Mercury detection based on label-free and isothermal enzyme-free amplified fluorescence platform

Ultrasensitive Electrochemiluminescence Biosensor Based on DNA-Bio-Bar-Code and Hybridization Chain Reaction Dual Signal Amplification for Exosomes Detection

Exosomes have received considerable attention as potent reference markers for the diagnosis of various neoplasms due to their close and direct relationship with the proliferation, adhesion, and migration of tumor. The ultrasensitive detection of cancer-derived low-abundance exosomes is imperative, but still a great challenge. Herein, we report an electrochemiluminescence (ECL) biosensor based on the DNA-bio-bar-code and hybridization chain reaction (HCR)-mediated dual signal amplification for the ultrasensitive detection of cancer-derived exosomes. In this system, two types of aptamers were modified on the magnetic nanoprobe (MNPs) and gold nanoparticles (AuNPs) with numerous bio-bar-code DNA, respectively, which formed "sandwich" structures in the presence of specific target exosomes. The "sandwich" structures were separated under magnetic field, and the numerous bio-bar-code DNA were released by dissolving AuNPs. The released bio-bar-code DNA triggered the HCR procedure to produce a good deal of long DNA duplex structure for embedding in hemin, which generated strong ECL signal in the presence of coreactors for ultrasensitive detection of exosomes. Under the optimal conditions, it exhibited a good linearly of exosomes ranging from 10 to 104 exosomes particle μL-1 with limit of detection down to 5.01 exosome particle μL-1. Furthermore, the high ratio of ECL signal and minor change of ECL intensity indicated the good specificity, stability, and repeatability of this ECL biosensor. Given the good performance for exosome analysis, this ultrasensitive ECL biosensor has a promising application in the clinical diagnosis of early cancers.

Detection of Streptavidin Based on Terminal Protection and Cationic Conjugated Polymer-Mediated Fluorescence Resonance Energy Transfer

In this paper, a fast and simple strategy for sensitive detection of streptavidin (SA) was proposed based on terminal protection of small molecule-linked DNA and cationic conjugated polymer-mediated fluorescence resonance energy transfer (FRET). In principle, we designed a biotin-labelled DNA probe (P1) as the recognitive probe of SA, along with a complementary DNA probe (P2) to form double-stranded DNA (dsDNA) with P1. SYBR Green I (SG I) as a fluorescent dye was further used to specifically bind to dsDNA to emit stronger fluorescence. The cationic poly[(9,9-bis(6′-N,N,N-triethy-lammonium)hexyl) fluorenylene phenylene dibromide] (PFP) acted as the donor to participate in the FRET and transfer energy to the recipient SG I. In the absence of SA, P1 could not hybridize with P2 to form dsDNA and was digested by exonuclease I (Exo I); thus, only a weak FRET signal would be observed. In the presence of SA, biotin could specifically bind to SA, which protected P1 from Exo I cleavage. Then, P1 and P2 were hybridized into dsDNA. Therefore, the addition of SG I and PFP led to obvious FRET signal due to strong electrostatic interactions. Then, SA can be quantitatively detected by monitoring FRET changes. As the whole reagent reaction was carried out in 1.5 mL EP and detected in the colorimetric dish, the operation process of the detection system was relatively simple. The response time for each step was also relatively short. In this detection system, the linear equation was obtained for SA from 0.1 to 20 nM with a low detection limit of 0.068 nM (S/N = 3). In addition, this strategy has also achieved satisfactory results in the application of biological samples, which reveals the application prospect of this method in the future.

Detection of coralyne and heparin by polymerase extension reaction using SYBR Green I

Polydeoxyadenosine (poly (dA)) has been extensively applied for detecting many drug molecules. Herein, we developed a sensitive method for detecting coralyne and heparin using a modified DNA probe with poly (dA) at one end. In the absence of coralyne, the DNA probe was digested by the Exonuclease I (Exo I), and therefore the SYBR Green I (SG I) emitted an extremely low fluorescent signal. While coralyne specifically binding to poly (dA) with strong propensity could remarkably restrain the disintegration of the DNA probe, through which as a template the second strand of DNA sequence was formed with the introduction of DNA polymerase. Therefore, the fluorescent signal of SG I was intensified to quantify coralyne. Based on this method, heparin can be determined due to its strong affinity towards coralyne. This method showed a linear range from 2 to 500 nM for coralyne with a low detection limit of 0.98 nM, and the linear range of heparin was from 1 to 100 nM when 1.25 nm was the detection limit. The proposed method was also implemented successfully in biological samples and showed a potential application for screening potential therapeutic molecules.

