Linear light-scattering of gold nanostars for versatile biosensing of nucleic acids and proteins using exonuclease III as biocatalyst to signal amplification

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

Redox-derivatization reaction-based rapid and sensitive determination of nitrite using resonance Rayleigh scattering method

It remains a problem for direct detection of small inorganic nitrite ions using resonance Rayleigh scattering (RRS) method based on the direct dye-binding reaction. In the present study, a redox-derivatization reaction taking only 5 min was introduced prior to nitrite detection. In the redox-derivatization reaction, nitrite ions were reduced by excess iodine ions to generate triiodide ions (I₃^-), which were further derivatized with a cationic dye (basic violet 1, BV1) to form the ion associates of I₃^--BV1. Therefore, the RRS signal was significantly enhanced, resulting from the increase of particle size and resonance-enhanced scattering effect. The analytical procedure was performed by just mixing nitrite, oxidant, acid, and dye all-in-one, avoiding the tediousness of a multi-step process or the preparation of nanoparticles. The whole detection process including the redox-derivatization reaction was less than 6 min. The reaction conditions such as concentration of hydrochloric acid, potassium iodide, and BV1, reaction time, and temperature were investigated. Under optimum conditions, the concentration of nitrite was linear with an RRS signal of I₃^--BV1 ion associates at 320 nm in the range of 0.015-1.2 mg/L. The limit of detection (LOD) was calculated to be 3.0 μg/L. The RRS method was applied to the determination of nitrite in real samples such as pork sausage, milk powder, and water with recovery of 95.2-112%. With advantages of rapidness, high sensitivity, and high selectivity, the method indicates potential applicability for detection of nitrite in complex samples. The method also provides an instructive protocol for detection of analytes that generate no/weak RRS enhancement after the direct dye-binding reaction. Graphical abstract.

Determination of the concentration of transcription factor by using exonuclease III-aided amplification and gold nanoparticle mediated fluorescence intensity: A new method for gene transcription related enzyme detection

Herein, we report a new probe for the determination of the concentration of NF-κB p50, one kind of DNA-binding transcription factors (TFs), by using Exonuclease III (Exo III)-aided amplification and gold nanoparticle mediated fluorescence intensity. Since TFs play critical roles in various biological processes, the detection of TFs can provide a lot of useful biological information for studding gene expression regulation related disease. In our system, in the presence of transcription factor, Exo III based amplification reaction was trigged. This enzymatic digestion results in the release of intermediate DNA and ultimately liberating the fluorophore (which, separated from the quencher of AuNP and BHQ2, now fluoresces). The released intermediate DNA then hybridizes with another strand3, whence the cycle starts anew. So, the fluorescence intensity reflects the NF-κB p50 concentration with a detection limit of 1.32 pM. Importantly, this method might be further extended to selectively detect various dsDNA-binding proteins by simply changing the binding-site sequences of strand1/strand2 duplex probes.

Sensitive detection of formamidopyrimidine-DNA glycosylase activity based on target-induced self-primed rolling circle amplification and magnetic nanoprobes

We developed a novel approach to determine formamidopyrimidine DNA glycosylase (FPG) activity by taking advantage of target-induced self-primed rolling circle amplification (RCA) and magnetic nanoprobes. Herein, a unique nick (8-oxoguanine, 8-oxoG) was positioned in duplex DNA containing P-circle and P1, which together serve as a FPG substrate, RCA template, and RCA primer probe. The presence of FPG specifically binds 8-oxoG and cleaves the P-circle into two parts, producing 5'-phosphoryl termini. A phosphodiester bond between the 5'-phosphoryl and 3'-hydroxyl termini was formed with the addition of T4 DNA ligase, producing an unnicked circular strand. Using the unnicked strand as the RCA template, the P1 hybridized with the circle probe as a primer will trigger the RCA process. The RCA reaction produces amounts of long tandem-repeat DNA tiles with multiple recognizing regions for the FAM modified DNA probes (FP) and biotin-modified DNA probes (BP). With the streptavidin-biotin interaction, the BPs and FPs can be easily immobilized on the surface of streptavidin-modified magnetic microbeads (MBs). Due to the RCA enhanced and highly-concentrated fluorescence accumulation on the MBs, an ultralow detection limit of 1.033 U mL-1 for FPG was obtained. Combined with the high tolerance capability of human blood serum owing to magnetic isolation, the FPG assays in human blood serum were also obtained using fluorescence and confocal laser scanning microscopy. These results indicate that this robust self-primed RCA combined with magnetic nanoprobes is an excellent candidate for quantitatively monitoring the FPG activity responsible for DNA oxidative damage-related clinical diagnosis and therapy.

