DNAzyme-Based Target-Triggered Rolling-Circle Amplification for High Sensitivity Detection of microRNAs

An electrochemical biosensor utilizing CRISPR/Cas12a amplification for the detection of E. coli

Electrochemical biosensors are frequently employed to identify harmful microbes and disease indicators. However, their practical applicability is constrained by poor signal amplification efficiency and immobilization processes on the probe surface. To get over these restrictions, we here integrated roll-cycling amplification (RCA) and CRISPR/Cas12a gene editing tools with electrochemical biosensors. We constructed an electrochemical biosensor based on RCA to activate the cleavage activity of Cas12a. First, by double-stranded nucleic acid aptamer (ds Apt) specifically binding to E. coli-2571, Apt-b was competitively isolated to bind to T4 ligase and produce circular DNA. This in turn activates RCA, which in turn activates the accessory cleavage activity of CRISPR/Cas12a, which in turn cleaves DNA sequences loaded onto the electrode, changing electrochemical signals. With a linear range of 1 × 102-1 × 107 CFU mL-1, a detection limit of 5.28 CFU mL-1, and experimental recoveries of 93.01-101.53%, the measured electrochemical signals were positively connected with the concentration of E. coli-2571 under the optimal experimental conditions. Therefore, by combining two approaches-RCA and CRISPR/Cas12a-our electrochemical biosensor was able to detect E. coli-2571 specifically and sensitively, providing new research opportunities for the detection of other harmful bacteria.

Reversible Ratiometric Electrochemiluminescence Biosensor Based on DNAzyme Regulated Resonance Energy Transfer for Myocardial miRNA Detection

Myocardial miRNAs in peripheral blood are closely related to the pathogenic process of myocardial infarction. Rapid identification and accurate quantification of myocardial miRNAs are of great significance to clinical interventions for treating cardiovascular lesions. Therefore, a ratiometric electrochemiluminescence (ECL) biosensor integrating DNAzyme with a resonance energy transfer (RET) system was designed to detect myocardial miRNA. The dual-signal system was composed of rA marked substrate strand functionalized CdTe quantum dots (QDs) as reductive-oxidative (R-O) emitters and Cy5-labeled strand-functionalized Ru(bpy)₃²⁺-filled silica nanoparticles (RuSi NPs) as oxidative-reductive (O-R) emitters. In the presence of target miRNA, DNAzyme was activated to cut substrate strands on the CdTe QDs and release triggers for opening hairpin probes. Then, the Cy5 molecule-labeled hairpin DNA on the RuSi NPs was opened to introduce Cy5 molecules and RuSi NPs into the system. The R-O ECL was quenched by ECL-RET between CdTe QDs and Cy5 molecules and the O-R ECL was introduced by the RuSi NPs. In this way, based on the simultaneous changing of the ECL signal, the dual-potential dynamic signal ratiometric ECL sensing platform was developed. By measuring the ratio of O-R ECL signal to R-O ECL signal, the concentration of miRNA-499 was accurately quantified in the range of 10 fM to 10 nM, and the detection limit was as low as 2.44 fM (S/N = 3). This DNAzyme guided dual-potential ratiometric ECL method provides a sensitive and reliable method for myocardial miRNA detection, and it has great potential in clinical diagnosis and treatment.

Rolling Circle Amplification-based Copper Nanoparticle Synthesis on Cyclic Olefin Copolymer Substrate and Its Application in Aptasensor

This study aimed to develop a label-free fluorescent aptasensor for the detection of diazinon (DZN) on a cyclic olefin copolymer (COC) substrate. The aptasensor design was based on rolling circle amplification (RCA) technology and the use of self-assembled copper nanoparticles (CuNPs). A dual-function (DF) probe, capable of binding to circular DNA and an aptamer, was designed and immobilized on a COC-bottom 96-well plate. An aptamer was used for selective recognition of DZN, and the specific site of the aptamer that strongly reacted with DZN was successfully identified using circular dichroism (CD) analysis. In presence of DZN, the aptamer and DZN formed a strong complex, thus providing an opportunity for hybridization of the DF probe and circular DNA, thereby initiating an RCA reaction. Repetitive poly thymine (T) sequence with a length of 30-mer, generated in the RCA reaction, served as a template for the synthesis of fluorescent copper nanoparticles, emitting an orange fluorescence signal (at approximately 620 nm) proportional to the amount of RCA product, within 10 min under UV irradiation. The CuNP fluorescence was imaged and quantified using an image analysis software. A linear correlation of the fluorescence signal was confirmed in the DZN concentration range of 0.1–3 ppm, with a detection limit of 0.15 ppm. Adoption of a label-free detection method, utilizing RCA and fluorescent CuNPs on COC substrates, reduced the need for complex equipment and requirements for DZN analysis, thereby representing a simple and rapid sensing method circumventing the limitations of current complex and labor-intensive methods.

