Visual detection of microRNA with lateral flow nucleic acid biosensor

Visual Detection of Dengue-1 RNA Using Gold Nanoparticle-Based Lateral Flow Biosensor

Dengue is a rapidly spreading mosquito-borne viral disease. Early diagnosis is important for clinical screening, medical management, and disease surveillance. The objective of this study was to develop a colorimetric lateral flow biosensor (LFB) for the visual detection of dengue-1 RNA using dextrin-capped gold nanoparticle (AuNP) as label. The detection was based on nucleic acid sandwich-type hybridization among AuNP-labeled DNA reporter probe, dengue-1 target RNA, and dengue-1 specific DNA capture probe immobilized on the nitrocellulose membrane. Positive test generated a red test line on the LFB strip, which enabled visual detection. The optimized biosensor has a cut-off value of 0.01 µM using synthetic dengue-1 target. Proof-of-concept application of the biosensor detected dengue-1 virus in pooled human sera with a cut-off value of 1.2 × 104 pfu/mL. The extracted viral RNA, when coupled with nucleic acid sequence-based amplification (NASBA), was detected on the LFB in 20 min. This study first demonstrates the applicability of dextrin-capped AuNP as label for lateral flow assay. The biosensor being developed provides a promising diagnostic platform for early detection of dengue infection in high-risk resource-limited areas.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

An aptamer-based hook-effect-recognizable three-line lateral flow biosensor for rapid detection of thrombin

In this paper, a three-line LFB was successfully developed by adding a thrombin line to a conventional two-line LFB for the detection of thrombin in a wide range of human serum. We introduced a thrombin line between the test line and the control line. The concentration of thrombin in the sample was quantitatively related to the signal formation on the three lines of the LFB. We can make use of signal on three lines to quantitative determinate the thrombin by data processing. The detection range of thrombin concentrations measured in 10 min was 1 nM to 100 μM and the LOD was 0.85 nM. Our approach paves way for rapid and sensitive thrombin detection and a superior device for testing in a wide range of physiological concentrations, which also can be used in other hook-effect-limited aptamers or antibodies based sandwich LFBs, and has a high accuracy even within the range of the hook-effect.

SERS based protocol using flow glass-hemostix for detection of neuron-specific enolase in blood plasma

An inexpensive and disposable lateral flow glass-hemostix (FGH) has been developed as an immunoassay, in which surface-enhanced Raman scattering (SERS) is utilized for sensing signal transduction.

Bioinspired DNA-Inorganic Hybrid Nanoflowers Combined with a Personal Glucose Meter for Onsite Detection of miRNA

Biomineralization is an important process in nature, by which living organisms participate in producing organic/inorganic hybrid materials and the resultant materials show sophisticated structures and excellent physical and chemical properties. Inspired by biomineralization, DNA-Cu₃(PO₄)₂ hybrid nanoflowers (HNFs) were prepared, which exhibited high stability, a high surface-to-volume ratio, and good DNA encapsulation ability. A facile thread platform for microRNA (miRNA) detection was fabricated by employing DNA-Cu₃(PO₄)₂ HNFs as captors, and the signal could be easily read out by a personal glucose meter. The fabricated biosensor could detect miRNA-21 quantitatively and a detection limit of 0.41 nM was achieved. Furthermore, miRNA in A549 cell lysate could also be detected without pretreatment. In this work, we achieved a fast, simple, low-cost method based on the bioinspired DNA-inorganic HNFs for the specific and sensitive detection of miRNA in both aqueous solution and biological samples, indicating its great promise in biomedical and clinical applications.

MicroRNA sensors based on gold nanoparticles

MicroRNAs (miRNAs) are small regulatory RNAs, the dysregulation of which has been associated with the progression of several human diseases, including cancer. Interestingly, these molecules can be used as biomarkers for early disease diagnosis and can be found in a variety of body fluids and tissue samples. However, their specific properties and very low concentrations make their detection rather challenging. In this regard, current detection methods are complex, cost-ineffective, and of limited application in point-of-care settings or resource-limited facilities. Recently, nanotechnology-based approaches have emerged as promising alternatives to conventional miRNA detection methods and paved the way for research towards sensitive, fast, and low-cost detection systems. In particular, due to their exceptional properties, the use of gold nanoparticles (AuNPs) has significantly improved the performance of miRNA biosensors. This review discusses the application of AuNPs in different miRNA sensor modalities, commenting on recently reported examples. A practical overview of each modality is provided, highlighting their future use in clinical diagnosis. Graphical abstract ᅟ.

