A plasmonic colorimetric strategy for visual miRNA detection based on hybridization chain reaction

Ultrasensitive Method Enables Liquid Biopsy for the Precise Detection of Circulating MicroRNAs

Due to invasive and serial examinations of bioactive molecules, liquid biopsy (LB) has emerged as a rapid and reliable solution for early disease detection and monitoring. Developing portable devices with high specificity and sensitivity for LB is highly valuable. To realize a generalized approach to increase the sensitivity of LB, we developed an ultrasensitive diagnostic biochip based on the amplification of miRNA by recombinase polymerase amplification and the significant enhancement of fluorescence signals by photonic crystal (PC) materials. The PCs-RPA biochip has a detection limit as low as 0.24 aM, a wide linear range of 8 orders of magnitude, and excellent specificity. Such advantages realize the accurate detection of circulating miRNAs with very low content in clinical serum samples for the precise diagnosis of nonsmall cell lung cancer.

Dual amplification-based ultrasensitive and highly selective colorimetric detection of miRNA

In this study, we combined a Pradeep Kumar (PK)-probe with a ligation-transcription-ramified RCA (LTR) dual-amplification system for the isothermal colorimetric detection of miRNA 25-3P, where the PK-probe transformed from its pink color to colorless in the presence of the amplification byproduct pyrophosphate (PPi), thereby allowing the simple naked-eye qualitative detection of the miRNA. Through this double-amplification strategy, the limit of detection reached as low as 91.4 aM-quite extraordinary sensitivity for a colorimetric miRNA detection system based on absorbance readings. Our detection system also operated with high specificity, the result of using two different target-selective ligation steps (linear DNA ligation and circular DNA ligation) mediated by SplintR ligase, and so could discriminate single-mismatched from perfectly matched target sequences. We suspect that this ultrasensitive and selective PK-probe/LTR dual-amplification system should be a great colorimetric diagnostic for the detection of any miRNA with high efficiency.

Advanced Self-Powered Biofuel Cells with Capacitor and Nanogenerator for Biomarker Sensing

Self-powered biofuel cells (BFCs) have evolved for highly sensitive detection of biomarkers such as noncodon micro ribonucleic acids (miRNAs) in the presence of interfering substrates. Self-charging supercapacitive BFCs for in vivo and in vitro cellular microenvironments represent the most prevalent sensing mechanism for diagnosis. Therefore, self-powered biosensing (SPB) with a capacitor and contact separation with a triboelectric nanogenerator (TENG) offers electrochemical and colorimetric dual-mode detection via improved electrical signal intensity. In this review, we discuss three major components: stretchable self-powered BFC design, miRNA sensing, and impedance spectroscopy. A specific focus is given to 1) assembling of sensors for biomarkers, 2) electrical output signal intensification, and 3) role of supercapacitors and nanogenerators in SPBs. We outline the key features of stretchable SPBs and the sequence of miRNA sensing by SPBs. We have emphasized the need of a supercapacitor and nanogenerator for SPBs in the context of advanced assembly of the sensing unit. Finally, we outline the role of impedance spectroscopy in the detection and estimation of biomarkers. We highlight key challenges in SPBs for biomarker sensing, which needs improved sensing accuracy, integration strategies of electrochemical biosensing for in vitro and in vivo microenvironments, and the impact of miRNA sensing on cancer diagnostics. This article attempts a specific focus on the accuracy and limitations of sensing unit for miRNA biomarkers and associated tool for boosting electrical signal intensity for a potential big step further.

Micro- and nanosystems for the detection of hemorrhagic fever viruses

Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.

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.

