrated that E.coli O157: H7 in milk could be accurately and conveniently measured with good performance. With the benefits of operation integration and strategy integration, our EA-Sensor shows advantages of high specificity, easy operation, efficient amplification and visualized readout, which offers a favorable point-of-care tool for E.coli O157: H7 or other pathogen detection in resource-constrained settings.

Aptamer-integrated nucleic acid circuits for biosensing: Classification, challenges and perspectives

Owing to their high programmability and modularity, autonomous enzyme-free nucleic acid circuits are attracting ever-growing interest as signal amplifiers with potential applications in developing highly sensitive biosensing techniques. Besides nucleic acid input, the biosensing scope of aptamer-integrated nucleic acids could be further expanded to non-nucleic targets by integrating nucleic acid circuits with aptamers-a class of functional oligonucleotides with binding capabilities toward specific targets. By coupling upstream target recognition with downstream signal amplification, aptamer-integrated nucleic acid circuits enable aptasensors with increased sensitivity and enhanced performances, which may act as powerful tools in various fields including environment monitoring, personal care, clinical diagnosis, etc. In designing aptamer-integrated nucleic acid circuits, smart integration between aptamer and nucleic acid circuits plays a crucial role in developing reliable circuits with good performances. To date, although there are plenty of published researches adopting aptamer-integrated nucleic acid circuits as amplifiers in biosensing systems, deep discussion or systematic review on rational design strategies for aptamer-integrated nucleic acid circuits is still lacking. To fill this gap, rational aptamer-nucleic acid circuits integration modes were classified and summarized for the first time based on reviewing the state of art of existing aptamer-integrated nucleic acid circuits. Moreover, theoretical updates in nucleic acid circuits designs and major challenges to be overcome in developing highly sensitive aptamer-integrated nucleic acids based biosensing systems are discussed in this review.

A versatile dynamic light scattering strategy for the sensitive detection of microRNAs based on plasmonic core-satellites nanoassembly coupled with strand displacement reaction

A low-cost, effective and enzyme-free sensing strategy for ultrasensitive microRNA (miRNA) detection was developed based on dynamic light scattering (DLS) coupled with strand displacement reaction (SDR). The combination of DLS and SDR was used to assess the size changes of core-satellites nanoassembly. This strategy realized the limit of detection (LOD) as low as 0.24 pM (S/N = 3) and the detection range of 5 pM-150 pM, which might urge this strategy as an ideal candidate for the sensitive detection of miRNA in the future. In addition, the proposed strategy could be successfully used to analyze target miRNA in various cancer cells, indicating that the developed SDR-DLS strategy has promising clinical implications for rapid and early diagnosis of cancer-related diseases.

Sensitive determination of DNA based on phosphate-dye interaction using photothermal lens technique

Photothermal lens spectrometry is a powerful optical detection technique that can be used to investigate biomolecules. In this work, for the first time to our knowledge, photothermal lens spectrometry was used for determination of nanomolar concentrations of three distinct deoxyribonucleic acid (DNA) strands using methylene blue as a labeling dye. Methylene blue interacts with phosphate groups of the DNA in lower DNA concentrations. It was observed that phosphate-methylene blue interaction had no obvious effect on methylene blue absorption and fluorescence spectra, but the photothermal lens spectrometry signal of methylene blue increased with DNA concentration. For this purpose, to evaluate the performance of the presented method, herring sperm DNA, Escherichia coli bacteria DNA, and partial 16S rRNA genes were examined. Under optimum conditions, photothermal lens spectrometry intensity of methylene blue increased linearly with DNA concentration when herring sperm DNA, Escherichia coli DNA, and 16S rRNA gene concentrations increased in the ranges of 0.1-250, 1-700, and 1-800  nmol L^-1, respectively. The corresponding detection limits were found to be 0.07, 0.71, and 0.56  nmol L^-1, respectively, and relative standard deviations for 50  nmol L^-1 of the tested samples were 2.59%, 4.95%, and 4.57%, respectively.

Enzyme-free amplified DNA assay: five orders of linearity provided by metal stable isotope detection

For the quantification of mutated genes at greatly varied concentrations in body fluids, nucleic acid amplification strategies are often challenged by limited dynamic linear ranges. The proposed metal stable isotope detection strategy demonstrates five orders of linear range and a lower attomol detection limit, showing promising potential in clinical diagnosis.

Gold nanoprobe-based non-crosslinking hybridization for molecular diagnostics: an update

INTRODUCTION

An update on the uses and applications of the non-cross-linking (NCL) hybridization assay based on the spectral modulation of gold nanoparticles (AuNPs) are presented, emphasizing DNA and RNA detection. Areas covered: Nanotechnology is strongly impacting the way we address diagnostics and therapeutics. In fact, nanoscale devices and particles have been used in a variety of platforms for improved biosensing and, more interestingly, for molecular diagnostics. AuNPs have been used in a great diversity of DNA and RNA detection strategies that are based on their nanoscale properties. Their unique optical properties have put them at the forefront of colorimetric sensing platforms. Among these, those relying on the NCL mechanism using DNA-modified AuNPs have shown remarkable versatility and simplicity for molecular detection of human pathogens, identification of single base alterations at the basis of human disease, gene expression, among others. Application of the NCL assay to molecular diagnostics will be discussed considering the challenges for validation and clinically relevant targets. Expert commentary: Integration of the NCL approach using AuNPs into chip biosensing platforms, projecting miniaturization and portability, will be addressed in terms of the future, i.e. clinical validation and translation to market.

Microplate Chemiluminescent Assay for DNA Detection Using Apoperoxidase-Oligonucleotide as Capture Conjugate and HRP-Streptavidin Signaling System

A covalent conjugate of horseradish apoperoxidase and amino-containing oligonucleotide was synthesized for the first time. Using the obtained conjugate as a capture reagent chemiluminescent microtiter plate-based assay for detection of 35-mer fragment of hepatitis B virus (HBV) DNA (proof-of-concept analyte) was developed. To detect the target DNA, a signaling system consisted of biotinylated reporter oligonucleotide and HRP-streptavidin conjugate was used. The high sensitivity of the assay was due to the enhanced chemiluminescence reaction, where 3-(10′-phenothiazinyl)propane-1-sulfonate/N-morpholinopyridine pair was used as an enhancer. Under the optimized conditions the limit of detection and a working range of the assay were 3 pM and 6⁻100 pM, respectively. The assay sensitivity was 1.6 × 10⁵ RLU/pM of target. The coefficient of variation (CV) for determination of HBV DNA within the working range was lower than 6%.