Lateral Flow Test for Visual Detection of Multiple MicroRNAs

The authors describe a rapid and low-cost approach for multiplex microRNA(miRNA) assay on lateral flow nucleic acid biosensor (LFNAB). The principle of assay is based on sandwich-type nucleic acid hybridization reactions to produce gold nanoparticle (GNP)-attached complexes (ssDNA-microRNA-ssDNA/GNPs), which are captured and visualized on the test zone of LFNAB. By designing three different test zones on LFNAB, simultaneous detection of microRNA-21, microRNA-155 and microRNA-210 was achieved with an adding-measuring model by using GNP as visual tag. The method was challenged by testing the microRNAs in spiked serum samples with satisfied results. In our perception, the test is a particularly valuable tool for clinical application and biomedical diagnosis, particularly in limited resource settings.

Biotin-exposure-based immunomagnetic separation coupled with nucleic acid lateral flow biosensor for visibly detecting viable Listeria monocytogenes

Infectious diseases caused by Listeria monocytogenes pose a great threat to public health worldwide. Therefore, a rapid and efficient method for L. monocytogenes detection is needed. In this study, a biotin-exposure-based immunomagnetic separation (IMS) method was developed. That is, biotinylated antibody was first targeted to L. monocytogenes. Then, streptavidin-functionalized magnetic nanoparticles were added and anchored onto L. monocytogenes cells indirectly through the strong noncovalent interaction between streptavidin and biotin. Biotin-exposure-based IMS exhibited an excellent capability to enrich L. monocytogenes. Specifically, more than 90% of L. monocytogenes was captured when the bacterial concentration was lower than 10⁴ colony-forming units (CFU)/mL. Importantly, the antibody dosage was reduced by 10 times of that in our previous study, which used antibody direct-conjugated magnetic nanoparticles. Propidium monoazide (PMA) treatment prior to PCR amplification could eliminate the false-positive results from dead bacteria and detected viable L. monocytogenes sensitively and specifically. For viable L.monocytogenes detection, enriched L. monocytogenes was treated with PMA prior to asymmetric PCR amplification. The detection limits of the combined IMS with nucleic acid lateral flow (NALF) biosensor for viable L. monocytogenes detection were 3.5 × 10³ CFU/mL in phosphate buffer solution and 3.5 × 10⁴ CFU/g in lettuce samples. The whole assay process of recognizing viable L. monocytogenes was completed within 6 h. The proposed biotin-exposure-mediated IMS combined with a disposable NALF biosensor platform posed no health risk to the end user, and possessed potential applications in the rapid screening and identification of foodborne pathogens.

Recent advances in microRNA detection

Recent advances in miRNA detection methods and new applications.

Challenges of the Nano-Bio Interface in Lateral Flow and Dipstick Immunoassays

Lateral flow assays (LFAs) are highly attractive for point-of-care (POC) diagnostics for infectious disease, food safety, and many other medical uses. The unique optical, electronic, and chemical properties that arise from the nanostructured and material characteristics of nanoparticles provide an opportunity to increase LFA sensitivity and impart novel capabilities. However, interfacing to nanomaterials in complex biological environments is challenging and can result in undesirable side effects such as non-specific adsorption, protein denaturation, and steric hindrance. These issues are even more acute in LFAs where there are many different types of inorganic-biological interfaces, often of a complex nature. Therefore, the unique properties of nanomaterials for LFAs must be exploited in a way that addresses these interface challenges.

A multiplex protein-free lateral flow assay for detection of microRNAs based on unmodified molecular beacons

Lateral flow assays (LFAs) have promising potentials for point-of-care applications. Recently, many LFAs have been reported that are based on hybridization of oligonucleotide strands. Mostly, biotinylated capture DNAs are immobilized on the surface of a nitrocellulose membrane via streptavidin interactions. During the assay, stable colorful complexes get formed that are visible by naked eyes. Here, we present an inexpensive and unique design of LFA that applies unmodified oligonucleotides at capture lines. The presented LFA do not utilize streptavidin or any other affinity protein. We employ structural switch of molecular beacons (MB) in combination with base stacking hybridization (BSH) phenomenon. The unique design of the reported LFA provided high selectivity for target oligonucleotides. We validated potential applications of the system for detection of DNA mimics of two microRNAs in multiplex assays.

