Exonuclease III-based target recycling for ultrasensitive homogeneous monitoring of HIV DNA using Ag(+)-coordinated hairpin probe

Exonuclease-based aptasensors: Promising for food safety and diagnostic aims

As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.

Isothermal nucleic acid amplification technology in HIV detection

Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.

Zettomole electrochemical HIV DNA detection using 2D DNA-Au nanowire structure, hemin/G-quadruplex and polymerase chain reaction multi-signal synergistic amplification

Multi-signal synergistically amplified electrochemical sensing of HIV DNA was proposed based on two-dimensional (2D) DNA-Au nanowire structure coupled with hemin/G-quadruplex and polymerase chain reaction (PCR). In the design, by using target HIV DNA as the template, PCR generated numbers of double-stranded DNA (dsDNA) with free single-stranded DNA (ssDNA) tails on one side and free G-quadruplex sequences on the other side. Then, the ssDNA tails of the PCR products were hybridized with the capture probe (CP) to introduce the hemin/G-quadruplex to the electrode surface as a redox-active reporter and to amplify the electrochemical signal as mimic peroxidase catalysis in the presence of H₂O₂. Meanwhile, (+)AuNPs were electrostatically adsorbed onto dsDNA surface for the formation of 2D DNA-Au nanowire structure, amplifying the electrochemical signal further as another mimic peroxidase and electric conductor together. By effectively combining these signal amplification processes, ultrasensitive HIV DNA detection was achieved with a detection limit of 1.3 aM, indicating that it has potential application in clinical diagnosis.

A visual detection of human immunodeficiency virus gene using ratiometric method enabled by phenol red and target-induced catalytic hairpin assembly

Relying on the specific coordination of Ag⁺ and mismatched cytosine-cytosine (C-C), the high-efficiency inhibition of urease by Ag⁺ ion, and the rapid and sensitive response of phenol red to pH, a sensitive ratiometric sensor has been designed for visual detection of human immunodeficiency virus gene (HIV DNA). This sensor utilizes the HIV DNA to initiate catalytic hairpin assembly (CHA) process, releasing Ag⁺ to inhibit subsequent urease-catalyzed urea hydrolysis and prevent the pH of the solution from rising. The CHA process and the absorbance ratio of phenol red at different wavelengths (A₅₅₉/A₄₃₂) amplify the signal, allowing the sensor to detect HIV DNA from 10 to 130 nM in a sensitive and highly selective manner with a low detection limit of 7.8 nM. In addition, this sensor can visually distinguish different concentrations of HIV DNA within a certain range and possesses a good recovery in 1% of serum samples, which will provide new ideas for biosensor design, dipstick test, blood test, and other clinical disease prevention.

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.

A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules

Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photoisomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.

Homogeneous and label-free electrochemiluminescence aptasensor based on the difference of electrostatic interaction and exonuclease-assisted target recycling amplification

The difference of electrostatic interaction between free Ru(phen)₃²⁺ and Ru(phen)₃²⁺ embedded in double strand DNA (dsDNA) to the negatively charged indium tin oxide (ITO) electrode has been applied to develop a homogeneous and label-free electrochemiluminescence (ECL) aptasensor for the first time. Ochratoxin A (OTA) has been chosen as the model target. The OTA aptamer is first hybridized with its complementary single strand DNA (ssDNA) to form dsDNA and then interacted with Ru(phen)₃²⁺ via the grooves binding mode to form dsDNA-Ru(phen)₃²⁺ complex, which remains negatively charged feature as well as low diffusion capacity to the negatively charged ITO electrode surface owing to the electrostatic repulsion. Meanwhile, the intercalated Ru(phen)₃²⁺ in the grooves of dsDNA works as an ECL signal reporter instead of the labor-intensive labeling steps and can generate much more ECL signal than that from the labeling probe. In the presence of target, the aptamer prefers to form an aptamer-target complex in lieu of dsDNA, which induces the releasing of Ru(phen)₃²⁺ from the dsDNA-Ru(phen)₃²⁺ complex into the solution. With the assistance of RecJ_f exonuclease (a ssDNA specific exonuclease), the released ssDNA and the aptamer in the target-complex were digested into mononucleotides. In the meantime, the target can be also liberated from OTA-aptamer complex and induce target cycling and large amount of free Ru(phen)₃²⁺ present in the solution. Since Ru(phen)₃²⁺ contains positive charges, which can diffuses easily to the ITO electrode surface because of electrostatic attraction, causing an obviously enhanced ECL signal detected. Under the optimal conditions, the enhanced ECL of the system has a linear relationship with the OTA concentration in the range of 0.01-1.0 ng/mL with a detection limit of 2 pg/mL. This innovative system not only expands the immobilization-free sensors in the electrochemiluminescent fields, but also can be developed for the detection of different targets easily with the same strategy by changing the aptamer used.

