Applying strand displacement amplification to quantum dots-based fluorescent lateral flow assay strips for HIV-DNA detection

2'-O-Methyl molecular beacon: a promising molecular tool that permits elimination of sticky-end pairing and improvement of detection sensitivity

An innovative 2'-O-methyl molecular beacon (MB) has been designed and prepared with improved thermal stability and unique nuclease resistance. The employment of 2'-O-methyl MBs helps efficiently suppress the background signal, while DNase I is responsible for the signal amplification and elimination of sticky-end pairing. The coupled use of 2'-O-methyl MBs and DNase I makes it possible to develop an enzyme-aided strategy for amplified detection of DNA targets in a sensitive and specific fashion. The analysis requires only mix-and-measure steps that can be accomplished within half an hour. The detection sensitivity is theoretically determined as 27.4 pM, which is nearly 200-fold better than that of the classic MB-based assay. This proposed sensing system also shows desired selectivity. All these features are of great importance for the design and application of MBs in biological, chemical, and biomedical fields.

Tutorial: design and fabrication of nanoparticle-based lateral-flow immunoassays

Lateral-flow assays (LFAs) are quick, simple and cheap assays to analyze various samples at the point of care or in the field, making them one of the most widespread biosensors currently available. They have been successfully employed for the detection of a myriad of different targets (ranging from atoms up to whole cells) in all type of samples (including water, blood, foodstuff and environmental samples). Their operation relies on the capillary flow of the sample throughout a series of sequential pads, each with different functionalities aiming to generate a signal to indicate the absence/presence (and, in some cases, the concentration) of the analyte of interest. To have a user-friendly operation, their development requires the optimization of multiple, interconnected parameters that may overwhelm new developers. In this tutorial, we provide the readers with: (i) the basic knowledge to understand the principles governing an LFA and to take informed decisions during lateral flow strip design and fabrication, (ii) a roadmap for optimal LFA development independent of the specific application, (iii) a step-by-step example procedure for the assembly and operation of an LF strip for the detection of human IgG and (iv) an extensive troubleshooting section addressing the most frequent issues in designing, assembling and using LFAs. By changing only the receptors, the provided example procedure can easily be adapted for cost-efficient detection of a broad variety of targets.

A Methodology for Ultrasensitive Detection of Sequence-Specific DNA or Uracil-DNA Glycosylase Activity

Ultrasensitive detection of sequence-specific DNA and uracil-DNA glycosylase (UDG) activity shows great practical significance in clinical diagnostic and biomedical studies. Here, a methodology based on a CRISPR/Cas12a system coupled with enhanced strand displacement amplification (E-SDA) was innovatively established for sequence-specific DNA or UDG activity detection. Sequence-specific DNA or DNA primers processed by UDG and Endonuclease IV can initiate E-SDA, generating auxiliary DNA chains, which act as activators to unlock the indiscriminate collateral cleavage activities (trans-cleavage) of the CRISPR/Cas12a. Then, the activated CRISPR/Cas12a, which intrinsically possesses the ability of significant signal amplification, can indiscriminately cleave the added cleavage reporters in the system. Thus, the multistep amplification of the method was obtained. Under the selected experimental conditions, the established method can achieve an actual sensitivity of sequence-specific DNA up to 100 aM within 2.5 h or ultralow UDG activity (3.1×10^-5 U/mL) detection within 3.5 h. We believe that the proposed method will have great potential for practical application in ultrasensitive detection of sequence-specific DNA or UDG activity.

Nanotechnology based strategies for HIV-1 and HTLV-1 retroviruses gene detection

Early detection of retroviruses including human T-cell lymphotropic virus and human immunodeficiency virus in the human body is indispensable to prevent retroviral infection propagation and improve clinical treatment. Until now, diverse techniques have been employed for the early detection of viruses. Traditional methods are time-consuming, resource-intensive, and laborious performing. Therefore, designing and constructing a selective and sensitive diagnosis system to detect serious diseases is highly demanded. Genetic detection with high sensitivity has striking significance for the early detection and remedy of disparate pathogenic diseases. The nucleic acid biosensors are based on the identification of specific DNA sequences in biological samples. Nanotechnology has an important impact on the development of sensitive biosensors. Different kinds of nanomaterials include nanoparticles, nanoclusters, quantum dots, carbon nanotubes, nanocomposites, etc., with different properties have been used to improve the performance of biosensors. Recently, DNA nanobiosensors are developed to provide simple, fast, selective, low-cost, and sensitive detection of infectious diseases. In this paper, the research progresses of nano genosensors for the detection of HIV-1 and HTLV-1 viruses, based on electrochemical, optical, and photoelectrochemical platforms are overviewed.

