Rolling circle amplification integrated with suspension bead array for ultrasensitive multiplex immunodetection of tumor markers

Immuno-Rolling Circle Amplification (Immuno-RCA): Biosensing Strategies, Practical Applications, and Future Perspectives

In the rapidly evolving field of life sciences and biomedicine, detecting low-abundance biomolecules, and ultraweak biosignals presents significant challenges. This has spurred a rapid development of analytical techniques aiming for increased sensitivity and specificity. These advancements, including signal amplification strategies and the integration of biorecognition events, mark a transformative era in bioanalytical precision and accuracy. A prominent method among these innovations is immuno-rolling circle amplification (immuno-RCA) technology, which effectively combines immunoassays with signal amplification via RCA. This process starts when a targeted biomolecule, such as a protein or cell, binds to an immobilized antibody or probe on a substrate. The introduction of a circular DNA template triggers RCA, leading to exponential amplification and significantly enhanced signal intensity, thus the target molecule is detectable and quantifiable even at the single-molecule level. This review provides an overview of the biosensing strategy and extensive practical applications of immuno-RCA in detecting biomarkers. Furthermore, it scrutinizes the limitations inherent to these sensors and sets forth expectations for their future trajectory. This review serves as a valuable reference for advancing immuno-RCA in various domains, such as diagnostics, biomarker discovery, and molecular imaging.

Rolling Circle Amplification-Enabled Ultrasensitive Point-of-Care Test Method for Aflatoxin B1 in the Environment and Food

Aflatoxin B1 (AFB1) contamination poses a fatal risk to human beings and urgently needs highly sensitive detection for environmental monitoring and food safety. However, the existing challenges are the unsatisfied sensitivity of the immunoassay methods and the complex matrix effect. Rolling circle amplification (RCA) is a promising method for nucleic acid isothermal amplification due to its high specificity and sensitivity. Herein, we constructed a general RCA-based point-of-care test method (RCA-POCT). With biotinylated antibodies, streptavidin, and biotinylated RCA primers, we realized the signal transduction and preliminary signal amplification. In this way, the fluorescent signal of the immunocomplex on the microwells was greatly enhanced. Under optimal conditions, we recorded sensitive detection limits for aflatoxin B1 (AFB1) of 1.94, 16.3, and 37.7 fg/mL (femtogram per microliter), and wide linear ranges with 5 × 10-6 to 5, 5 × 10-5 to 5, and 5 × 10-5 to 5 ng/mL in the irrigation water, field soil, and peanut samples, respectively. Satisfactory recovery, specificity, repeatability, and reproducibility were observed. The RCA-POCT was validated by comparing it to the HPLC method. This work provides a general RCA-assisted detection method for AFB1 in the environment and food.

Highly sensitive "off-on" sensor based on MXene and magnetic microspheres for simultaneous detection of lung cancer biomarkers - Neuron specific enolase and carcinoembryonic antigen

In this work, a highly sensitive lung cancer biomarkers detection probe was developed based on Ag and MXene co-functionalized magnetic microspheres. By using carboxyl magnetic microspheres as carrier, MXene was coated repeatedly by Poly (allylamine hydrochloride) (PAH) as interlayer adhesive, and silver particles grown on the surface of MXene in situ can efficiently improve the sensitivity of the probe. The detection of neuron specific enolase (NSE) is mainly through the formation of a specific complex between NSE antigen and antibody, and the release of antibody labeled with amino carbon quantum dots (CQDs) from the surface of Ag nanoparticles (AgNPs), so that the fluorescence is restored and "OFF-ON" is formed. The biosensor exhibits excellently wide linear range (0.0001-1500 ng/mL) and the limit of detection (LOD) is up to 0.03 pg/mL, which is superior to most tumor marker probes based on fluorescence mechanism. Furthermore, we constructed dual detection strategy for NSE and carcinoembryonic antigen (CEA) simultaneously.

Dual-Encoded Affinity Microbead Signature Combinatorial Profiling for Acute Myocardial Infarction High-Sensitivity Diagnosis

The early diagnosis of acute myocardial infarction (AMI) is dependent on the combined feedback of multiple cardiac biomarkers. However, it remains challenging to precisely detect multicardiac biomarkers in complex blood early due to the lack of sensitive and specific diagnostic indicators and the low abundance and small size of associated biomarkers with high specificity (such as microRNAs). To make matters worse, spectral overlap significantly limits the multiplex analysis of cardiac biomarkers by fluorescent probes, leading to bias in the diagnosis of myocardial infarction. Herein, we developed a method for simultaneous detection of miRNAs and protein biomarkers using size- and color-coded microbeads that carry signature for target capture. We also constructed a microfluidic chip with different spacer arrays that segregate these microbeads in different chip regions according to their size to produce signature signals, indicating the level of different biomarkers. The signals on the microbeads were hugely amplified by catalytic hairpin assembly and rolling circle amplification. Notably, this strategy enables the simultaneous and in situ sensitive profiling of six kinds of biomarkers via adding two different fluorescent labels, removing the limitations of spectral overlap. We envision that the strategy has great potential for application in clinical diagnosis for AMI.