Cascaded multiple amplification strategy for ultrasensitive detection of HIV/HCV virus DNA

Ultrasensitive detection of HIV and HCV virus DNA is of great importance for early accurate diagnostics and therapy of HIV virus-infected patients. Herein, to our best knowledge, it is the first to use DNA cascaded multiple amplification strategy for ultrasensitive detection of HIV virus DNA with G-quadruplex-specific fluorescent or colorimetric probes as signal carriers. The developed strategy also exhibited universal applicability for HCV virus DNA detection. After reaction for about 4h, high sensitivity and specificity can be achieved at both fluorescent and colorimetric strategies (limit of detection (LOD) of 10 fM and 0.5pM were reached for fluorescent and colorimetric detection, respectively). And the single-based mismatched DNA even can be distinguished by naked eyes. It is believed that the cascaded multiple amplification strategy presents a huge advance in sensing platform and potential application in future clinical diagnosis.

Silver-functionalized g-C3N4 nanohybrids as signal-transduction tags for electrochemical immunoassay of human carbohydrate antigen 19-9

A simple and feasible electrochemical immunosensing platform was developed for highly efficient screening of a disease-related protein (human carbohydrate antigen 19-9, CA 19-9 used in this case) using silver-functionalized g-C3N4 nanosheets (Ag/g-C3N4) as signal-transduction tags. Initially, Ag/g-C3N4 nanohybrids were synthesized by combining thermal polymerization of the melamine precursor with the photo-assisted reduction method. Thereafter, the as-synthesized Ag/g-C3N4 nanohybrids were utilized for the labeling of the anti-CA 19-9 detection antibody by using a typical carbodiimide coupling method. The assay was carried out on a capture antibody-modified glassy carbon electrode in a sandwich-type detection mode. The detectable signal mainly derived from the voltammetric characteristics of the immobilized nanosilver particles on the g-C3N4 nanosheets within the applied potentials. Under the optimal conditions, the voltammetric peak currents increased with the increasing amount of target CA 19-9, and exhibited a wide linear range from 5.0 mU mL(-1) to 50 U mL(-1) with a detection limit of 1.2 mU mL(-1). Our strategy also displayed good reproducibility, precision and specificity. The results of the analysis of clinical serum specimens were in good accordance with the results obtained by an enzyme-linked immunosorbent assay (ELISA) method. The newly developed immunosensing system is promising for enzyme-free and cost-effective analysis of low-abundance proteins.

DNA tetrahedron and star trigon nanostructures for target recycling detection of nucleic acid

We develop an electrochemical method for the target recycling detection of nuclei acid by constructing DNA tetrahedron and star trigon nanostructures.

Homogeneous electrochemical detection of ochratoxin A in foodstuff using aptamer-graphene oxide nanosheets and DNase I-based target recycling reaction

A simple and feasible homogeneous electrochemical sensing protocol was developed for the detection of ochratoxin A (OTA) in foodstuff on the immobilization-free aptamer-graphene oxide nanosheets coupling with DNase I-based cycling signal amplification. Thionine-labeled OTA aptamers were attached to the surface of nanosheets because of the strong noncovalent binding of graphene oxide nanosheets with nucleobases and aromatic compounds. The electronic signal was acquired via negatively charged screen-printed carbon electrode (SPCE) toward free thionine molecules. Initially, the formed thionine-aptamer/graphene nanocomposites were suspended in the detection solution and far away from the electrode, thereby resulting in a weak electronic signal. Upon addition of target OTA, the analyte reacted with the aptamer and caused the dissociation of thionine-aptamer from the graphene oxide nanosheets. The newly formed thionine-aptamer/OTA could be readily cleaved by DNase I and released target OTA, which could retrigger thionine-aptamer/graphene nanocomposites with target recycling to generate numerous free thionine molecules. Free thionine molecules were captured by negatively charged SPCE, each of which could produce an electrochemical signal within the applied potentials. Under optimal conditions, graphene-based aptasensing platform could exhibit good electrochemical responses for the detection of OTA at a concentration as low as 5.6pg/mL. The reproducibility, precision and selectivity of the system were acceptable. Importantly, the method accuracy was comparable with commercialized OTA ELISA kit when using for quantitative monitoring of contaminated wheat samples.