Enzyme-free visualization of nucleic acids during HIV infection by octopus-like DNA

It is highly desirable to develop a facile approach for the detection of the human immunodeficiency virus (HIV). To address this need, an octopus-like DNA (OLD) is designed in a one-pot method by direct folding of nine short single strands of DNA (ssDNA), which can be used to capture all the conserved HIV-1 gene efficiently though the sticky arms. The branched OLD was applied for the enzyme-free detection of HIV-1 nucleic acid and the visualization of the virus during HIV infection. The total detection procedure can be finished within 2 h with high specificity, making the OLD system a valuable tool for the rapid detection of HIV virus and further biomedical application.

Quantum Dot Bioconjugates for Diagnostic Applications

Quantum dots (QDs) are a special type of engineered nanomaterials with outstanding optoelectronic properties that make them as a very promising alternative to conventional luminescent dyes in biomedical applications, including biomolecule (BM) targeting, luminescence imaging and drug delivery. A key parameter to ensure successful biomedical applications of QDs is the appropriate surface modification, i.e. the surface of the nanomaterials should be modified with the appropriate functional groups to ensure stability in aqueous solutions and it should be conjugated with recognition elements capable of ensuring an efficient tagging of the BMs of interest. In this review we summarize the most relevant strategies used for surface modification of QDs and for their conjugation to BMs in preparation of their application in nanoplatforms for luminescent BM sensing and imaging-guided targeting. The applications of conjugations of photoluminescent QDs with different BMs in both in vitro and in vivo chemical sensing, immunoassays or luminescence imaging are reviewed. Recent progress in the application of functionalized QDs in ultrasensitive detection in bioanalysis, diagnostics and imaging strategies are reported. Finally, some key future research goals in the progress of bioconjugation of QDs for diagnosis are identified, including novel synthetic approaches, the need for exhaustive characterization of bioconjugates and the design of signal amplification schemes.

An enzyme-free electrochemical sandwich DNA assay based on the use of hybridization chain reaction and gold nanoparticles: application to the determination of the DNA of Helicobacter pylori

An ultrasensitive enzyme-free electrochemical sandwich DNA biosensor is described for the detection of ssDNA oligonucleotides. A DNA sequence derived from the genom of Helicobacter pylori was selected as a model target DNA. The DNA assay was realized through catching target DNA on capture DNA immobilized gold electrode; then labeling the target DNA with reporter DNA (rpDNA) and initiator DNA (iDNA) co-modified gold nanoparticles (AuNPs). The high density of iDNAs serves as one of the amplification strategies. The iDNA triggers hybridization chain reaction (HCR) between two hairpins. This leads to the formation of a long dsDNA concatamer strand and represents one amplification strategy. The electrochemical probe [Ru(NH₃)₅L]²⁺, where L stands for 3-(2-phenanthren-9-ylvinyl)pyridine, intercalated into dsDNA chain. Multiple probe molecules intercalate into one dsDNA chain, serving as one amplification strategy. The electrode was subjected to differential pulse voltammetry for signal acquisition, and the oxidation peak current at -0.28 V was recorded. On each AuNP, 240 iDNA and 25 rpDNA molecules were immobilized. Successful execution of HCR at the DNA-modified AuNPs was confirmed by gel electrophoresis and hydrodynamic diameter measurements. Introduction of HCR significantly enhances the DNA detection signal intensity. The assay has two linear ranges of different slopes, one from 0.01 fM to 0.5 fM; and one from 1 fM to 100 fM. The detection limit is as low as 0.68 aM. Single mismatch DNA can be differentiated from the fully complementary DNA. Conceivably, this highly sensitive and selective assay provides a general method for detection of various kinds of DNA. Graphical abstractSchematic representation of the detection and the amplification principles of the electrochemical sandwich DNA assay. Purple curl: Captured DNA; Green curl: Reporter DNA; Orange curl: HCR initiator DNA; Yellow solid-circle: Gold nanoparticle; H1 and H2: Two hairpin DNA; [Ru(NH₃)₅L]²⁺: Signal probe.

