Traditional and new applications of the HCR in biosensing and biomedicine

Improved Catalytic Activity of Spherical Nucleic Acid Enzymes by Hybridization Chain Reaction and Its Application for Sensitive Analysis of Aflatoxin B1

Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule.

Chemiluminescent plate assay of microRNA-155 coupled with catalytic hairpin assembly with oligonucleotide release (CHAOR)

A heterogeneous sensitive microRNA-155 assay based on a new isothermal amplification method, called catalytic hairpin assembly with oligonucleotide release (CHAOR), was developed. The principle of CHAOR was studied by non-denaturing electrophoresis. To detect the amplification product, a polyperoxidase-streptavidin conjugate (molar ratio 1:80) and an enhanced chemiluminescence reaction were used, which made it possible to increase assay sensitivity. The detection limit of microRNA-155 assay was 0.4 pM. The coefficient of variation of the chemiluminescent signal, formed upon the heterogeneous determination of miRNA-155, was less than 12 % within the working range. The efficiency of CHAOR as an amplification method was similar to that of traditional CHA, as miRNA-155 assays based on CHAOR and CHA had similar analytical parameters. In addition, the proposed assay was highly specific. Contrary to traditional CHA, CHAOR, one of whose products is a single-stranded oligonucleotide, can be used in analytical methods based on cascade amplification.

Accurate and sensitive low-density lipoprotein (LDL) detection based on the proximity ligation assisted rolling circle amplification (RCA)

Metabolic-associated fatty liver disease (MAFLD) is one of the leading causes of mortality from chronic diseases worldwide, and it is strongly linked to dyslipidemia. Dyslipidemia typically presents as an elevated concentration of low density lipoprotein (LDL). Hence, accurate quantification of LDL particles is crucial for predicting the risks of cardiovascular illnesses. Nevertheless, conventional techniques can merely provide indirect measurements of LDL particle concentrations through the detection of cholesterol or proteins within LDL particles, and they often require significant effort and time. Therefore, an accurate and effective method for identifying intact LDL particles is highly desired. We have devised a method that allows for the measurement of LDL concentration without the need for isolation. This method relies on proximity ligation rolling circle amplification (RCA). This technique enables the direct and precise measurement of the concentration of "actual" LDL particles, rather than measuring the cholesterol content inside LDL. It has a detection limit of 7.3 μg dL-1, which also meets the requirements for analyzing lipoproteins in clinical samples. Hence, this platform exhibits immense potential in clinical applications and health management.

Exonuclease-III Assisted the Target Recycling Coupling with Hybridization Chain Reaction for Sensitive mecA Gene Analysis by Using PGM

In the field of neonatal infections nursing, methicillin-resistant Staphylococcus aureus (MRSA) is a major bacterial pathogen. Here, we present a portable biosensor for MRSA detection that is both highly sensitive and portable, owing to its implementation on the personal glucose meter (PGM) platform. The H probe was fixed on the magnetic bead for mecA gene analysis. A blunt 3' terminus appeared in the MBs-H probe when the mecA gene was present. Exonuclease-III (Exo-III) recognized the blunt terminus and cleaved it, freeing the mecA gene and so facilitating target recycling. In the meantime, the remaining H probe-initiated hybridization chain reaction (HCR) led to the desired signal amplification. Portable quantitative detection of mecA gene is possible because PGM can read the quantity of invertase tagged on HCR product. After optimizing several experimental parameters, such as the concentration of Exo-III and incubation time, the constructed sensor is extremely sensitive, with a detection limit of 2 CFU/mL. The results from this sensitive PGM-based sensor are in agreement with those obtained from plate counting methods, suggesting that it can be used to accurately assess the MRSA content in artificial clinical samples. In addition, the PGM sensor can significantly cut down on time spent compared to plate counting techniques. The manufactured sensor provides a promising option for accurate identification of pathogenic bacteria.

Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection

Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.

The Application of Hybridization Chain Reaction in the Detection of Foodborne Pathogens

Today, with the globalization of the food trade progressing, food safety continues to warrant widespread attention. Foodborne diseases caused by contaminated food, including foodborne pathogens, seriously threaten public health and the economy. This has led to the development of more sensitive and accurate methods for detecting pathogenic bacteria. Many signal amplification techniques have been used to improve the sensitivity of foodborne pathogen detection. Among them, hybridization chain reaction (HCR), an isothermal nucleic acid hybridization signal amplification technique, has received increasing attention due to its enzyme-free and isothermal characteristics, and pathogenic bacteria detection methods using HCR for signal amplification have experienced rapid development in the last five years. In this review, we first describe the development of detection technologies for food contaminants represented by pathogens and introduce the fundamental principles, classifications, and characteristics of HCR. Furthermore, we highlight the application of various biosensors based on HCR nucleic acid amplification technology in detecting foodborne pathogens. Lastly, we summarize and offer insights into the prospects of HCR technology and its application in pathogen detection.

Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1

Traditional hybridization chain reaction (HCR) as a popular isothermal amplification technique shows some inevitable disadvantages in bioanalysis due to its relatively slow kinetics, which could be markedly promoted when the HCR initiator occurs under tension. Herein, a poly DNA tetrahedrons (pTDNs)-mediated HCR was successfully constructed to make its initiator in a stretched state by long-range electrostatic forces owing to the superimposed electrostatic interactions derived from the synthesized pTDNs, and it was hypothesized that it could remarkably enhance HCR performance, which was testified by theoretical simulations and experimental studies. Consequently, pTDNs-mediated HCR was applied to develop a novel immunoassay for rapid and sensitive detection of aflatoxin B1 as a proof-of-concept, and its signal amplification was attributed to the increased G4 DNAzyme that loaded on the second antibody. Our work paves a promising way using simple DNA frameworks alone to heighten HCR kinetics for reaction speed improvement and signal amplification in bioanalysis.