Paper-Based Surface-Enhanced Raman Scattering Lateral Flow Strip for Detection of Neuron-Specific Enolase in Blood Plasma

An inexpensive and disposable paper-based lateral flow strip (PLFS) has been developed as an immunoassay, in which surface-enhanced Raman scattering (SERS) is utilized for sensing signal transduction. The Au nanostar@Raman Reporter@silica sandwich nanoparticles are developed as the SERS probes, which is the key to the high sensitivity of the device. Compared with a colorimetric PLFS, the SERS-PLFS exhibits superior performance in terms of sensitivity and limit of detection (LOD) in a blood plasma-containing sample matrix. In addition, the SERS-PLFS has been successfully used for detection of neuron-specific enolase (NSE), a traumatic brain injury (TBI) protein biomarker, in diluted blood plasma samples, achieving a LOD of 0.86 ng/mL. Moreover, the SERS-PLFS was successfully employed to measure the NSE level in clinical blood plasma samples taken from deidentified TBI patients. This work demonstrates that the SERS-PLFS has great potential in assisting screening of TBI patients in the point-of-care setting.

Free-Energy-Driven Lock/Open Assembly-Based Optical DNA Sensor for Cancer-Related microRNA Detection with a Shortened Time-to-Result

Quantification of cancer biomarker microRNAs (miRs) by exquisitely designed biosensors with a short time-to-result is of great clinical significance. With immobilized capture probes (CPs) and fluorescent-labeled signal probes (SPs), surface-involved sandwich-type (SST) biosensors serve as powerful tools for rapid, highly sensitive, and selective detection of miR in complex matrices as opposed to the conventional techniques. One key challenge for such SST biosensors is the existence of false-negative signals when the amount of miRs exceeds SPs in solution phase for a surface with a limited number of CP. To meet this challenge, a dynamic lock/open DNA assembly was designed to rationally program the pathway for miR/SP hybrids. Based on secondary structure analysis and free-energy assessment, a "locker" strand that partially hybridizes with target miR by two separated short arms was designed to stabilize target miR, preventing possible false-negative signals. The strategy was demonstrated on a fiber-based fluorescent DNA-sensing platform. CP/miR/SP sandwiches formed on the fiber surface would generate fluorescent signals for quantitative analysis. The developed SST biosensor was able to detect miR Hsa let-7a with a detection limit of 24 pM. The applicability of this free-energy-driven lock/open assembly-based optical DNA sensor was further confirmed with spiked human urine and serum samples.

Fluorescent carbon nanoparticle-based lateral flow biosensor for ultrasensitive detection of DNA

We report a fluorescent carbon nanoparticle (FCN)-based lateral flow biosensor for ultrasensitive detection of DNA. Fluorescent carbon nanoparticle with a diameter of around 15nm was used as a tag to label a detection DNA probe, which was complementary with the part of target DNA. A capture DNA probe was immobilized on the test zone of the lateral flow biosensor. Sandwich-type hybridization reactions among the FCN-labeled DNA probe, target DNA and capture DNA probe were performed on the lateral flow biosensor. In the presence of target DNA, FCNs were captured on the test zone of the biosensor and the fluorescent intensity of the captured FCNs was measured with a portable fluorescent reader. After systematic optimizations of experimental parameters (the components of running buffers, the concentration of detection DNA probe used in the preparation of FCN-DNA conjugates, the amount of FCN-DNA dispensed on the conjugate pad and the dispensing cycles of the capture DNA probes on the test-zone), the biosensor could detect a minimum concentration of 0.4 fM DNA. This study provides a rapid and low-cost approach for DNA detection with high sensitivity, showing great promise for clinical application and biomedical diagnosis.

Fabrication of calix[4]arene-attached mesoporous ammonium molybdophosphate–silica hybrid and its application as an adsorbent for cesium ions

The cesium cation is a common contaminant in medical and industrial products as well as in nuclear wastes, and it can present a serious risk to human health.

