Simple Amplifier Coupled with a Lanthanide Labeling Strategy for Multiplexed and Specific Quantification of MicroRNAs

Entropy driven-based catalytic biosensors for bioanalysis: From construction to application-A review

The rapid advancement of precision medicine and the continuous emergence of novel pathogens have presented new challenges for biosensors, necessitating higher requirements. Target amplification technology serves as the core component in biosensor construction. Enzyme-based amplification methods are often sensitive and selective but involve relatively complex operational steps, whereas enzyme-free amplification methods offer simplicity but frequently fail to meet both sensitivity and selectivity simultaneously. Existing research has confirmed that entropy-driven catalyst (EDC) biosensors not only fulfills the demands for sensitivity and selectivity concurrently but also offers ease of operation and flexibility in construction. In this review, we summarize the key advantages of EDC, explore how to construct DNA nanomachines based on these advantages to achieve intracellular detection and simultaneous detection of multiple targets, as well as point-of-care testing (POCT) to address practical issues in clinical diagnosis and treatment. We also anticipate potential challenges, propose corresponding solutions, and outline future development directions for EDC-based biosensors in practical clinical applications. We firmly believe that EDC sensors will emerge as a crucial branch within the realm of biosensor development.

Dual-Amplification Single-Particle ICP-MS Strategy Based on Strand Displacement Amplification-CRISPR/Cas12a Amplification for Homogeneous Detection of miRNA

MicroRNAs (miRNAs) regulate a myriad of biological processes and thus have been regarded as useful biomarkers in biomedical research and clinical diagnosis. The specific and highly sensitive detection of miRNAs is of significant importance. Herein, a sensitive and rapid dual-amplification elemental labeling single-particle inductively coupled plasma-mass spectrometry (spICP-MS) analytical method based on strand displacement amplification (SDA) and CRISPR/Cas12a was developed for miRNA-21 detection. Taking gold nanoparticles (AuNPs) as the elemental labels, the Au NP probe initially hybridized with linker DNA, forming large aggregates. In the absence of target miRNA-21, large aggregates of AuNPs will produce high pulse signals in spICP-MS detection. In the presence of the target miRNA-21, it triggered the SDA reaction, and the SDA products activated CRISPR/Cas12a's trans-cleavage activity to cleave the linker DNA, resulting in disassembly of the AuNP aggregates. The AuNP aggregates with smaller size displayed lower pulse signals in spICP-MS detection. Under the optimal conditions, a good relationship between the average pulse signal intensity of AuNP aggregates and the concentration of miRNA-21 was obtained in the range of 0.5 fmol L-1-100 pmol L-1 with a quantification limit as low as 0.5 fmol L-1. The developed method was successfully used for determination of miRNA-21 in human breast cancer cell lines (SK-BR-3 and MCF-7) and real blood samples from breast cancer patients. It is versatile, can be adapted to detect other targets by modifying the specific sequence of the SDA template chain that is complementary to the analytes, and offers a promising strategy for detecting various biomarkers with high sensitivity and specificity.

An enzyme-free and label-free multiplex detection of miRNAs by entropy-driven circuit coupled with capillary electrophoresis

MicroRNAs (miRNAs) are currently recognized as important biomarkers for the early diagnosis and prognostic treatment of cancer. Herein, we developed a simple and label-free method for the multiplex detection of miRNAs, based on entropy-driven circuit (EDC) amplification and non-gel sieving capillary electrophoresis-LED induced fluorescence detection (NGCE-LEDIF) platform. In this system, three different lengths of fuel chains were designed to catalyze three EDC, targeting miRNA-21, miRNA-155, and miRNA-10b, respectively. In the presence of target miRNA, the EDC cycle amplification reaction was triggered, generating numerous stable double-strands products (F-DNA/L-DNA). Since the three miRNAs correspond to three different lengths of F-DNA/L-DNA, they can be easily isolated and detected by NGCE. This strategy has good sensitivity, with detection limits of 68 amol, 292.2 amol, and 394 amol for miRNA-21, miRNA-155, and miRNA-10b, respectively. Additionally, this method has good specificity and can effectively distinguish single-base mismatches of miRNA. The recoveries of the three miRNAs in deproteinized healthy human serum ranged from 91.28 % to 108.4 %, with a relative standard deviation (RSD) of less than 7.9 %. This method was further applied to detect cellular miRNAs in human breast cancer (MCF-7) cell extracts, revealing an up-regulation of miRNA-21, miRNA-155, and miRNA-10b in MCF-7 cells. The successful spiked recovery in human serum and RNA extraction from MCF-7 cells underscores the practicality of this method. Therefore, this strategy has broad application prospects in biomedical research.