Enzyme-free homogeneous electrochemical biosensor for DNA assay using toehold-triggered strand displacement reaction coupled with host-guest recognition of Fe3O4@SiO2@β-CD nanocomposites

Taking advantages of the toehold-triggered strand displacement reaction (TSDR) and host-guest interaction of β-cyclodextrin (β-CD), a facile enzyme-free and homogeneous electrochemical sensing strategy was designed for the sensitive assay of target DNA using Fe₃O₄@SiO₂@β-CD nanocomposites and ferrocene-labeled hairpin DNA (H-1) as the capture and electrochemical probes, respectively. Upon addition of target molecule, the initiated TSDR process induced the conformational change of H-1, and subsequently stimulated the dynamic assembly of assist probes (A-1 and A-2) to generate H-1:A-1:A-2 duplex along with the release of target sequence. The released target could drive the next TSDR recycling and finally result in the formation of numerous DNA duplex. After the molecular recognition of Fe₃O₄@SiO₂@β-CD nanocomposites, a large number of duplex were easily separated from the supernatant solution under an external magnetic field, which led to a decreased H-1 concentration in residual solution, concomitant with a remarkable reduction of peak current. Under the optimized conditions, wide linear range (1-5000 pM), low detection limit (0.3 pM), desirable reproducibility, good selectivity, and satisfactory practical analysis were obtained by the combination of the superior recognition capability of β-CD, TSDR-induced signal amplification, and homogeneous electroanalytical method. The proposed detection strategy could offer a universal approach for the monitoring of various biological analytes via the rational design of probe sequences.

Application of a cation-exchange reaction of CuS nanoparticles and fluorescent copper nanoparticles in a DNA biosensor

A novel detection method based on the cation-exchange reaction of CuS nanoparticles (CuS NPs) combined with poly T-templated fluorescent Cu nanoparticles (Cu NPs) was developed. First, CuS NPs-magnetic bead conjugates were prepared through the hybridization of DNA. Competition with target DNA resulted in the release of CuS NPs, and exonuclease III catalysis could lead to recycling of the target DNA. Then, the CuS NPs released into the supernatant were subjected to a cation-exchange reaction after the addition of AgNO₃. The obtained Cu²⁺ could form fluorescent Cu NPs using poly T DNA as a template. The fluorescence intensity of the Cu NPs could be used to determine the concentration of the target DNA. To further increase the detection sensitivity, two types of DNA decorated magnetic beads were used. After Exo III digestion for two cycle processes, more CuS NPs entered the supernatant. Hence, a stronger fluorescence intensity was found after the cation-exchange reaction and the formation of fluorescent Cu NPs. The developed method is convenient and low cost with good sensitivity and selectivity.

A novel detection method based on cation-exchange of CuS nanoparticles combined with poly T-templated fluorescent Cu nanoparticles was developed and applied to the exonuclease III catalyst DNA biosensor.

Rapid and label-free fluorescence bioassay for microRNA based on exonuclease III-assisted cycle amplification

A new assay for the rapid and simple detection of microRNA based on G-quadruplex and Exonuclease III (ExoIII) dual signal amplification was constructed.

Strategy for the detection of mercury ions by using exonuclease III-aided target recycling

A new method for the detection of Hg²⁺ by using an Exo III and G-quadruplex-based strategy was reported here.

Aptamer-initiated on-particle template-independent enzymatic polymerization (aptamer-OTEP) for electrochemical analysis of tumor biomarkers

Herein, an aptamer-initiated on-particle template-independent enzymatic polymerization (aptamer-OTEP) strategy for electrochemical aptasensor (E-aptasensor) is developed for analysis of cancer biomarker carcino-embryonic antigen (CEA). A pair of DNA aptamers is employed which can be specifically bond with CEA simultaneously. One of the aptamer is thiolated at 3'-terminal and immobilized onto the gold electrode as a capture probe, while the other one has a thiol group at its 5'-terminal and is modified onto the gold nanoparticles surface to form a nanoprobe. In the present of target, the two aptamers can "sandwich" the target, thus the nanoprobe is attached to the electrode. Then terminal deoxynucleotidyl transferase (TdT) is employed to catalyze the incorporation of biotin labeled dNTPs into the 3'-OH terminals of the DNA aptamer on the nanoprobe. The as-generated long DNA oligo tentacles allow specific binding of numerous avidin modified horseradish peroxidase (Av-HRP), resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide and sharply increasing electrochemical signals. Taking advantage of the enzyme based nucleic acid amplification and nanoprobe, this strategy is demonstrated to possess the outstanding amplification efficiency.

Gold nanoparticles as sensitive optical probes

Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.

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

A new homogeneous electrochemical sensing strategy based on exonuclease III-assisted target recycling amplification was utilized for simple, rapid and highly sensitive detection of human immunodeficiency virus (HIV) DNA on an immobilization-free Ag(I)-assisted hairpin DNA through the cytosine-Ag(+)-cytosine coordination chemistry. The assay involved target-induced strand-displacement reaction accompanying dissociation of the chelated Ag(+) in the hairpins and exonuclease III-triggered target recycling. Initially, the added target DNA hybridized with hairpin DNA to disrupt the Ag(I)-coordinated hairpin probe and releases the coordinated Ag(+) ion. Then, the newly formed DNA double-stranded DNA could be cleaved by exonuclease III, and released target HIV DNA, which retriggered the strand-displacement reaction with the hairpin for target recycling, thereby resulting in formation of numerous free Ag(+) ions in the detection cell. The released Ag(+) ions can be readily captured by the negatively charged electrode, and subsequent anodic-stripping voltammetric detection of the captured Ag(+) ions are conducted to form the anodic current for the production of the electronic signal within the applied potential. Under optimal conditions, the exonuclease III-based sensing system exhibited good electrochemical responses for the detection of HIV DNA at a concentration as low as 23 fM.