Printed Electrochemical Strip for the Detection of miRNA-29a: A Possible Biomarker Related to Alzheimer’s Disease

The development of electrochemical strips, as extremely powerful diagnostic tools, has received much attention in the field of sensor analysis and, in particular, the detection of nucleic acids in complex matrixes is a hot topic in the electroanalytical area, especially when directed toward the development of emerging technologies, for the purpose of facilitating personal healthcare. One of the major diseases for which early diagnosis is crucial is represented by Alzheimer’s disease (AD). AD is a progressive neurodegenerative disease, and it is the most common cause of dementia worldwide. In this context microRNAs (miRNAs), which are small noncoding RNAs, have recently been highlighted for their promising role as biomarkers for early diagnosis. In particular, miRNA-29 represents a class of miRNAs known to regulate pathogenesis of AD. In this work we developed an electrochemical printed strip for the detection of miRNA-29a at low levels. The architecture was characterized by the presence of gold nanoparticles (AuNPs) and an anti-miRNA-29a probe labeled with a redox mediator. The novel analytical tool has been characterized with microscale thermophoresis and electrochemical methods, and it has been optimized by selection of the most appropriate probe density to detect low target concentration. The present tool was capable to detect miRNA-29a both in standard solution and in serum, respectively, down to 0.15 and 0.2 nM. The platform highlighted good repeatability (calculated as the relative standard deviation) of ca. 10% and satisfactory selectivity in the presence of interfering species. This work has the objective to open a way for the study and possible early diagnosis of a physically and socially devastating disease such as Alzheimer’s. The results demonstrate the suitability of this approach in terms of ease of use, time of production, sensitivity, and applicability.

SERS Based Lateral Flow Assay for Rapid and Ultrasensitive Quantification of Dual Laryngeal Squamous Cell Carcinoma-Related miRNA Biomarkers in Human Serum Using Pd-Au Core-Shell Nanorods and Catalytic Hairpin Assembly

Non-invasive early diagnosis is of great significant in disease pathologic development and subsequent medical treatments, and microRNA (miRNA) detection has attracted critical attention in early cancer screening and diagnosis. However, it was still a challenge to report an accurate and sensitive method for the detection of miRNA during cancer development, especially in the presence of its analogs that produce intense background noise. Herein, we developed a surface-enhanced Raman scattering (SERS)–based lateral flow assay (LFA) biosensor, assisted with catalytic hairpin assembly (CHA) amplification strategy, for the dynamic monitoring of miR-106b and miR-196b, associated with laryngeal squamous cell carcinoma (LSCC). In the presence of target miRNAs, two hairpin DNAs could self-assemble into double-stranded DNA, exposing the biotin molecules modified on the surface of palladium (Pd)–gold (Au) core–shell nanorods (Pd-AuNRs). Then, the biotin molecules could be captured by the streptavidin (SA), which was fixed on the test lines (T1 line and T2 line) beforehand. The core–shell spatial structures and aggregation Pd-AuNRs generated abundant active “hot spots” on the T line, significantly amplifying the SERS signals. Using this strategy, the limits of detections were low to aM level, and the selectivity, reproducibility, and uniformity of the proposed SERS-LFA biosensor were satisfactory. Finally, this rapid analysis strategy was successfully applied to quantitatively detect the target miRNAs in clinical serum obtained from healthy subjects and patients with LSCC at different stages. The results were consistent with the quantitative real-time PCR (qRT-PCR). Thus, the CHA-assisted SERS-LFA biosensor would become a promising alternative tool for miRNAs detection, which showed a tremendous clinical application prospect in diagnosing LSCC.

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.

Smartphone-Based Device for Colorimetric Detection of MicroRNA Biomarkers Using Nanoparticle-Based Assay

The detection of microRNAs (miRNAs) is emerging as a clinically important tool for the non-invasive detection of a wide variety of diseases ranging from cancers and cardiovascular illnesses to infectious diseases. Over the years, miRNA detection schemes have become accessible to clinicians, but they still require sophisticated and bulky laboratory equipment and trained personnel to operate. The exceptional computing ability and ease of use of modern smartphones coupled with fieldable optical detection technologies can provide a useful and portable alternative to these laboratory systems. Herein, we present the development of a smartphone-based device called Krometriks, which is capable of simple and rapid colorimetric detection of microRNA (miRNAs) using a nanoparticle-based assay. The device consists of a smartphone, a 3D printed accessory, and a custom-built dedicated mobile app. We illustrate the utility of Krometriks for the detection of an important miRNA disease biomarker, miR-21, using a nanoplasmonics-based assay developed by our group. We show that Krometriks can detect miRNA down to nanomolar concentrations with detection results comparable to a laboratory-based benchtop spectrophotometer. With slight changes to the accessory design, Krometriks can be made compatible with different types of smartphone models and specifications. Thus, the Krometriks device offers a practical colorimetric platform that has the potential to provide accessible and affordable miRNA diagnostics for point-of-care and field applications in low-resource settings.

