Fluorescence biosensor to detect microRNAs via integrating DNA hairpins transition mediated strand displacement amplification with primer exchange reaction

Herein, we constructed a fluorescence biosensor for the ultra-sensitive analysis of microRNAs (miRNAs) by combining DNA hairpins transition triggered strand displacement amplification (DHT-SDA) with primer exchange reaction (PER). Target miRNA initiated DHT-SDA to facilitate the generation of multiple single-stranded DNA (ssDNA) as PER primer, which was extended into a long ssDNA. The biosensor is successfully utilized in detecting miRNAs with high sensitivity (limit of detection for miRNA-21 was 58 fM) and a good linear relationship between 100 nM and 100 fM. By simply changing the DNA hairpin sequence, the constructed biosensor can be extended to analyze another miRNAs. Moreover, the biosensor has the feasibility of detecting miRNAs in real samples with satisfactory accuracy and reliability. Therefore, the fluorescent biosensor has great application potential in clinical diagnosis.

Highly sensitive SERS platform for pathogen analysis by cyclic DNA nanostructure@AuNP tags and cascade primer exchange reaction

The capacity to identify small amounts of pathogens in real samples is extremely useful. Herein, we proposed a sensitive platform for detecting pathogens using cyclic DNA nanostructure@AuNP tags (CDNA) and a cascade primer exchange reaction (cPER). This platform employs wheat germ agglutinin-modified Fe3O4@Au magnetic nanoparticles (WMRs) to bind the E. coli O157:H7, and then triggers the cPER to generate branched DNA products for CDNA tag hybridization with high stability and amplified SERS signals. It can identify target pathogens as low as 1.91 CFU/mL and discriminate E. coli O157:H7 in complex samples such as water, milk, and serum, demonstrating comparable or greater sensitivity and accuracy than traditional qPCR. Moreover, the developed platform can detect low levels of E. coli O157:H7 in mouse serum, allowing the discrimination of mice with early-stage infection. Thus, this platform holds promise for food analysis and early infection diagnosis.

An electrochemical biosensor to assay Trop-2 of breast cancer cells fabricated by methylene blue-assisted assembly of DNA nanoparticles

Human trophoblast surface cell antigen 2 (Trop-2) on the tumor cell membrane can not only serve as the target for chemotherapy drugs, but also as a biomarker for typing and prognosis of breast cancer; however, assay of Trop-2 is seriously hampered due to the limitations of available tool. Herein, we have designed and fabricated an electrochemical biosensor for the assay of Trop-2 based on methylene blue (MB)-assisted assembly of DNA nanocomposite particles (DNPs). Specially, the recognition between Trop-2 and its aptamer may activate the primer exchange reaction (PER) on an electrode surface to produce long single-strand DNA (ssDNA) which can be self-assembled into DNPs by electrostatic interaction between negative charged DNA and positive charged and electro-active MB molecules which can also be used to give electrochemical signal. By using this electrochemical biosensor, ultrasensitive detection of tumor cells with high Trop-2 expressions can be conducted, with the limit of detection (LOD) of 1 cell/mL. Moreover, this biosensor can be further used for accurately profiling Trop-2 expression of tumor cells in mouse tissues, suggesting its great potential in the precise definition of breast cancer.

Design strategies and advanced applications of primer exchange reactions in biosensing: A review

Early disease diagnosis relies on the sensitive detection and imaging of biomarkers. Signal amplification is one of the most commonly used methods to improve detection sensitivity. Primer exchange reaction (PER) is a novel signal amplification technique that has garnered attention because of its simple and sensitive features. The classical PER involves a single catalytic hairpin, which enables the attachment of custom sequences to the primer chain, generating a long repeat sequence that can bind numerous signaling molecules and achieve powerful signal amplification. Currently, numerous PER-based signal amplification strategies are available that can improve detection sensitivity and promote the development of the signal amplification field. This review focuses on the mechanism of typical PER, the diversification of PER, and PER-based biosensors for various targets. Finally, the challenges and prospects of PER development are discussed.

Multifunctional dumbbell probes-based logic circuits: microRNAs logic detection and tumor cells identification

BACKGROUND

The powerful logic processing capability of DNA logic circuits over multiple input signals perfectly meets the demands of multi-biomarker-based clinical diagnostics. As important biomarkers for cancer diagnosis and treatment, the orthogonal differential expression of microRNAs (miRNAs) in different diseases and different cancer cells makes the precise logical detection of multiple miRNAs particularly critical.

RESULTS

Therefore, we constructed two fundamental "AND" and "OR" logic gates and one "AND-OR" logic gate on the basis of our proposed multifunctional dumbbell probes. These logic gates allowed for the logical profiling of multiple cancer-associated miRNAs. In addition, by making simple adjustments to the functional modules of multifunctional dumbbell probes, the three logic gates we proposed could be easily transformed without the use of sophisticated probe design. Remarkably, these logic gates, in particular the "AND-OR" logic gate, were able to compute several miRNAs simultaneously, demonstrating excellent cell identification capabilities.