Graphene oxide and enzyme-assisted dual-cycling amplification method for sensitive fluorometric determination of DNA

A fluorometric method is described for the determination of DNA. It involves the use of graphene oxide (GO), exonuclease III (Exo III), and two specially designed fluorophore-labeled hairpin probes (HP1 and HP2). Different from other GO-based DNA assays, the method takes advantage of the distinct binding abilities of GO with hairpin DNA probes and single nucleotides. GO serves as a strong quencher for fluorescent labels to ensure a very low background signal. Two reaction cycles mediated by Exo III are employed to enhance the signals. The combination of GO-induced quenching and Exo III-mediated dual regeneration of analytes leads to a detection limit as low as 1 pM for the model analyte human hemochromatosis protein (HFE) gene. The method is also applicable for the determination of HFE gene spiked into fetal bovine serum. Graphical abstract Schematic representation of a GO-based, Exo III-assisted method for dual-signal amplified detection of DNA, for which human haemochromatosis protein (HFE) gene is designed as the model target. The assay involves graphene oxide (GO), exonuclease (Exo III), and two specially designed, fluorophore-labelled hairpin probes (HP1 and HP2).

DNA-programming multicolor silver nanoclusters for sensitively simultaneous detection of two HIV DNAs

A novel DNA-stabilized silver nanoclusters (AgNCs)-based label-free fluorescent platform for simultaneously detecting two human immunodeficiency virus oligonucleotides (HIV DNAs) was developed. The sensing platform was established based on fluorescence enhancement of guanine (G)-rich and the phenomenon in the process of two silver nanoclusters (AgNCs) forming a nanoclusters dimer. The probe (AgNCs/G) utilized for HIV-1 detection adopted an effective conformation based on enhancement effect of G-rich sequence (at 500 nm ex / 565 nm em) while the probe (AgNCs/AgNCs) for HIV-2 generated fluorescence signals (at 580 nm ex / 630 nm em) with bright fluorescence only in nanoclusters dimer. The nanoprobe shows high selectivity for multiplexed analysis of target DNA with a detection limit of 11 pM, respectively. Moreover, this is the first time to use the affectivity of fluorescent AgNCs and two HIV DNAs simultaneous detection integrated into a novel method, which shows a great promise in biomedical research and early clinical diagnosis.

Enrichment-Stowage-Cycle Strategy for Ultrasensitive Electrochemiluminescent Detection of HIV-DNA with Wide Dynamic Range

Sensitive detection of human immunodeficiency virus DNA (HIV-DNA) is essential for timely diagnosis and cure of the illness. Herein, a novel "enrichment-stowage-cycle" strategy was proposed to fabricate a multiple amplified electrochemiluminecence (ECL) biosensor for HIV-DNA detection. On the basis of the enrichment role of magnetic nanobeads, assembly role of copolymer nanospheres and strand displacement amplification (SDA), the processes were named as "enrichment", "stowage", and "cycle", respectively. The method employed electrochemiluminescent nanospheres (ENs) as signal labels by assembling three layers of CdSe/ZnS quantum dots (QDs) onto the surface of copolymer nanospheres. Compared to QDs, the same concentration of ENs can the enhance the ECL intensity by about 11.3-fold. SDA could further amplify the signals by about 3.77-fold, possessing high sensitivity for low-abundant biomarkers detection. The integration of magnetic separation improved detection specificity and stability, making the method possible for practical application. On the basis of magnetic separation, ENs and SDA, the ECL biosensor realized ultrasensitive detection of 39.81 fM HIV-DNA, which was more sensitive than other HIV-DNA analytical methods, with a wide dynamic range of 0.05 pM to 50 nM. The successful detection of HIV-DNA in complex samples with good sensitivity and accuracy indicated its potential utilization in early judgment of diseases and fabrication of signal amplification platforms.