Dual Catalytic Hairpin Assembly-Based Automatic Molecule Machine for Amplified Detection of Auxin Response Factor-Targeted MicroRNA-160

MicroRNA160 plays a crucial role in plant development by negatively regulating the auxin response factors (ARFs). In this manuscript, we design an automatic molecule machine (AMM) based on the dual catalytic hairpin assembly (D-CHA) strategy for the signal amplification detection of miRNA160. The detection system contains four hairpin-shaped DNA probes (HP1, HP2, HP3, and HP4). For HP1, the loop is designed to be complementary to miRNA160. A fragment of DNA with the same sequences as miRNA160 is separated into two pieces that are connected at the 3′ end of HP2 and 5′ end of HP3, respectively. In the presence of the target, four HPs are successively dissolved by the first catalytic hairpin assembly (CHA1), forming a four-way DNA junction (F-DJ) that enables the rearrangement of separated DNA fragments at the end of HP2 and HP3 and serving as an integrated target analogue for initiating the second CHA reaction, generating an enhanced fluorescence signal. Assay experiments demonstrate that D-CHA has a better performance compared with traditional CHA, achieving the detection limit as low as 10 pM for miRNA160 as deduced from its corresponding DNA surrogates. Moreover, non-target miRNAs, as well as single-base mutation targets, can be detected. Overall, the D-CHA strategy provides a competitive method for plant miRNAs detection.

Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection

Rolling circle amplification (RCA) and loop mediated isothermal amplification (LAMP) were combined to establish the rolling circle and loop mediated isothermal amplification (RC-LAMP) method for miRNA detection. With the participation of Bst 2.0 DNA Polymerase, the method enabled RCA and LAMP amplification to occur simultaneously without thermal cycling. The limit of detection of RC-LAMP was 500 amol/L, which is comparable to previously reported amplification strategies. Moreover, its upper limit of quantitation was higher and showed a stronger resistance to matrix interference. Therefore, it is possible to detect low concentrations of miRNA in samples by increasing the total RNA added. Owing to its facile detection mode and simple operation, this method has great potential in clinical sample detection.

Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions

Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.

Mesoporous gold-silver alloy films towards amplification-free ultra-sensitive microRNA detection

Herein, we report the preparation of mesoporous gold (Au)-silver (Ag) alloy films through the electrochemical micelle assembly process and their applications as microRNA (miRNA) sensors. Following electrochemical deposition and subsequent removal of the templates, the polymeric micelles can create uniformly sized mesoporous architectures with high surface areas. The resulting mesoporous Au-Ag alloy films show high current densities (electrocatalytic activities) towards the redox reaction between potassium ferrocyanide and potassium ferricyanide. Following magnetic isolation and purification, the target miRNA is adsorbed directly on the mesoporous Au-Ag film. Electrochemical detection is then enabled by differential pulse voltammetry (DPV) using the [Fe(CN)6]3-/4- redox system (the faradaic current for the miRNA-adsorbed Au-Ag film decreases compared to the bare film). The films demonstrate great advantages towards miRNA sensing platforms to enhance the detection limit down to attomolar levels of miR-21 (limit of detection (LOD) = 100 aM, s/n = 3). The developed enzymatic amplification-free miniaturized analytical sensor has promising potential for RNA-based diagnosis of diseases.

Recent Progress in Plasmonic Biosensing Schemes for Virus Detection

The global burden of coronavirus disease 2019 (COVID-19) to public health and global economy has stressed the need for rapid and simple diagnostic methods. From this perspective, plasmonic-based biosensing can manage the threat of infectious diseases by providing timely virus monitoring. In recent years, many plasmonics’ platforms have embraced the challenge of offering on-site strategies to complement traditional diagnostic methods relying on the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). This review compiled recent progress on the development of novel plasmonic sensing schemes for the effective control of virus-related diseases. A special focus was set on the utilization of plasmonic nanostructures in combination with other detection formats involving colorimetric, fluorescence, luminescence, or Raman scattering enhancement. The quantification of different viruses (e.g., hepatitis virus, influenza virus, norovirus, dengue virus, Ebola virus, Zika virus) with particular attention to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reviewed from the perspective of the biomarker and the biological receptor immobilized on the sensor chip. Technological limitations including selectivity, stability, and monitoring in biological matrices were also reviewed for different plasmonic-sensing approaches.