Exonuclease III-assisted fluorometric aptasensor for the carcinoembryonic antigen using graphene oxide and 2-aminopurine

A reliable fluorometric assay is described for the determination carcinoembryonic antigen (CEA) using exonuclease III (Exo III) and a 2-aminopurine binding aptamer. In the absence of CEA, dsDNA is degraded by Exo III, and free 2-AP (which has a blue fluorescence with excitation/emission maxima of 310/365 nm) is released. Strong fluorescence is generated after addition of graphene oxide (GO) to the solution. However, the 2-AP modified DNA (T2) cannot be degraded in the presence of CEA by Exo III due to the interaction between CEA and aptamer T1. Hence, only weak fluorescence can be detected after addition of GO. In this system, CEA can be quantified in the 0.05 - 2 ng·mL^-1 concentration range with a detection limit of 30 pg·mL^-1 (at S/N = 3). The method was successfully applied to analyze serum samples for CEA. Graphical Abstract An exonuclease III-assisted fluorometric aptasensor has been developed for the detection of carcinoembryonic antigen using graphene oxide and 2-aminopurine.

A visual and sensitive Hg2+ detection strategy based on split DNAzyme amplification and peroxidase-like activity of hemin-graphene composites

A visual and sensitive Hg²⁺ detection strategy was developed based on split DNAzyme amplification and hemin-graphene oxide composites (H-GNs). Two split DNAzyme sequences can form two entire enzyme-strands DNA (E-DNA) by T-Hg²⁺-T interaction. The E-DNA can bind with the loop of molecular beacon (MB) to form Mg²⁺-dependent DNAzyme structure. The formed DNAzyme can circularly cleave the loop of MB, resulting large amount of DNA fragments. The resultant DNA fragments can prevent H-GNs from aggregation by adsorbing on its surface. Consequently, the supernate with large amount of H-GNs shows dark blue color after chromogenic reaction. This strategy shows a linear range from 50 pM to 1200 pM. The limit detection can be low to 33 pM. This strategy provides a visual and enzyme-free amplification mode for quick and sensitive screen of Hg²⁺.

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.

Branch-Migration Based Fluorescent Probe for Highly Sensitive Detection of Mercury

Detection of heavy metals is of great importance for food safety and environmental analysis. Among various heavy metal ions, mercury ion is one of the most prevalent species. The methods for detection of mercury were numerous, and the T-Hg-T based assay was promising due to its simplicity and compatibility. However, traditional T-Hg-T based methods mainly relied on multiple T-Hg-T to produce enough conformational changes for further detection, which greatly restrained the limit of detection. Hence, we established a branch-migration based fluorescent probe and found that single T-Hg-T could produce strong signals. The sensing mechanism of our method in different reaction modes was explored, and the detection limits were determined to be 18.4 and 14.7 nM in first-order reaction mode and mixed reaction mode, respectively. Moreover, coupled with Endonuclease IV assisted signal amplification, the detection limit could be 1.2 nM, lower than most DNA based fluorometric assays. For practicability, the specificity of our assay toward different interfering ions was investigated and detection of Hg²⁺ in deionized water and lake water was also achieved with similar recoveries compared to those of atomic fluorescence spectrometry, which demonstrated the practicability of our method in real samples. Definitely, the proposed branch migration probe would be a promising substitution for current DNA probes based on recognition of multiple T-Hg-T and we anticipate it to be widely adopted in food and environmental analysis.

The detection of mercury ion using DNA as sensors based on fluorescence resonance energy transfer

Mercury ion (Hg²⁺) is a heavy metal that can cause serious water pollution. With the accumulation of large quantities in lakes, rivers, freshwater and aquatic life, Hg²⁺ can pass through the food chain, entering the human body and endangering health. Hg²⁺ detection has therefore become important thereby attracting extensive interests. Currently, several DNA-based sensors have been used for Hg²⁺ detection because they are not easy to degrade and are very stable. This paper summarizes the application of some DNA-based sensors based on fluorescence resonance energy transfer (FRET), analyzes their characteristic, and compares their sensitivity. Future perspectives and possible challenges in this area are also outlined.

Highly fluorescent carbon quantum dots as nanoprobes for sensitive and selective determination of mercury (II) in surface waters

A novel carbon quantum dots (CQDs) was successfully prepared through one-step green hydrothermal method using polyacrylamide as carbon source. The prepared CQDs were characterized using TEM, XRD, XPS, FT-IR, UV-Vis, and fluorescence spectroscopy. The CQDs was demonstrated as nanoprobes for mercury ion detection, moreover, it demonstrated excitation-dependent and superior stability in acidic and alkaline media. Besides, the probe exhibited a good linearity range (0.25-50μM) and a low detection limit (13.48nM). These attractive properties indicated that this novel CQDs can adapt to a variety of complex pH environment, which had extensive prospect and promising application for detection of mercury ions in complex water samples.