One-step colorimetric detection of an antibody based on protein-induced unfolding of a G-quadruplex switch

Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments

Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.

Development of DNA Biosensors Based on DNAzymes and Nucleases

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

Recent developments of nanoenzyme-based colorimetric sensors for heavy metal detection and the interaction mechanism

This work highlights the application and interaction mechanism of metal nanoparticles, metal oxides, metal sulfides, graphene-based nanomaterials and G-quadruplex, etc. in nanoenzyme-based colorimetric sensors.

Colorimetric detection of hydrogen peroxide and glucose by exploiting the peroxidase-like activity of papain

Papain, a natural plant protease that exists in the latex of Carica papaya, catalyzes the hydrolysis of peptide, ester and amide bonds. In this work, we found that papain displayed peroxidase-like activity and catalyzed the oxidation of 3,3',5',5'-tetramethylbenzidine (TMB) in the presence of H2O2. This results in the formation of a blue colored product with an absorption maximum at 652 nm. The effects of experimental parameters including pH and reaction temperature on catalytic activity of papain were investigated. The increase of absorbance induced by the catalytic effect of papain offers accurate detection of H2O2 in the range of 5.00-90.0 μM, along with a detection limit of 2.10 μM. A facile colorimetric method for glucose detection was also proposed by combining the glucose oxidase (GOx)-catalyzed glucose oxidation and papain-catalyzed TMB oxidation, which exhibited a linear response in the range of 0.05-0.50 mM with a detection limit of 0.025 mM. The method proposed here displayed excellent selectivity, indicating that common coexisting substances (urea, uric acid, ascorbic acid, maltose, lactose and fructose) in urine did not interfere with detection of glucose. More importantly, the suggested method was successfully used to precisely detect the glucose concentration in human urine samples with recoveries over 96.0%.

Proximity-induced hybridization chain assembly with small-molecule linked DNA for single-step amplified detection of antibodies

A novel and versatile platform for single-step amplified fluorescence detection of antibodies via specific proximity-induced hybridization chain assembly is developed.

A transparent paper-based platform for multiplexed bioassays by wavelength-dependent absorbance/transmittance

The present work describes the rational design of a paper-based biosensing platform for multi-target detection with low cost and high sensitivity by wavelength-dependent absorbance/transmittance.

A new colorimetric assay method for the detection of anti-hepatitis C virus antibody with high sensitivity

A sensitive colorimetric assay method has been proposed for the detection of antibody by specifically assembling tandemly repeated DNAzymes on its “Y”-shaped structure, which has been used to determine anti-HCV Ab in serum with high sensitivity.

Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure

A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2-) by H2O2 to generate green ABTS•- radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2-. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0-250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.

Affinity Binding-Induced Hg2+ Release and Quantum Dot Doping for General, Label-Free, and Homogenous Fluorescence Protein Assay

Herein, a general protein conversion and analysis strategy was developed for homogeneous, label-free, and sensitive protein detection, on the basis of the affinity binding-induced Hg²⁺ release for protein conversion, and the succeeding Hg²⁺ doping-induced ZnSe quantum dot (QD) photoluminescence for signal readout. Two DNA motifs were designed, each of which was conjugated with a protein-specific recognition ligand. The mercury ions were initially introduced into one DNA motif by T-Hg²⁺-T interaction. The Hg²⁺ releasing was then accomplished after protein recognition-initiated strand exchange reaction between two DNA motifs. Then, the simultaneous incorporation of the released Hg²⁺ into ZnSe QD resulted in a doping-dependent fluorescence emission at 560 nm correlated with protein analysis. The protein assay is outperformed only by a simple one-step mixing operation but no separation or washing steps. Also, the use of doped QD as a fluorogenic reporter can avoid the fluorophore and/or quencher labeling, and eliminate complex DNA manipulation procedures for signal readout or amplification involved in most existing nucleic acid-based protein conversion and analysis methods. The versatile and sensitive detection toward multivalent proteins was verified with the detection limits achieved at 0.034 nM for anti-Dig antibody, 0.012 nM for streptavidin, and 0.025 nM for thrombin. Thus, it shows great promise for protein analysis to accommodate the applications in disease diagnosis, biomarker screening, and clinical medicine.

Instrument-free visual detection of tetracycline on an autocatalytic DNA machine using a caged G-quadruplex as the signal reporter

An instrument-free visual biosensor for the amplified detection of tetracycline has been successfully constructed using an autocatalytic DNA machine as the signal amplifier and a caged G-quadruplex as the signal reporter. The assay is ultrasensitive, enabling the visual detection of trace levels of tetracycline as low as 1 pM without instrumentation.