A label-free colorimetric isothermal cascade amplification for the detection of disease-related nucleic acids based on double-hairpin molecular beacon

Label-free fluorescent aptasensor for chloramphenicol based on hybridization chain reaction amplification and G-quadruplex/N-methyl mesoporphyrin IX complexation

The use of the broad-spectrum antibiotic chloramphenicol (CAP) in food is strictly regulated or banned in many countries. Herein, for the sensitive, rapid, and specific detection of CAP in milk, a label-free fluorescence strategy was established based on guanine (G)-quadruplex/N-methyl mesoporphyrin IX (NMM) complex formation and hybridization chain reaction (HCR) amplification. In this system, CAP can specifically bind to an aptamer (Apt) to release an Apt-C sequence from double-stranded DNA (Apt·Apt-C). Apt-C, can further hybridize with a functional hairpin DNA probe to release a primer sequence. The released primer sequence causes HCR and the formation of a nicked double-helix polymer, which contains G-quadruplex DNA. The recognition of G-quadruplex DNA by the NMM fluorochrome results in fluorescence enhancement. Consequently, CAP can be quantitatively detected by measuring the fluorescence intensity at 612 nm. The reliability of the aptasensor method was confirmed by comparison with an enzyme-linked immunosorbent assay. The proposed aptasensor was found to have a limit of detection of 0.8 pg mL⁻¹ for CAP. Moreover, when the aptasensor was applied to the detection of CAP in milk samples, the average recoveries were 99.8–108.3% with relative standard deviations of 4.5–5.2%. Thus, this CAP detection method, which is rapid with high sensitivity and selectivity, has considerable potential for a wide range of food analysis applications.

For the sensitive and specific detection of CAP in milk, a label-free fluorescence strategy was established based on guanine (G)-quadruplex/N-methyl mesoporphyrin IX (NMM) complex formation and hybridization chain reaction (HCR) amplification.

Construction of a CRISPR-Biolayer Interferometry Platform for Real-Time, Sensitive, and Specific DNA Detection

The clustered regularly interspaced short palindromic repeats (CRISPR) technology has been widely applied for nucleic acid detection because of its high specificity. By using the highly specific and irreversible bond between HaloTag and its alkane chlorine ligand, we modified dCas9 (deactivated CRISPR/Cas9) with biotin as a biosensor to detect nucleic acids. The CRISPR biosensor was facilely prepared to adequately maintain its DNA-recognition capability. Furthermore, by coupling biolayer interferometry (BLI) with the CRISPR biosensor, a real-time, sensitive, and rapid digital system called CRISPR-BLI was established for the detection of double-stranded DNA. The CRISPR biosensor immobilised on the biolayer could recruit the target DNA onto the biosensor surface and change its optical thickness, resulting in a shift in the interference pattern and responding signal of the BLI. The CRISPR-BLI system was further applied to detect the ALP gene of Escherichia coli DH5α combined with a polymerase chain reaction, which demonstrated a linear range from 20 to 20 000 pg and a low detection limit (1.34 pg). The CRISPR-BLI system is a promising approach for rapid and sensitive detection of target DNA analytes.

Highly sensitive fluorescence biosensing of BCR-ABL1 fusion gene based on exponential transcription-triggered hemin catalysis

Simple, sensitive and specific detection of the transcription level of BCR-ABL1 mRNA possesses vital clinical significance in diagnosis and treatment of chronic myeloid leukemia (CML). In this study, an innovative fluorescence biosensing methodology has been developed for sensitive and specific detection of BCR-ABL1 mRNA by integrating high-efficiency of exponential transcription and superior catalytic performance of DNA-grafted hemin. Exponential transcription was triggered by BCR-ABL1 mRNA to produce plenty of RNA products. They can specifically hybridize with circular dual-labeled hemin (DLH) probe to dissociate the intramolecular hemin dimmers into highly active hemin monomers for catalyzing fluorescence substrate tyramine. This exponential transcription-triggered hemin catalysis (ET-HC) strategy showed highly sensitive and specific for BCR-ABL1 detection with a limit of detection at 0.5 aM and a good linear range from 2 aM to 200 fM. This method was successfully applied to directly detect as low as 0.001% e13a2 transcript isoforms from complex genomic RNA extraction. Compared with clinical routine, the overall process is a thermostatic reaction and eliminates additional reverse transcription operation. Therefore, the developed ET-HC strategy might provide a promising alternative tool for precise diagnosis and personalized treatment of CML.