Establishment and Application of a Dual Immunoassay Method Based on ICP-MS for Stable Element Labeling Antibodies

BACKGROUND

To establish a dual immunoassay based on inductively coupled plasma mass spectrometry (ICP-MS) with stable element labeling antibodies for the simultaneous detection of alpha-fetoprotein (AFP) and prostate-specific antigen (PSA) in serum and evaluate its performance and clinical sample validation.

METHODS

The immunoassay system based on the double antibody sandwich method was established using magnetic beads as solid-phase carriers and rare earth elements europium (Eu) and samarium (Sm) as element tags. The test conditions were optimized. According to the Clinical Laboratory Standards Institute (CLSI) guidelines and the "Guidelines for Performance Validation of Clinical Chemistry Quantitative Testing Procedures," performance validation was conducted using the established method, followed by clinical sample validation.

RESULTS

The LOD and AMR for AFP were 0.76 ng/mL and 1.5-1200 ng/mL, respectively; the LOD and AMR for PSA were 0.41 ng/ mL and 0.5-250 ng/ mL, respectively. The intra-batch precision for AFP and PSA was all less than 3.33%, and the inter-batch precision for AFP and PSA was all less than 4.97%. The recoveries of AFP and PSA were 95.08%-104.18% and 97.65%-100.72%, respectively. The correlation coefficients between the established and the CLIA methods were r = 0.9930 for AFP and r = 0.9852 for PSA.

CONCLUSIONS

We have developed a dual immunoassay method based on ICP-MS, which can quantitatively detect AFP and PSA in serum within a single analysis. This method exhibits good precision, a wide linear range, and high specificity, meeting the requirements for clinical sample detection and holding potential for clinical application.

Recombinase Polymerase Amplification and Target-Triggered CRISPR/Cas12a Assay for Sensitive and Selective Hepatitis B Virus DNA Analysis Based on Lanthanide Tagging and Inductively Coupled Plasma Mass Spectrometric Detection

Herein, we report a target-triggered CRISPR/Cas12a assay by coupling lanthanide tagging and inductively coupled plasma mass spectrometry (ICP-MS) for highly sensitive elemental detection. Hepatitis B virus (HBV) DNA was chosen as a model analyte, and recombinase polymerase amplification (RPA) was used for target amplification. The double-stranded RPA amplicons containing a 5' TTTG PAM sequence can be recognized by Cas12a through a specific CRISPR RNA, activating the trans-cleavage activity of CRISPR/Cas12a and nonspecific cleavage of terbium (Tb)-ssDNA modified on magnetic beads (MBs). Following magnetic separation and acid digestion, the released Tb3+ ions were quantitated by ICP-MS and correlated to the concentration of HBV DNA. Taking advantage of the accelerated cleavage of Tb-ssDNA attached to the MB particles, RPA for target amplification, and ICP-MS for highly selective signal readout, this method permits the detection of 1 copy/μL of HBV DNA in serum with high specificity and holds great promise in the early diagnosis of viral infections or tumor development.

Primer exchange reaction assisted CRISPR/Cas9 cleavage for detection of dual microRNAs with electrochemistry method

An electrochemical sensor assisted by primer exchange reaction (PER) and CRISPR/Cas9 system (PER-CRISPR/Cas9-E) was established for the sensitive detection of dual microRNAs (miRNAs). Two PER hairpin (HP) were designed to produce a lot of extended PER products, which could hybridize with two kinds of hairpin probes modified on the electrode and initiate the cleavage of two CRISPR/Cas9 systems guided by single guide RNAs (sgRNAs) with different recognition sequences. The decrease of the two electrochemical redox signals indicated the presence of dual-target miRNAs. With the robustness and high specificity of PER amplification and CRISPR/Cas9 cleavage system, simultaneous detection of two targets was achieved and the detection limits for miRNA-21 and miRNA-155 were 0.43 fM and 0.12 fM, respectively. The developed biosensor has the advantages of low cost, easy operation, and in-situ detection, providing a promising platform for point-of-care detection of multiple miRNAs.