Progress in Procalcitonin Detection Based on Immunoassay

Procalcitonin (PCT) serves as a crucial biomarker utilized in diverse clinical contexts, including sepsis diagnosis and emergency departments. Its applications extend to identifying pathogens, assessing infection severity, guiding drug administration, and implementing theranostic strategies. However, current clinical deployed methods cannot meet the needs for accurate or real-time quantitative monitoring of PCT. This review aims to introduce these emerging PCT immunoassay technologies, focusing on analyzing their advantages in improving detection performances, such as easy operation and high precision. The fundamental principles and characteristics of state-of-the-art methods are first introduced, including chemiluminescence, immunofluorescence, latex-enhanced turbidity, enzyme-linked immunosorbent, colloidal gold immunochromatography, and radioimmunoassay. Then, improved methods using new materials and new technologies are briefly described, for instance, the combination with responsive nanomaterials, Raman spectroscopy, and digital microfluidics. Finally, the detection performance parameters of these methods and the clinical importance of PCT detection are also discussed.

Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates

As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.

Evaluation of Immuno-Rolling Circle Amplification for Multiplex Detection and Profiling of Antigen-Specific Antibody Isotypes

Antibody characterization is essential for understanding the immune system and development of diagnostics and therapeutics. Current technologies are mainly focusing on the detection of antigen-specific immunoglobulin G (IgG) using bulk singleplex measurements, which lack information on other isotypes and specificity of individual antibodies. Digital immunoassays based on nucleic acid amplification have demonstrated superior performance by allowing the detection of single molecules in a multiplex and sensitive manner. In this study, we demonstrate for the first time an immuno-rolling circle amplification (immuno-RCA) assay for the multiplex detection of three antigen-specific antibody isotypes (IgG, IgA, and IgM) and its integration with microengraving. To validate this approach, we used the autoimmune disease immune-mediated thrombotic thrombocytopenic purpura (iTTP) as the model disease with anti-ADAMTS13 autoantibodies as the diagnostic target molecules. To identify the anti-ADAMTS13 autoantibody isotypes, we designed a pool of three unique antibody-oligonucleotide conjugates for identification and subsequent amplification and visualization via RCA. To validate this approach, we first confirmed an assay specificity of >88% and a low limit of detection of 0.3 ng/mL in the spiked buffer. Subsequently, we performed a dilution series of an iTTP plasma sample for the multiplex detection of the three isotypes with higher sensitivity compared to an enzyme-linked immunosorbent assay. Finally, we demonstrated single-cell analysis of human B cells and hybridoma cells for the detection of secreted antibodies using microengraving and achieved a detection of 23.3 pg/mL secreted antibodies per hour. This approach could help to improve the understanding of antibody isotype distributions and their roles in various diseases.

Simultaneous detection of multiple exosomal microRNAs for exosome screening based on rolling circle amplification

Exosomal microRNAs (miRNAs) have attracted great attention as predictive and prognostic biomarkers of cancer. Profiling of miRNAs plays a key role in the effective diagnosis of cancers. However, simultaneous quantification of multiple miRNAs is challenging due to their homology and low abundance especially in exosomes. Here, we developed a sensitive detection method for multiple exosomal miRNAs with the help of rolling circle amplification (RCA). In contrast of the traditional ways, this method takes the advantages of both the multiplex sensing ability and the simplicity of RCA. Specifically, multiple exosomal miRNAs from different cell lines were replicated simultaneously through RCA and detected using designed molecular beacons (MBs). miRNA-21, miRNA-122 and miRNA-155 were chosen as the targets, which are overexpressed in cancers. Normalized fluorescence intensities of MB were used to imply the relative concentrations of these miRNAs. The obtained relative miRNAs expression levels could be used to distinguish the breast cancer exosome from normal one. If the varieties of the detected exosomal miRNAs are abundant enough, the concentration ratios of miRNAs could basically indicate the corresponding exosome and exosome screening could be realized. Such exosomal miRNA profiling and exosome screening can assist cancer diagnosis, which is promising in clinical application.