Chaperone Copolymer Assisted G-Quadruplex-Based Signal Amplification Assay for Highly Sensitive Detection of VEGF

Vascular endothelial growth factor (VEGF) is a critical biomarker in the angiogenesis of several cancers. Nowadays, novel approaches to rapid, sensitive, and reliable VEGF detection are urgently required for early cancer diagnosis. Cationic comb-type copolymer, poly(L-lysine)-graft-dextran (PLL-g-Dex) accelerates DNA hybridization and chain exchange reaction while stabilizing the DNA assembly structure. In this work, we examined the chaperone activity of PLL-g-Dex to assist G-quadruplex-based fluorescent DNA biosensors for sensitive detection of VEGF. This convenient and effective strategy is based on chitosan hydrogel, c-myc, Thioflavin T (ThT), VEGF aptamer, and its partially complementary strand. The results show that chaperone copolymer PLL-g-Dex significantly promotes the accumulation of G-quadruplex and assembles into G-wires, allowing an effective signal amplification. Using this method, the detection limit of VEGF was as low as 23 pM, better than many previous works on aptamer-based VEGF detection. This chaperone copolymer-assisted signal amplification strategy has potential applications in the highly sensitive detection of target proteins, even including viruses.

Single-Molecule Detection of Nucleic Acids via Liposome Signal Amplification in Mass Spectrometry

A single-molecule detection method was developed for nucleic acids based on mass spectrometry counting single liposome particles. Before the appearance of symptoms, a negligible amount of nucleic acids and biomarkers for the clinical diagnosis of the disease were already present. However, it is difficult to detect extremely low concentrations of nucleic acids using the current methods. Hence, the establishment of an ultra-sensitive nucleic acid detection technique is urgently needed. Herein, magnetic beads were used to capture target nucleic acids, and liposome particles were employed as mass tags for single-particle measurements. Liposomes were released from magnetic beads via photocatalytic cleavage. Hence, one DNA molecule corresponded to one liposome particle, which could be counted using mass spectrometric measurement. The ultrasensitive detection of DNA (10^-18 M) was achieved using this method.

Establishment and Application of Ligation Reaction-Based Method for Quantifying MicroR-156b

Microribonucleic acids (miRNAs) play significant roles in the regulation of biological processes and in responses to biotic or abiotic environmental stresses. Therefore, it is necessary to quantitatively detect miRNAs to understand these complicated biological regulation mechanisms. This study established an ultrasensitive and highly specific method for the quantitative detection of miRNAs using simple operations on the ground of the ligation reaction of ribonucleotide-modified deoxyribonucleic acid (DNA) probes. This method avoids the complex design of conventional reverse transcription. In the developed assay, the target miRNA miR156b was able to directly hybridize the two ribonucleotide-modified DNA probes, and amplification with universal primers was achieved following the ligation reaction. As a result, the target miRNA could be sensitively measured even at a detection limit as low as 0.0001 amol, and differences of only a single base could be detected between miR156 family members. Moreover, the proposed quantitative method demonstrated satisfactory results for overexpression-based genetically modified (GM) soybean. Ligation-based quantitative polymerase chain reaction (PCR) therefore has potential in investigating the biological functions of miRNAs, as well as in supervising activities regarding GM products or organisms.

Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection

The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.

The fluorescent probe-based recombinase-aided amplification for rapid detection of Escherichia coli O157:H7

Escherichia coli O157:H7 (E. coli O157:H7) is a common foodborne morbigenous microorganism, which can spread through fecal-oral transmission. Humans can be infected by ingesting foods and water contaminated with E. coli O157:H7, which can cause various symptoms. In present study, we have successfully developed a quick and hypersensitive fluorescent probe-based Recombinase-aided amplification (RAA) method and applied in E. coli O157:H7 detection at 39 °C in 20 min. The sensitivity of the assay in pure E. coli O157:H7 suspension was 5.6 × 10⁰ CFU/mL. The fluorescent probe-based RAA assay was further applied in three samples, and the limit of detection (LOD) in skimmed milk, lettuces and lake water was 5.4 × 10¹ CFU/mL, 7.9 × 10¹ CFU/mL and 5.2 × 10¹ CFU/mL, separately. This method showed a high sensitivity and short detection time, which has the feasible application in on-site test in real samples.