Visual detection of thrombin using a strip biosensor through aptamer-cleavage reaction with enzyme catalytic amplification

A new class of strip biosensors has been established based on well-distributed thrombin aptamer-linked gold nanoparticle aggregates, which will undergo a cracking reaction when the target recognizes its homologous aptamer. Combining the aptamer-cleavage reaction with the enzyme catalytic amplification system, our proposed lateral flow strip biosensor (LFB) is capable of visually detecting 6.4 pM of thrombin without instrumentation within 12 minutes. Under the optimal conditions, the quantitative detection of thrombin by a portable strip reader exhibited a linear relationship between the peak area and the concentration of thrombin in the range of 6.4 pM-500 nM with a detection limit of 4.9 pM, which is three orders of magnitude lower than that of the aptamer-functionalized gold nanoparticle-based LFB (2.5 nM, Xu et al., Anal. Chem., 2009, 81, 669-675). As the aptamers have no special requirements and the gold nanoparticles can also be replaced by other metallic nanoparticles, this method for strip sensing is expected to be generally applicable in point of care testing, home testing, medical diagnostics, clinical diagnosis, and environmental monitoring.

Application of a SERS-based lateral flow immunoassay strip for the rapid and sensitive detection of staphylococcal enterotoxin B

A novel surface-enhanced Raman scattering (SERS)-based lateral flow immunoassay (LFA) biosensor was developed to resolve problems associated with conventional LFA strips (e.g., limits in quantitative analysis and low sensitivity). In our SERS-based biosensor, Raman reporter-labeled hollow gold nanospheres (HGNs) were used as SERS detection probes instead of gold nanoparticles. With the proposed SERS-based LFA strip, the presence of a target antigen can be identified through a colour change in the test zone. Furthermore, highly sensitive quantitative evaluation is possible by measuring SERS signals from the test zone. To verify the feasibility of the SERS-based LFA strip platform, an immunoassay of staphylococcal enterotoxin B (SEB) was performed as a model reaction. The limit of detection (LOD) for SEB, as determined with the SERS-based LFA strip, was estimated to be 0.001 ng mL(-1). This value is approximately three orders of magnitude more sensitive than that achieved with the corresponding ELISA-based method. The proposed SERS-based LFA strip sensor shows significant potential for the rapid and sensitive detection of target markers in a simplified manner.

A SERS-based lateral flow assay biosensor for highly sensitive detection of HIV-1 DNA

User-friendly lateral flow (LF) strips have been extensively used for point-of-care (POC) self-diagnostics, but they have some limitations in their detection sensitivity and quantitative analysis because they only identify the high cut-off value of a biomarker by utilizing color changes that are detected with the naked eye. To resolve these problems associated with LF strips, we developed a novel surface-enhanced Raman scattering (SERS)-based LF assay for the quantitative analysis of a specific biomarker in the low concentration range. Herein, human immunodeficiency virus type 1 (HIV-1) DNA was chosen as the specific biomarker. Raman reporter-labeled gold nanoparticles (AuNPs) were employed as SERS nano tags for targeting and detecting the HIV-1 DNA marker, as opposed to using bare AuNPs in LF strips. It was possible to quantitatively analyze HIV-1 DNA with high sensitivity by monitoring the characteristic Raman peak intensity of the DNA-conjugated AuNPs. Under optimized conditions, the detection limit of our SERS-based lateral flow assay was 0.24 pg/mL, which was at least 1000 times more sensitive compared to colorimetric or fluorescent detection methods. These results demonstrate the potential feasibility of the proposed SERS-based lateral flow assay to quantitatively detect a broad range of genetic diseases with high sensitivity.

Ultratrace DNA Detection Based on the Condensing-Enrichment Effect of Superwettable Microchips

A sensitive nucleic acid detection platform based on superhydrophilic microwells spotted on a superhydrophobic substrate is fabricated. Due to the wettability differences, ultratrace DNA molecules are enriched and the fluorescent signals are amplified to allow more sensitive detection. The biosensing interface based on superwettable materials provides a simple and cost-effective way for ultratrace DNA sensing.

