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Karenia mikimotoi is a globally distributed, toxic, bloom-forming dinoflagellate. The development of rapid, precise and sensitive detection methods is essential for the field monitoring of this harmful alga. In this study, exponential rolling circle amplification (E-RCA) and double-ligation E-RCA (dlE-RCA) were established for the detection of K. mikimotoi. The partial large subunit rDNA (D1–D2) of K. mikimotoi was PCR amplified, cloned and then sequenced. The resultant sequence was used to perform alignment analysis for species-specific regions and consequently design padlock probes and primers for E-RCA and dlE-RCA. Both E-RCA and dlE-RCA detection protocols were established and their parameters were optimized. dlE-RCA can avoid self-cyclization of PLP compared with E-RCA. The optimized parameters were as follows: ligation temperature, 61 °C; ligation time, 60 min (E-RCA)/30 min (dlE-RCA); amplification temperature, 61 °C (E-RCA)/64 °C (dlE-RCA); and amplification time, 30 min (E-RCA)/40 min (dlE-RCA). Specificity tests showed that both E-RCA and dlE-RCA were specific for K. mikimotoi. Sensitivity comparison indicated that E-RCA was 10-fold more sensitive than PCR and the sensitivity of dlE-RCA was comparable with that of PCR. Tests with simulated field samples suggested that the developed E-RCA and dlE-RCA obtained detection limits of 1 and 10 cells, respectively. Positive E-RCA and dlE-RCA could be confirmed by visual observation of coloration reaction with the addition of fluorescent SYBR Green I dye to the reaction tube. The developed E-RCA and dlE-RCA were also efficient for field samples with target cell densities ranging from 1 cell mL−1 to 1000 cells mL−1. These results suggest that the established E-RCA and dlE-RCA detection protocols show promising applications in the field monitoring of K. mikimotoi.

Rolling circle replication (RCR), including rolling circle amplification (RCA) and rolling circle transcription (RCT), is an isothermal enzymatic reaction. Because of its high amplification efficiency, RCR is a powerful biosensing tool for detecting biomolecules. In recent years, RCR has also been extended to the field of bioimaging to better understand biological pathways. Furthermore, RCR provides a simple technique to design and generate DNA/RNA structures with unique advantages in delivering drugs and enhanced targeting ability. In this review, we introduce the fundamentals of RCR and describe the most recent advances in RCR-based detection methods and delivery vehicles for biosensing, bioimaging, and biomedicine. Finally, some challenges and further opportunities of RCR-based biotechnology are discussed. Rolling circle replication (RCR) is an isothermal nucleic acid amplification approach that holds great potential in biotechnology.RCR can serve as a powerful biosensing platform for the detection of various biomolecules in bioanalysis and diagnosis.In bioimaging, RCR can provide a unique perspective in comprehensive understanding of biological processes and effective diagnosis of diseases.Programmable, biodegradable RCR-based assemblies have been used as versatile advanced drug carriers for targeted theranostics.

Recombinant protein polymers with repeat sequences of specific amino acids can be regarded as sustainable functional materials that can be designed using genetic engineering. However, synthesizing genes encoding these proteins is significantly time‐consuming and labor‐intensive owing to the difficulty of using common gene synthesis tools, such as restriction enzymes and PCR primers. To overcome these obstacles, a novel method is proposed herein: seamless cloning of rolling‐circle amplicons (SCRCA). This method involves one‐pot preparation of repetitive‐sequence genes with overlapping ends for cloning, facilitating the easy construction of the desired recombinants. SCRCA is used to synthesize 10 genes encoding hydrophilic resilin‐like and hydrophobic elastin‐like repeat units that induce liquid‐liquid phase separation. SCRCA shows higher transformation efficiency and better workability than conventional methods, and the time and budget required for SCRCA are comparable to those required for non‐repetitive‐sequence gene synthesis. Additionally, SCRCA facilitates the construction of a repeat unit library at a low cost. The library shows considerably higher diversity than that of the current state‐of‐the‐art method. By combining this library construction with the directed evolution concept, an elastin‐like protein polymer with the desired functions can be rapidly developed. SCRCA can greatly accelerate research on protein polymers. A new gene synthesis method consisting of rolling‐circle amplification and seamless cloning facilitates the advanced design of protein polymers with repetitive sequences. This method is more cost‐effective and user‐friendly than conventional methods. Using this method, a library of polymers with different repeat units can be easily constructed. This enables the rapid development of functional protein polymers through directed evolution.

The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.