Protein detection based on rolling circle amplification sensors

Rolling circle amplification (RCA) is an isothermal process under the action of DNA polymerases. Large-scale DNA templates have been generated using RCA for target detection. Some signal amplification strategies including optical sensors and electrochemical sensors based on RCA have been applied to achieve sensitive detection. Sensors based on RCA have attracted increasing interest. Advances in RCA-based sensors for protein detection are reviewed in this paper. The advantages and detection mechanisms of sensors based on RCA are revealed and discussed. Finally, possible challenges and future perspectives are also outlined.

Development of a multi-channel magnetic bead micro-probe assay for high-throughput detection of zearalenone in edible and medicinal Coix seed

A multi-channel magnetic bead micro-probes assay (MBPA) based on indirect competitive principle was developed for high-throughput detection of zearalenone (ZEA) in edible and medicinal Coix seed. This strategy introduced magnetic beads as the carriers, the specific primary antibodies as the capture probes for targets and the secondary antibodies functionalized goat anti-mouse immunoglobulin G labeled fluorescein isothiocyanate as the fluorescence signal probes. Through the competitive reaction of ZEA in Coix seed samples and that covalently coupled on the surface of MBs with their specific antibodies, as well as fast magnetic separation and sensitive fluorescence detection, the developed MBPA strategy allowed low limit of detection (2.03 ng/mL) with broad dynamic range (2.03-440.67 ng/mL), as well as excellent accuracy with the average recovery rate of 96.39% and relative standard deviation (RSD) of 5.48% for ZEA. 36 samples could realize simultaneous analysis in one operation within less than 20 min only needing 50 μL of solution and 30 s of sampling, avoiding large consumption of time and organic solvents. Multiple centrifugation and cleanup steps were omitted because of magnetic separation, avoiding the loss of targets. Diverse capture and fluorescent probes can be randomly bound onto the surface of MBs, making the MBPA strategy a promising tool for on-site high-throughput monitoring of various trace hazard factors in food safety, and environmental monitoring.

Determination of plasma β-amyloids by rolling circle amplification chemiluminescent immunoassay for noninvasive diagnosis of Alzheimer's disease

A rolling circle amplification chemiluminescence immunoassay (RCA-CLIA) was developed for precise quantitation of Aβ in plasma. Capture antibodies conjugated with magnetic beads and detection antibodies with collateral single-stranded DNA (ssDNA) were bound to Aβ42/Aβ40 antigens to form a typical double-antibody sandwich structure. The RCA reaction was triggered by the addition of ssDNA, which generated products with a large number of sites for the binding of acridinium ester (AE)-labeled detection probes, thereby realizing the purpose of the amplification. The RCA-CLIA method had higher sensitivity than conventional CLIA without loss of specificity. Under optimum conditions, the linear range of Aβ42 and Aβ40 detection was 3.9-140 pg/mL and 3.9-180 pg/mL, respectively, with corresponding low detection limits of 1.99 pg/mL and 3.14 pg/mL, respectively. Plasma Aβ42 and Aβ40 were detected in the blood of 21 AD patients and 22 healthy people, wherein this ratio could significantly distinguish AD patients from healthy individuals with a sensitivity of 90.48% and specificity of 63.64% for a cutoff value of 154. The Aβ42/Aβ40 ratio of plasma acts as an accurate indicator for AD diagnosis; therefore, detection of plasma Aβ using the RCA-CLIA exhibits great potential in noninvasive diagnosis and progressive assessment of AD.

Recent advances in rolling circle amplification-based biosensing strategies-A review

Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.

Critical Review: digital resolution biomolecular sensing for diagnostics and life science research

One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.

Polydopamine nanosphere@silver nanoclusters for fluorescence detection of multiplex tumor markers

There is an increasing demand to establish a convenient and stable analytical methodology for screening multiplex tumor markers in early diagnosis of cancers. In this work, an innovative fluorescence method is proposed for simultaneous detection of alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA). A polydopamine nanosphere@silver nanocluster (PDAN@AgNC) system is introduced for fluorescence quenching and recovery. The AgNCs with different emissions are synthesized using different DNA templates, which also contain aptamer sequences towards AFP and CEA, respectively. These single-stranded DNA sequences could be adsorbed on the surface of the PDAN through π-π stacking, which results in the quenching of AgNCs. However, in the presence of the corresponding tumor marker, the aptamer/target complex forms which releases AgNCs from the surface of the PDAN and the recovered fluorescence could be used to indicate the concentration of the tumor marker. This PDAN@AgNC system has been validated preliminarily to screen human serum samples with excellent results. Taking advantages of simplicity, enzyme/antibody-free nature, low cost and convenient operation, the proposed biosensor has great potential to be used in biomedical research studies and clinical diagnosis.