Enzyme-Free Amplification by Nano Sticky Balls for Visual Detection of ssDNA/RNA Oligonucleotides

Visual detection of nucleic acids provides simple and rapid screening for infectious diseases or environmental pathogens. However, sensitivity is the current bottleneck, which may require enzymatic amplification for targets in low abundance and make them incompatible with detection at resource-limited sites. Here we report an enzyme-free amplification that provides a sensitive visual detection of ssDNA/RNA oligonucleotides on the basis of nano "sticky balls". When target oligonucleotides are present, magnetic microparticles (MMPs) and gold nanoparticles (AuNPs) were linked together, allowing the collection of AuNPs after magnetic attraction. Subsequently, the collected AuNPs, which carry many oligonucleotides, were used as the sticky balls to link a second pair of MMPs and polymer microparticles (PMPs). Thus, because the magnetic field can attract the MMPs as well as the linked PMPs to the sidewall, the reduction of suspended PMPs yields a change of light transmission visible by the naked eye. Our results demonstrate that the limit of detection is 10 amol for ssDNAs (228 fM in 45 μL) and 75 amol for ssRNAs (1.67 pM in 45 μL). This method is also compatible with the serum environment and detection of a microRNA, miR-155, derived from human breast cancer cells. With significantly improved sensitivity for visual detection, it provides great potential for point-of-care applications at resource-limited sites.

Clinical evaluation of circulating microRNA-25 level change in sepsis and its potential relationship with oxidative stress

OBJECTIVE

To investigated the circulating microRNA expression profile in sepsis and its clinical evaluation.

METHODS

70 patients with sepsis and 30 patients with SIRS were selected and their blood samples were collected. Using liquid bead array with 3 statistical analysis approaches analyzed the circulating microRNA expression profiles, for confirming the data of liquid bead array, qRT-PCR was performed. The prognostic value of the changed microRNA in sepsis was determined and compared with CRP and PCT by analyzing the receiver operating characteristic (ROC) curves. To reveal whether the selected microRNAs could predict the outcome of patients, 28 d survival rate were calculated using Kaplan-Meier curves. Furthermore, the level of malondialdehyde (MDA), activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in plasma were detected and the relationship with the changed microRNA was determined.

RESULTS

By integrating data from liquid bead array, we ultimately identified 6 microRNAs that were consistently changed in both of 3 statistical analysis approaches, however, only the change of microRNA-25 was significant according to the qPCR's result. The area under ROC curve showed that the clinical accuracy of microRNA-25 for sepsis diagnosis was better than CRP and PCT (AUG=0.806, 0.676 and 0.726, P<0.05).The decrease in level of microRNA-25 was correlated with the severity of sepsis, SOFA score, CRP and PCT level, meanwhile, microRNA-25 level can be used for predicting the prognosis of patients, the patients with microRNA-25 level ≤0.492 had a lower 28 d survival rate. Moreover, Decreased microRNA-25 level was related to the level of oxidative stress indicators in sepsis patients.

CONCLUSIONS

MicroRNA-25 can be used as a biomarker for the diagnosis and assessment of sepsis. Meanwhile, microRNA-25 level may be associated with oxidative stress in patients with sepsis, and it is expected to become a target for anti-oxidation therapy.

Sensitive and multiplexed on-chip microRNA profiling in oil-isolated hydrogel chambers

Although microRNAs (miRNAs) have been shown to be excellent indicators of disease state, current profiling platforms are insufficient for clinical translation. Here, we demonstrate a versatile hydrogel-based microfluidic approach and novel amplification scheme for entirely on-chip, sensitive, and highly specific miRNA detection without the risk of sequence bias. A simulation-driven approach is used to engineer the hydrogel geometry and the gel-reaction environment is chemically optimized for robust detection performance. The assay provides 22.6 fM sensitivity over a three log range, demonstrates multiplexing across at least four targets, and requires just 10.3 ng of total RNA input in a 2 hour and 15 minutes assay.

Plasmon-enhanced optical sensors: a review

Surface plasmon resonance (SPR) has found extensive applications in chemi-sensors and biosensors. Plasmons play different roles in different types of optical sensors. SPR transduces a signal in a colorimetric sensor through shifts in the spectral position and intensity in response to external stimuli. SPR can also concentrate the incident electromagnetic field in a nanostructure, modulating fluorescence emission and enabling plasmon-enhanced fluorescence to be used for ultrasensitive detection. Furthermore, plasmons have been extensively used for amplifying a Raman signal in a surface-enhanced Raman scattering sensor. This paper presents a review of recent research progress in plasmon-enhanced optical sensing, giving emphasis on the physical basis of plasmon-enhanced sensors and how these principles guide the design of sensors. In particular, this paper discusses the design strategies for nanomaterials and nanostructures to plasmonically enhance optical sensing signals, also highlighting the applications of plasmon-enhanced optical sensors in healthcare, homeland security, food safety and environmental monitoring.

MicroRNA Detection: Current Technology and Research Strategies

The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.