HIV biosensors for early diagnosis of infection: The intertwine of nanotechnology with sensing strategies

Human immunodeficiency virus (HIV) is a lentivirus that leads to acquired immunodeficiency syndrome (AIDS). With increasing awareness of AIDS emerging as a global public health threat, different HIV testing kits have been developed to detect antibodies (Ab) directed toward different parts of HIV. A great limitation of these tests is that they can not detect HIV antibodies during early virus infection. Therefore, to overcome this challenge, a wide range of biosensors have been developed for early diagnosis of HIV infection. A significant amount of these studies have been focused on the application of nanomaterials for improving the sensitivity and accuracy of the sensing methods. Following an introduction into this field, a first section of this review covers the synthesis and applicability of such nanomaterials as metal nanoparticles (NPs), quantum dots (QDs), carbon-based nanomaterials and metal nanoclusters (NCs). A second larger section covers the latest developments concerning nanomaterial-based biosensors for HIV diagnosis, with paying a special attention to the determination of CD4⁺ cells as a hall mark of HIV infection, HIV gene, HIV p24 core protein, HIV p17 peptide, HIV-1 virus-like particles (VLPs) and HIV related enzymes, particularly those that are passed on from the virus to the CD⁴⁺ T lymphocytes and are necessary for viral reproduction within the host cell. These studies are described in detail along with their diverse principles/mechanisms (e.g. electrochemistry, fluorescence, electromagnetic-piezoelectric, surface plasmon resonance (SPR), surface enhanced Raman spectroscopy (SERS) and colorimetry). Despite the significant progress in HIV biosensing in the last years, there is a great need for the development of point-of-care (POC) technologies which are affordable, robust, easy to use, portable, and possessing sufficient quantitative accuracy to enable clinical decision making. In the final section, the focus is on the portable sensing devices as a new standard of POC and personalized diagnostics.

Lateral and Vertical Flow Assays for Point-of-Care Diagnostics

Lateral flow assays (LFAs) have been the pillar of rapid point-of-care (POC) diagnostics due to their simplicity, rapid process, and low cost. Recent advances in sensitivity, selectivity, and chemical stability enhancement have ensured the foothold of LFAs in commercial POC diagnostics. This paper reviews recent developments in labeling strategies and detection methods of LFAs. Moreover, vertical flow assays (VFAs) have emerged as an alternate paper-based assay due to faster detection time and unique multiplexing capabilities. Smartphones as LFA readers have been transformed into a universal integrated platform for imaging, data processing, and storage, providing quantitative results in low-resource settings. Commercial LFAs and VFAs products are evaluated with regards to their performance, market trends, and regulatory issues. The future outlook of the flow-based assays for POC diagnostics is also discussed.

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.

A graphene oxide-based paper chip integrated with the hybridization chain reaction for peanut and soybean allergen gene detection

Allergen genes of the peanut and soybean were selected as model targets. Four hairpin DNA probes, H1, H2, H3, H4 were designed. Cy3-labeled H1 and H2 were used to detect peanut DNA, while FAM-labeled H3 and H4 were used to detect soybean DNA. Graphene oxide (GO) was used as the adsorption material for capturing the hairpin probes, and as a selective fluorescence quencher to reduce the background signal. To develop an allergen gene detection system with a GO-based paper chip format, we integrated the hybridization chain reaction (HCR) with fluorescence resonance energy transfer (FRET) in our design. The results showed that in the absence of peanut DNA (TP) and soybean DNA (TS), the detection probes attached to the GO surface, which quenched their fluorescence. In the presence of TP or TS, however, complementary probe binding to the targets initiated HCR, producing long double-stranded DNA products that could not be absorbed onto the GO surface. Hence, a strong red or green fluorescent signal was generated. The detection limit for both peanut and soybean DNA was 1 nM using this method, indicating the high sensitivity of our approach. This method also exhibited good specificity and a single chip could be used to simultaneously detect two different targets.

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.

A label-free and double recognition-amplification novel strategy for sensitive and accurate carcinoembryonic antigen assay

Herein, a label-free and double recognition-amplification (LDRA) strategy for carcinoembryonic antigen (CEA) detection was developed, based on a new designed dual-function messenger probe (DMP) coalescing with DNA tetrahedron probes (DTPs) and hybridization chain reaction (HCR). The DMP possess dual-function to replace CEA for specific interface hybridization and initiate hybridization chain reaction. The interfacial hybridization event was quantitatively converted to an electrochemical signal by using hemin/G-quadruplex (h-Gx) formed after the hybridization chain reaction. Self-assembled DNA tetrahedron probes, which were readily decorated on an electrode surface as a scaffold with rigid support and ordered orientation, enabled the highly efficient strands hybridization and greatly increased target accessibility as well as significantly decreased noise. The proposed assay integrated dual recognition processes and HCR signal amplification processes, achieving the identification of low concentration of CEA as detection limit of 18.2 fg mL^-1 (S/N = 3) and wider linearity range of 0.0001 ng mL^-1-50 ng mL^-1. A new electrochemical sensing method was proposed for CEA detection and used in real clinical samples. The obtained results were good consistency with those of clinical diagnosis.