A sensitive fluorometric sensor for Ag+ based on the hybridization chain reaction coupled with a glucose oxidase dual-signal amplification strategy

In this work, an efficient and sensitive fluorometric sensor was developed to detect silver ions (Ag⁺). It is based on the cytosine–Ag⁺–cytosine (C–Ag⁺–C) structure via a dual-signal amplification strategy using glucose oxidase (GOx) and the hybridization chain reaction (HCR). A silver-coated glass slide (SCGS) acts as an ideal material for separation. Cytosine rich (C-rich) capture DNA (C-DNA) assembled themselves on the SCGS via Ag–S bonds and hybridized with signal DNA (S-DNA) to trigger the HCR. With specific base-pairing, the S-DNA and HCR products bind on the SCGS. Then, the GOx–biotin–streptavidin (SA) complexes bind to the HCR products through SA–biotin interactions. Owing to the formation of a particular C–Ag⁺–C structure between two neighboring C-rich C-DNA on the SCGS, the C-DNA/S-DNA/HP1-GOx/HP2-GOx complex gradually moved away from the SCGS as the concentration of Ag⁺ increased and the combined GOx fell into the buffer. H₂O₂ could be generated during the oxidation of glucose, catalyzed by GOx in the buffer. Afterward, H₂O₂ could oxidize the substrate (3-(p-hydroxyphenyl)-propanoic acid) when Horseradish peroxidase was present, giving rise to blue fluorescence. The proposed strategy reached a limit of detection (LOD) of 1.8 pmol L⁻¹ with a linear detection range of 5 to 1000 pmol L⁻¹ for Ag⁺. Moreover, this assay has been commendably used for the detection of Ag⁺ in actual samples with fairly good results.

An assay for Ag⁺ based on a C–Ag⁺–C structure by utilizing a HCR/GOx dual-signal amplification strategy and SCGS as an ideal separation material.

Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor

Most methods for the detection of nucleic acids require many reagents and expensive and bulky instrumentation. Here, we report the development and testing of a graphene-based field-effect transistor that uses clustered regularly interspaced short palindromic repeats (CRISPR) technology to enable the digital detection of a target sequence within intact genomic material. Termed CRISPR-Chip, the biosensor uses the gene-targeting capacity of catalytically deactivated CRISPR-associated protein 9 (Cas9) complexed with a specific single-guide RNA and immobilized on the transistor to yield a label-free nucleic-acid-testing device whose output signal can be measured with a simple handheld reader. We used CRISPR-Chip to analyse DNA samples collected from HEK293T cell lines expressing blue fluorescent protein, and clinical samples of DNA with two distinct mutations at exons commonly deleted in individuals with Duchenne muscular dystrophy. In the presence of genomic DNA containing the target gene, CRISPR-Chip generates, within 15 min, with a sensitivity of 1.7 fM and without the need for amplification, a significant enhancement in output signal relative to samples lacking the target sequence. CRISPR-Chip expands the applications of CRISPR-Cas9 technology to the on-chip electrical detection of nucleic acids.

Palindromic molecular beacon-based intramolecular strand-displacement amplification strategy for ultrasensitive detection of K-ras gene

The sensitive detection of tumor proto-oncogenes is indispensable because the early diagnosis and accurate treatment of genetic diseases is the key guarantee of patients' health. In this study, we proposed a novel palindromic molecular beacon (PMB) that it bases on the signal amplification strategy for ultrasensitive detection of Kras gene codon 12. PMB is designed to have two palindromic fragments at its two ends, one of which is locked via folding into a hairpin structure and the other promotes the formation of PMB duplex via intermolecular self-hybridization. Target DNA can hybridize to the loop portion of PMB and release the palindromic fragment at the 3' end. Within the PMB duplex, the two palindromic fragments released hybridize with each other and serve as polymerization primer responsible for the strand-displacement amplification (SDA). Namely, hybridized target DNA can be displaced and initiates the next round of reactions, making the polymerization/displacement/hybridization process go forward circularly. As a result, a large number of polymerization products are produced, dramatically enhancing optical signal. Because primer hybridization and polymerization-based displacement occur within PMB duplex, the reaction process is called intramolecular strand-displacement amplification (ISDA). Via utilizing the newly-proposed PMB-based ISDA strategy, the target K-ras gene could be detected down to 10 pM with a wide response range of 1 × 10^-11-1.5 × 10^-7 M, and point mutations are easily distinguished, realizing the ultrasensitive, highly selective detection of K-ras gene. This impressive sensing paradigm demonstrates a new concept of signal amplification for the detection of disease-related genes only via using a simple way to efficiently amplify optical signal.