SIGNIFICANCE

Overall, this work provided a new idea for accurately distinguishing multiple cell types and showed great application prospects.

A fluorescent sensor based on strand displacement amplification and primer exchange reaction coupling for label-free detection of miRNA

MicroRNAs (miRNAs) are closely associated with human disease occurrence, including cancers, diabetes, inflammation, heart diseases, and viral infections, and their rapid and accurate detection is vital for the diagnosis and treatment of these diseases. Based on one-step reaction of strand displacement amplification (SDA) and primer exchange reaction (PER), a label-free and highly sensitive miRNA-21 detection strategy was developed. In this strategy, the target miRNA-21 binds directly to the hairpin template, triggering the SDA reaction and generating a large number of single strand DNAs as primers for PER amplification. With the help of polymerase, plenty of G-quadruplex fragments of different lengths were accumulated, and the organic dye thioflavin T selectively binds to these G-quadruplex fragments to produce a strong fluorescent signal. There is a wide detection range in this method, miRNA-21 can be detected in the range of 10 fM - 1 nM, the detection limit is low (1.25 fM). This method has good specificity and can effectively distinguish single-base mismatches of miRNA. In addition, the versatility of the method was validated by changing the target recognition site of SDA template.

A programmable DNA nanodevice for colorimetric detection of DNA methyltransferase activity using functionalized hemin/G-quadruplex DNAzyme

The measurement of DNA methyltransferase (MTase) activity and screening of DNA MTase inhibitors holds significant importance for the diagnosis and therapy of methylation-related illness. Herein, we developed a colorimetric biosensor (PER-FHGD nanodevice) to detect DNA MTase activity by integrating the primer exchange reaction (PER) amplification and functionalized hemin/G-quadruplex DNAzyme (FHGD). By replacing the native hemin cofactor into the functionalized cofactor mimics, FHGD has exhibited significantly improved catalytic efficiency, thereby enhancing the detection performance of the FHGD-based system. The proposed PER-FHGD system is capable of detecting Dam MTase with excellent sensitivity, exhibiting a limit of detection (LOD) as low as 0.3 U/mL. Additionally, this assay demonstrates remarkable selectivity and ability for Dam MTase inhibitors screening. Furthermore, using this assay, we successfully detect the Dam MTase activity both in serum and in E. coli cell extracts. Importantly, this system has the potential to serve as a universal strategy for FHGD-based diagnosis in point-of-care (POC) tests, by simply altering the recognition sequence of the substrate for other analytes.

Sensitive analysis of miRNAs via primer exchange reaction integrated with hairpin catalytic reaction

MicroRNAs (miRNAs) can serve as potential biological targets for early screening, targeted therapy, and prognosis in ovarian cancer (OC). However, sensitive and reliable quantification and identification of miRNA remain a huge challenge. Herein, we proposed a simple and reliable approach for the ultra-sensitive detection of miRNA by integrating endonuclease-III (Exo-III) assisted signal recycle, primer exchange reaction (PER), and hairpin catalytic reaction (HCR). In this method, target miRNA specifically binds with toehold sequence to form a blunt 3' terminus in the detection probe (dumbbell probe) that can be recognized by Exo-III, and to initiate subsequent signal amplifications. Based on this, the approach is successfully utilized in detecting OC related miRNAs with high sensitivity (limit of detection for miRNA-211 was 13 aM) and stability. By simply changing the toehold sequence in detection probe, the established approach can be easily extended to other miRNA detection. We believe that the platform is robust in detecting OS related biomarkers and is promising in renovating cancer diagnostic tools.

Target-initiated autonomous synthesis of metal-ion dependent DNAzymes for label-free and amplified fluorescence detection of kanamycin in milk samples

Accurate and sensitive monitoring of the abused antibiotics is vital because excessive antibiotics in human body can cause toxicity to kidney or lead to potential loss of hearing. In this work, we described a label-free and highly sensitive fluorescent aptasensing platform for detecting kanamycin in milk samples based on the synchronization signal amplification of primer exchange reaction (PER) and metal-ion dependent DNAzyme. The target kanamycin binds the aptamer sequence hybridized on a hairpin template and initiates PER for autonomous synthesis of Mg²⁺-dependent DNAzyme sequences with aid of Bst-DNA polymerase at isothermal conditions. Such a synthesis process can be repeated many times to produce lots of DNAzymes to cyclically cleave the rA site in the signal hairpin substrates under the assistance of Mg²⁺ cofactor to liberate numerous free G-quadruplex fragments. The organic dye thioflavin T (ThT) further associates with these G-quadruplex fragments to yield substantially intensified fluorescence for sensitive detection of kanamycin with a low detection limit of 0.36 nM. In addition, the developed aptamer sensing method also shows a good selectivity for kanamycin against other interfering antibiotics, and can realize the monitoring of kanamycin added in milk samples, highlighting its potential for sensitive monitoring of trace amount of kanamycin for food safety applications.