Isothermal amplification (IA) is a nucleic acid amplification technology (NAAT) that has contributed significantly to the healthcare system. The combination of NAAT with a suitable detection platform resulted in higher sensitivity, specificity, and rapid disease diagnosis. Traditional NAAT, such as polymerase chain reaction (PCR), is widely applied in the general healthcare system but is rarely accessed in resource-limited hospitals. Some IA methods provide a rapid, sensitive, specific, and simple method for disease diagnosis. However, not all IA techniques have been regularly used in clinical applications because different biomarkers and sample types affect either the enzyme in the IA system or sample preparation. This review focuses on the application of some IA techniques that have been applied in the medical field and have the potential for use at points of care.

Extrachromosomal circular DNAs (eccDNAs) carrying random genomic segments are broadly found across different cancer types, but their molecular functions and impact in gastric cancer (GC) are rarely known. In this study, we aimed to investigate the potential role of eccDNA in GC. Using the Circle-seq strategy, we observed the eccDNA abundance in gastric cancer tissues (GCT) was aberrantly higher than that of normal adjacent tissues (NAT). The high abundance of eccDNAs carrying oncogene-segments in GCT may represent the DNA damage products of amplified oncogenes. Analysis of GCT over-represented eccDNA carrying enhancer (eccEnhancer) based on data from FANTOM5 project combined with TCGA database suggested the GC over-represented eccEnhancers may contribute to development of GC. GC over-represented eccDNAs carrying pre-miRNA (eccMIR) were enriched to multiple cancer-relevant signal pathways by KEGG analysis. We then synthesized the top six GC over-represented eccMIRs and found four of them enabled high expression of miRNAs and down-regulation of miRNA-target genes in MGC803 cells. Furthermore, we observed the inheritance of GC over-represented eccMIRs benefited host cell proliferation and promoted the aggressive features of host cells. Altogether, this study revealed the GC over-represented eccDNAs carrying functional genomic segments were related to the carcinogenesis of GC and presented the capability to facilitate cancer progression, suggesting the cancerous eccDNAs may serve as a dynamic reservoir for genome plasticity and rapid adaptive evolution of cancer. Therefore, blocking the pathways for eccDNAs generation may provide a novel therapeutic strategy for the treatment of gastric cancer.

Mercury ions (Hg[sup.2+]), a heavy metal contaminant of strong biotoxicity, pose a serious threat to ecosystems and human health in aquatic environments. Developing highly sensitive and specific detection methods is therefore of great importance. This study presents a novel label-free fluorescent biosensor for Hg[sup.2+] by ingeniously coupling target-induced aptamer switching with rolling circle amplification (RCA). Upon Hg[sup.2+] binding, the conformational change releases a sequestered primer to initiate RCA, generating G-quadruplex-rich DNA products that produce a strong “turn-on” signal with N-methylmesoporphyrin IX (NMM). Under optimized conditions, the assay exhibits excellent linearity from 10 to 1000 nM with a detection limit of 3.2 nM, along with high selectivity over competing metal ions. Validation using spiked environmental water samples yielded accurate and reproducible recoveries in the range of 93.8% to 106.0%. With its operational simplicity, high sensitivity, and robust performance in complex matrices, this label-free strategy offers a reliable and promising platform for detecting Hg[sup.2+] in environmental waters.

Accurate and efficient detection of pathogenic bacteria plays a crucial role in the diagnosis of infectious diseases. However, rapid and highly sensitive detection of specific bacteria in clinical samples remains challenging. In this study, we developed a ratiometric dual‐signal electrochemical biosensor for ultrasensitive detection of pathogenic bacteria, based on an aptamer recognition‐induced rolling circle amplification (RCA)/G‐quadruplex strategy. On the surface of a gold electrode chip, we used an aptamer sequence (P1) conjugated to ferrocene (Fc) to capture the target bacterium. This capture released a different, previously bound sequence (P2) sequence that initiated the RCA/G‐quadruplex cascade, which, in the presence of potassium ions, was able to bind the electrochemical indicator methylene blue (MB). We integrated the signals from the loss of Fc and the appearance of MB (IMB/IFC ratio) to quantify the target bacteria concentration. This biosensor showed excellent detection performance and specificity, with a detection limit of 10 CFU/mL. Notably, it showed great diagnostic potential for clinical infectious diseases caused by pathogenic bacteria in precise/personalized medicine applications. Principles used in a ratiometric dual‐signal electrochemical biosensor for ultrasensitive detection of pathogenic bacteria based on aptamer recognition‐induced rolling circle amplification (RCA)/G‐quadruplex strategy.

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.