Solution of Equations Based on Analog DNA Strand Displacement Circuits

Deoxyribonucleic acid (DNA) strand displacement can be used to build complex functional circuits due to its highly modular and programmable properties. While DNA strand displacement is most often used to solve logic problems, it can also be used to compute the roots of equations. In this paper, we present the design of novel architectures for catalysis, degradation, and annihilation in ideal formal reaction modules, and we translate these reaction modules to DNA networks. These ideal formal or DNA reaction modules are suitable for building analog circuits for solving tasks. The computing analog DNA circuits are assessed by solving a linear equation, a one-variable quadratic equation, and a set of two simultaneous linear equations. The results were evaluated by simulation.

Visual detection of Fusarium proliferatum based on asymmetric recombinase polymerase amplification and hemin/G-quadruplex DNAzyme

A one-step and instrument-free visual method was established based on asymmetric recombinase polymerase amplification coupled with hemin/G-quadruplex DNAzyme for the detection of Fusarium proliferatum.

Asymmetric recombinase polymerase amplification and hemin/G-quadruplex DNAzyme-based visual detection of F. proliferatum is demonstrated.

Rapid Detection of Severe Fever with Thrombocytopenia Syndrome Virus via Colloidal Gold Immunochromatography Assay

To develop the point-of-care testing method to facilitate the clinical detection of severe fever with thrombocytopenia syndrome virus (SFTSV), colloidal gold paper-based lateral flow immunochromatography test strips (LFITSs) have been fabricated for the rapid detection for the first time. The pH value and the amount of monoclonal antibody to prepare colloidal gold nanoparticle-labeled monoclonal antibody bioconjugates were optimized. In addition, 0.4% bovine serum albumin was considered to be the best concentration for blocking nitrocellulose membranes. Under optimal conditions, the limit of detection for SFTSV was as low as 1 ng/mL depending on a visual line. Meanwhile, the entire detection process required no more than 10 min with a volume of only 50 μL of the analyte solution. Moreover, paper-based LFITSs were evaluated in real samples of human serum of patients with satisfactory results. In addition, all strips were of high stability and specificity. In the light of advantages such as simple, portable, rapid, and low cost, the developed LFITSs will extensively come into service, especially in remote areas.

Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection

Antibiotics are a type of antimicrobial drug with the ubiquitous presence in foodstuff that effectively applied to treat the diseases and promote the animal growth worldwide. Chloramphenicol as one of the antibiotics with the broad action spectrum against Gram-positive and Gram-negative bacteria is widely applied for the effective treatment of infectious diseases in humans and animals. Unfortunately, the serious side effects of chloramphenicol, such as aplastic anemia, kidney damage, nausea, and diarrhea restrict its application in foodstuff and biomedical fields. Development of the sufficiently sensitive methods to detect chloramphenicol residues in food and clinical diagnosis seems to be an essential demand. Biosensors have been introduced as the promising tools to overcome the requirement. As one of the newest types of the biosensors, aptamer-based biosensors (aptasensors) are the efficient sensing platforms for the chloramphenicol monitoring. In the present review, we summarize the recent achievements of the accessible aptasensors for qualitative detection and quantitative determination of chloramphenicol as a candidate of the antibiotics. The present chloramphenicol aptasensors can be classified in two main optical and electrochemical categories. Also, the other formats of the aptasensing assays like the high performance liquid chromatography (HPLC) and microchip electrophoresis (MCE) have been reviewed. The enormous interest in utilizing the diverse nanomaterials is also highlighted in the fabrication of the chloramphenicol aptasensors. Finally, some results are presented based on the advantages and disadvantages of the studied aptasensors to achieve a promising perspective for designing the novel antibiotics test kits.