Symmetric exponential amplification reaction-based DNA nanomachine for the fluorescent detection of nucleic acids

By introducing palindromic sequences into the classical exponential amplification reaction (EXPAR), we constructed a new palindromic fragment-incorporated multifunctional hairpin probe (P-HP)-mediated symmetric exponential amplification reaction (S-EXPAR), to significantly reduce the background signal caused by inherent nonspecific amplification. A G-triplex/ThT complex was used as the signal reporter for the proposed label-free DNA nanomachine. The P-HP consists of five functional regions: a C-rich region (C), a target DNA recognition region (T′), two nicking sites (X′) and a palindromic fragment (P). When target DNA (T) hybridizes with P-HP, the palindromic fragment at the 3′ end of P-HP is fully exposed. Then, the P-HP/T duplexes hybridize with each other through the exposed P, and EXPAR occurs automatically and continuously on both sides of P under the synergistic effect of polymerase and nicking endonuclease. This is called the S-EXPAR assay. In this system, one T converts to a large number of G-triplex fragments, which can combine with ThT within a short time. The G-triplex/ThT complexes formed act as the signal reporter in a label-free and environmentally friendly format. In this way, the limit of detection of this method is as low as 10 pM with a dynamic response range of 10 pM to 300 nM. In addition, this method can detect other nucleic acids by simply changing the T′ region of the P-HP. Thus, the proposed DNA nanomachine is a potential alternative method for nucleic acid detection.

This label-free and ultra-low background signal DNA nanomachine was based on P-HP mediated S-EXPAR and the G-triplex/ThT complex.

Inverted mirror image molecular beacon-based three concatenated logic gates to detect p53 tumor suppressor gene

Mutation of p53 tumor suppressor gene represents one of the early molecular events in tumor initiation and progression. Although molecular computing holds tremendous potential with important applications in diagnosis, prognosis and treatment of human diseases at the molecular level, designing molecular logic gates to implement cascade amplification via operating autonomously for the detection of point mutations still remains challenging. In this contribution, we developed a three concatenated logic gates (TCLG) to perform multiple strand displacement amplification (m-SDA) for screening the cancer-related point mutations only via designing an innovative molecular beacon (MB). Specifically, using p53 gene as model target, extending the two ends of a MB via adding two fragments with the same sequence achieves two unique terminal single-stranded (ss) overhangs. After self-folding of MB into hairpin structure, the two overhangs exhibit a near inverted mirror image (IM) relationship if taking the base nature and direction into account. For this, the probe is called IM-MB. Because cascade SDAs can occur on IM-MB and promote each other, the target gene can be detected down to 10 pM. Along this line, the TCLG circuit was proposed, and two primers and target gene serve as the indispensable input signals. Utilizing this logic circuit, the point mutation or absence of target gene can be sensitively screened. Moreover, its potential application in the recognition of point mutations in complex biomatrix has been demonstrated via blind test. The proof-of-concept scheme is expected to provide new insight into the development of DNA-based molecular logic gates and their applications in basic research, medical diagnosis and precise treatment and treatment of genetic diseases.

Development of small molecule biosensors by coupling the recognition of the bacterial allosteric transcription factor with isothermal strand displacement amplification

Here, we demonstrate an easy-to-implement and general biosensing strategy by coupling the small-molecule recognition of the bacterial allosteric transcription factor (aTF) with isothermal strand displacement amplification (SDA) in vitro. Based on this strategy, we developed two biosensors for the detection of an antiseptic, p-hydroxybenzoic acid, and a disease marker, uric acid, using bacterial aTF HosA and HucR, respectively, highlighting the great potential of this strategy for the development of small-molecule biosensors.