Sensing Biomarkers with Plasmonics

The detection of biomarkers is critical for enabling early disease diagnosis, monitoring the progression, and tracking the effectiveness of therapeutic intervention. Plasmonic sensors exhibit a broad range of analytical capabilities, from the rapid generation of colorimetric readouts to single-molecule sensitivity in ultralow sample volumes, which have led to their increased exploration in bioanalysis and point-of-care applications. This perspective presents selected accounts of recent developments on the different types of plasmonic sensing platforms, the pervasive challenges, and outlook on the pathway to translation. We highlight the sensing of upcoming biomarkers, including microRNA, circulating tumor cells, exosomes, and cell-free DNA, and discuss the opportunity of utilizing plasmonic nanomaterials and tools for biomarker detection beyond biofluids, such as in tissues, organs, and disease sites. The integration of plasmonic biosensors with established and upcoming technologies of instrumentation, sample pretreatment, and data analysis will help realize their translation to clinical settings for improving healthcare and enhancing the quality of life.

Hydrogel-Based Colorimetric Assay for Multiplexed MicroRNA Detection in a Microfluidic Device

Although microRNA (miRNA) expression levels provide important information regarding disease states owing to their unique dysregulation patterns in tissues, translation of miRNA diagnostics into point-of-care (POC) settings has been limited by practical challenges. Here, we developed a hydrogel-based microfluidic platform for colorimetric profiling of miRNAs, without the use of complex external equipment for fluidics and imaging. For sensitive and reliable measurement without the risk of sequence bias, we employed a gold deposition-based signal amplification scheme and dark-field imaging, and seamlessly integrated a previously developed miRNA assay scheme into this platform. The assay demonstrated a limit of detection of 260 fM, along with multiplexing of small panels of miRNAs in healthy and cancer samples. We anticipate this versatile platform to facilitate a broad range of POC profiling of miRNAs in cancer-associated dysregulation with high-confidence by exploiting the unique features of hydrogel substrate in an on-chip format and colorimetric analysis.

Cationic copolymer-chaperoned DNAzyme sensor for microRNA detection

Multi-component nucleic acid enzymes (MNAzymes) are allosteric deoxyribozymes that are activated upon binding of a specific nucleic acid effector. MNAzyme activity is limited due to an insufficient assembly of the MNAzyme and its turnover. In this work, we describe the successful improvement of MNAzyme reactivity and selectivity by addition of cationic copolymers, which exhibit nucleic acid chaperone-like activity. The copolymer allowed a 210-fold increase in signal activity and a 95-fold increase in the signal-to-background selectivity of MNAzymes constructed for microRNA (miRNA) detection. The selectivity of the MNAzyme for homologous miRNAs was demonstrated in a multiplex format in which isothermal reactions of two different MNAzymes were performed. In addition, the copolymer permitted miRNA detections even in the presence of a ribonuclease which is ubiquitous in environments, indicating the protective effect of the copolymer against ribonucleases.

Highly Sensitive in Vitro Diagnostic System of Pandemic Influenza A (H1N1) Virus Infection with Specific MicroRNA as a Biomarker

Several microRNAs (miRNAs) have been reported to be closely related to influenza A virus infection, replication, and immune response. Therefore, the development of the infectious-disease detection system using miRNAs as biomarkers is actively underway. Herein, we identified two miRNAs (miR-181c-5p and miR-1254) as biomarkers for detection of pandemic influenza A H1N1 virus infection and proposed the catalytic hairpin assembly-based in vitro diagnostic (CIVD) system for a highly sensitive diagnosis; this system is composed of two sets of cascade hairpin probes enabling to detect miR-181c-5p and miR-1254. We demonstrated that CIVD kits could not only detect subnanomolar levels of target miRNAs but also distinguish even single-base mismatches. Moreover, this CIVD kit has shown excellent detection performance in real intracellular RNA samples and confirmed results similar to those of conventional methods (microarray and quantitative real-time polymerase chain reaction).