The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology

DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.

Rational design of nonlinear hybridization immunosensor chain reactions for simultaneous ultrasensitive detection of two tumor marker proteins

Sensitive biomarker detection techniques are beneficial for both disease diagnosis and postoperative examinations. The nonlinear hybridization chain reaction (NHCR) is widely used as an output signal amplification technique for biosensor platforms. A novel hairpin-free NHCR was developed in this study as a flow cytometric immunoassay to detect alpha-fetoprotein (AFP) and prostate specific antigen (PSA). First, the target AFP is captured on magnetic beads (MBs) that are modified with capture antibodies. Then, the prepared biotin-streptavidin-biotin (B-S-B) system, which links biotinylated detection antibodies and biotinylated trigger DNA together through the high affinity between biotin-streptavidin interaction, is added to label the target AFP, forming a sandwich complex with three trigger DNA chains. Each trigger DNA chain grows a dendritic DNA nanostructure following a nonlinear hybridization chain reaction. As the substrate flue chains are labeled with fluorophores, the self-assembly process of dendritic DNA is accompanied by the continuous release of fluorophores. Dendrites with strong fluorescence then form on the surface of MBs. Finally, the target AFP is quantified by analyzing the fluorescent MBs using flow cytometry. The proposed immunoassay has a high selectivity along with isothermal, enzyme-free, and exponential amplification efficiency. It shows a limit of detection (LOD) of 1.74 pg mL^-1. The proposed biosensor was also successfully used to quantitatively detect AFP in serum samples. It may be utilized to detect multiple tumor markers simultaneously by changing the size of MBs and antibody-antigen pairs. Most tumor markers are only related to tumor diagnosis but without specificity, so the combined detection of multiple tumor markers can improve the accuracy of early tumor diagnoses.

Self-assembly of DNA-hyperbranched aggregates catalyzed by a dual-targets recognition probe for miRNAs SERS detection in single cells

MicroRNAs (miRNAs) are very important for the early diagnosis and prognosis of tumors. In this work, we achieved the simultaneous detection of microRNA-155 (miR-155) and microRNA-21 (miR-21) with a dual target recognition probe (DRP) based on the nonlinear hybridization chain reaction (HCR). The multi-branched DNA products, three-dimensional multi-hotspot DNA dendrimers (3DmhD) were used in the amplification of the target miRNAs signal. The DRP is constructed with a core of gold nanocages (AuNCs), modified by nucleic acid probes and labeled with Raman signaling molecules ROX and Cy3. Experiments demonstrated that DRP could activate the multi-branched DNA reaction and generate 3DmhD in the presence of miR-155 and miR-21, which can achieve effective amplification of miR-21 and miR-155. When Surface Enhanced Raman Scattering (SERS) analysis was performed on 3DmhD, the multi-hot spot effect of 3DmhD significantly enhanced the signals of ROX and Cy3, allowing ultra-sensitive detection of miR-21 and miR-155 in vitro. To our delight, DRP also exhibited sensitive specificity and significant signal amplification for intracellular miRNAs. These results revealed that DRP has the potential to screen tumor cells by analyzing the expression levels of intracellular miRNAs.

Biosensors based on functional nucleic acids and isothermal amplification techniques

In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.

Recent Progress on Techniques in the Detection of Aflatoxin B1 in Edible Oil: A Mini Review

Contamination of agricultural products and foods by aflatoxin B1 (AFB1) is becoming a serious global problem, and the presence of AFB1 in edible oil is frequent and has become inevitable, especially in underdeveloped countries and regions. As AFB1 results from a possible degradation of aflatoxins and the interaction of the resulting toxic compound with food components, it could cause chronic disease or severe cancers, increasing morbidity and mortality. Therefore, rapid and reliable detection methods are essential for checking AFB1 occurrence in foodstuffs to ensure food safety. Recently, new biosensor technologies have become a research hotspot due to their characteristics of speed and accuracy. This review describes various technologies such as chromatographic and spectroscopic techniques, ELISA techniques, and biosensing techniques, along with their advantages and weaknesses, for AFB1 control in edible oil and provides new insight into AFB1 detection for future work. Although compared with other technologies, biosensor technology involves the cross integration of multiple technologies, such as spectral technology and new nano materials, and has great potential, some challenges regarding their stability, cost, etc., need further studies.

Label- and enzyme-free plasmon-enhanced single molecule fluorescence detection of HIV DNA fragments based on a catalytic hairpin assembly

We developed a label- and enzyme-free single molecule fluorescence counting strategy for HIV DNA fragments detection. The nucleic acid biosensor consists of a 5' terminal connected with a triangular gold nanoplate, 3' terminal rich in guanine hairpin probe (HP1) and a hairpin probe HP2 complementary to the partial sequence of HP1. Without the existence of the target DNA, the DNA fragment rich in the guanine region is locked in a hairpin structure and cannot form a G-quadruplex, hence NMM exhibits a low fluorescence signal. When the target DNA exists, the hairpin assembly will trigger a strand displacement amplification reaction that produces a great number of G-quadruplexes, and the fluorescence brightness of NMM will be enhanced. The plasmon resonance effect of the triangular gold nanoplates will further amplify the fluorescence signal. This method can analyze the target DNA with high sensitivity and selectivity, and the detection limit is 0.83 fM. The analysis of the HIV DNA fragments in diluted human serum samples was successfully achieved, and the recovery rate was 92%-104%. Because of its easy operation and low cost, it has broad development potential in biochemical analysis and clinical applications.