Multicolor and Ultrasensitive Enzyme-Linked Immunosorbent Assay Based on the Fluorescence Hybrid Chain Reaction for Simultaneous Detection of Pathogens

Various pathogens may coexist in one sample; however, detection methods that rely on traditional selective culture media or immune agents designed specifically for a certain target are unsuitable for multiple targets. It is important to develop a simultaneous and sensitive detection method for multiple pathogens. Here, a multicolor and ultrasensitive enzyme-linked immunosorbent assay (ELISA) platform based on the fluorescence hybridization chain reaction (HCR) was developed. In the assay, multicolor fluorescence concatemers formed as signal amplifiers and signal reporters in the presence of target pathogens. When HCR occurred, Escherichia coli O157:H7, Salmonella serotype Choleraesuis, and Listeria monocytogenes were detected simultaneously with three different fluorescences. Additionally, the limits of detection for E. coli O157:H7, Salmonella Choleraesuis, and L. monocytogenes were 3.4 × 10¹, 6.4 × 10⁰, and 7.0 × 10¹ CFU/mL, respectively. The assay achieved ultrasensitive, specific, and simultaneous detection of three pathogens and can be applied to the detection of pathogens in milk samples. Therefore, this multicolor and ultrasensitive ELISA platform has great potential in the application of simultaneous detection of pathogens.

Surface Plasmon Resonance for Biomarker Detection: Advances in Non-invasive Cancer Diagnosis

Biomarker-based cancer analysis has great potential to lead to a better understanding of disease at the molecular level and to improve early diagnosis and monitoring. Unlike conventional tissue biopsy, liquid biopsy allows the detection of a large variety of circulating biomarkers, such as microRNA (miRNA), exosomes, circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and proteins, in an easily accessible and minimally invasive way. In this review, we describe and evaluate the relevance and applicability of surface plasmon resonance (SPR) and localized SPR (LSPR)-based platforms for the detection of different classes of cancer biomarkers in liquid biopsy samples. Firstly, we critically discuss unsolved problems and issues in capturing and analyzing biomarkers. Secondly, we highlight current challenges which need to be resolved in applying SPR biosensors into clinical practice. Then, we mainly focus on applications of SPR-based platforms that process a patient sample aiming to detect and quantify biomarkers as a minimally invasive liquid biopsy tool for cancer patients appearing over the last 5 years. Finally, we describe the analytical performances of selected SPR biosensor assays and their significant advantages in terms of high sensitivity and specificity as well as accuracy and workflow simplicity.

Research advances in the detection of miRNA

MicroRNAs (miRNAs) are a family of endogenous, small (approximately 22 nucleotides in length), noncoding, functional RNAs. With the development of molecular biology, the research of miRNA biological function has attracted significant interest, as abnormal miRNA expression is identified to contribute to serious human diseases such as cancers. Traditional methods for miRNA detection do not meet current demands. In particular, nanomaterial-based methods, nucleic acid amplification-based methods such as rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), strand-displacement amplification (SDA) and some enzyme-free amplifications have been employed widely for the highly sensitive detection of miRNA. MiRNA functional research and clinical diagnostics have been accelerated by these new techniques. Herein, we summarize and discuss the recent progress in the development of miRNA detection methods and new applications. This review will provide guidelines for the development of follow-up miRNA detection methods with high sensitivity and specificity, and applicability to disease diagnosis and therapy.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

Dual cycle amplification and dual signal enhancement assisted sensitive SERS assay of MicroRNA

A sensitive surface-enhanced Raman scattering (SERS) approach has been developed for detection of microRNA (miRNA) based on target-triggered dual signal amplification including strand displancement amplification (SDA) and hybridization chain reaction (HCR). With the assistant of polymerase and nicking endonuclease (NEase), target miRNA combines with the single stranded template DNA to generate a great amount of trigger DNA which can induce HCR. Coupled the dual cycle amplification of SDA and HCR with the dual enhancement of gold nanoparticles (AuNPs), a low detection limit of 0.5 fM for miRNA is obtained using the proposed strategy. With high sensitivity, universality, rapid analysis, and high selectivity, this method has a great potential for detecting biomolecules with trace amounts in bioanalysis and clinical biomedicine.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

Localized surface plasmon resonance based biosensing

INTRODUCTION

Bioanalytical sensing based on the principle of localized surface plasmon resonance experiences is currently an extremely rapid development. Novel sensors with new kinds of plasmonic transducers and innovative concepts for the signal development as well as read-out principles were identified. This review will give an overview of the development of this field. Areas covered: The focus is primarily on types of transducers by preparation or dimension, factors for optimal sensing concepts and the critical view of the usability of these devices as innovative sensors for bioanalytical applications. Expert commentary: Plasmonic sensor devices offer a high potential for future biosensing given that limiting factors such as long-time stability of the transducers, the required high sensitivity and the cost-efficient production are addressed. For higher sensitivity, the design of the sensor in shape and material has to be combined with optimal enhancement strategies. Plasmonic nanoparticles from bottom-up synthesis with a post-synthetic processing show a high potential for cost-efficient sensor production. Regarding the measurement principle, LSPRi offers a large potential for multiplex sensors and can provide a high-throughput as well as highly paralleled sensing. The main trends are expected towards optimal LSPR concepts which represent cost-efficient and robust point-of-care solutions, and the use of multiplexed devices for clinical applications.

Methods and novel technology for microRNA quantification in colorectal cancer screening

The screening and diagnosis of colorectal cancer (CRC) currently relies heavily on invasive endoscopic techniques as well as imaging and antigen detection tools. More accessible and reliable biomarkers are necessary for early detection in order to expedite treatment and improve patient outcomes. Recent studies have indicated that levels of specific microRNA (miRNA) are altered in CRC; however, measuring miRNA in biological samples has proven difficult, given the complicated and lengthy PCR-based procedures used by most laboratories. In this manuscript, we examine the potential of miRNA as CRC biomarkers, summarize the methods that have commonly been employed to quantify miRNA, and focus on novel strategies that can improve or replace existing technology for feasible implementation in a clinical setting. These include isothermal amplification techniques that can potentially eliminate the need for specialized thermocycling equipment. Additionally, we propose the use of near-infrared (NIR) probes which can minimize autofluorescence and photobleaching and streamline quantification without tedious sample processing. We suggest that novel miRNA quantification tools will be necessary to encourage new discoveries and facilitate their translation to clinical practice.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Ultrasensitive Detection of MicroRNAs with Morpholino-Functionalized Nanochannel Biosensor

Here, we demonstrate a phosphorodiamidate morpholino oligos (PMO)-functionalized nanochannel biosensor for label-free detection of microRNAs (miRNAs) with ultrasensitivity and high sequence specificity. PMO, as a capture probe, was covalently anchored on the nanochannel surface. Because of the neutral character and high sequence-specific affinity of PMO, hybridization efficiency between PMO and miRNAs was enhanced, thus largely decreasing background signals and highly improving the detection specificity and sensitivity. The miRNAs detection was realized through observing the change of surface charge density when PMO/miRNAs hybridization occurred. Not only could the developed biosensor specifically discriminate complementary miRNAs (Let-7b) from noncomplementary miRNAs (miR-21) and one-base mismatched miRNAs (Let-7c), but also it could detect target miRNAs in serum samples. In addition, this nanochannel-based biosensor attained a reliable limit of detection down to 1 fM in PBS and 10 fM in serum sample, respectively. It is expected that such a new method will benefit miRNA detection in clinical diagnosis.

Ultrasensitive colorimetric detection of circulating tumor DNA using hybridization chain reaction and the pivot of triplex DNA

This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA. Nevertheless, in the absence of ctDNA, no HCR happens. Thus, no triplex DNA and G-Quadruplex structure is formed, producing a negligible background. The colorimetric sensing platform is successfully applied in complex biological environments such as human blood plasma for ctDNA detection, with a detection limit corresponding to 0.1 pM. This study unambiguously uses triplex DNA forming as the pivot to integrate nucleic acid amplification and DNAzymes for producing a highly sensitive signal with low background.