Amplification-Free Strategy for miRNA Quantification in Human Serum Using Single Particle ICP-MS and Gold Nanoparticles as Labels

MicroRNAs (miRNAs), which are short single-stranded RNA sequences between 18 and 24 nucleotides, are known to play a crucial role in gene expression. Changes in their expression are not only involved in many diseases but also as a response to physiological changes, such as physical exercise. In this work, a new analytical strategy for the sensitive and specific analysis of miRNA sequences in human plasma is presented. The developed strategy does not depend on any nucleic acid amplification process and can be obtained in direct correlation to the number of events obtained by using single-particle ICP-MS measurements. The high selectivity of the assay (up to single nucleotide polymorphisms) can be achieved by a double hybridization process of the target miRNA with a complementary capture oligonucleotide that is conjugated to a magnetic microparticle and simultaneously with a complementary reporter oligonucleotide conjugated to a gold nanoparticle. Thanks to the novel approach followed in this method, the stoichiometry of the oligonucleotide-nanoparticle conjugates does not need to be addressed for the quantification of the target miRNA, which also represents a big advantage over other similar methods. The optimized method is applied to the determination of a miRNA as a biomarker of physical exercise in non-spiked human serum samples, and the results are validated against rt-qPCR. The achieved sensitivity permits the direct differentiation among sedentary and sportive subjects. This general platform can be easily applied to any other sequence by only modifying the capture and reporter oligonucleotides, paving the way for multiple clinically interesting applications.

Label-free detection of biomolecules using inductively coupled plasma mass spectrometry (ICP-MS)

Bioassays using inductively coupled plasma mass spectrometry (ICP-MS) have gained increasing attention because of the high sensitivity of ICP-MS and the various strategies of labeling biomolecules with detectable metal tags. The classic strategy to tag the target biomolecules is through direct antibody-antigen interaction and DNA hybridization, and requires the separation of the bound from the unbound tags. Label-free ICP-MS techniques for biomolecular assays do not require direct labeling: they generate detectable metal ions indirectly from specific biomolecular reactions, such as enzymatic cleavage. Here, we highlight the development of three main strategies of label-free ICP-MS assays for biomolecules: (1) enzymatic cleavage of metal-labeled substrates, (2) release of immobilized metal ions from the DNA backbone, and (3) nucleic acid amplification-assisted aggregation and release of metal tags to achieve amplified detection. We briefly describe the fundamental basis of these label-free ICP-MS assays and discuss the benefits and drawbacks of various designs. Future research is needed to reduce non-specific adsorption and minimize background and interference. Analytical innovations are also required to confront challenges faced by in vivo applications.

Miniaturized ascorbic acid assay platform based on point discharge atomic emission spectrometry coupling with gold filament enrichment

BACKGROUND

Miniaturized microplasma-based atomic emission spectrometry (AES) has been extensively used for element analysis in recent years due to the advantages of low power consumption, low gas consumption, relatively low manufacturing and running cost, and the potential for real-time and field analysis. However, few applications in bioassay detection have been reported based on microplasma AES systems because of their relatively low sensitivity and the absence of indirect analytical strategies. It is still a challenge to develop a simple, sensitive, and portable microplasma-based AES bioassay approach.

RESULTS

In this work, a portable analytical system was designed based on point discharge chemical vapor generation atomic emission spectrometry (PD-CVG-AES) coupling with gold filament enrichment. The detection of ascorbic acid (AA) was realized indirectly by means of the highly sensitive analysis of Hg2+. The measurement was based on Ag + can decrease the concentration of Hg2+ by forming Ag-Hg amalgam in the presence of the reductant SnCl2, while AA can pre-reduce Ag + to Ag0, leading to the generation of silver nanoparticles (Ag NPs). The pre-reduce procedure can decrease the generation of Ag-Hg amalgam, resulting in the recovery of Hg2+ signal. The dissociative Hg2+ was further detected by PD-CVG-AES combination of gold filament enrichment, which significantly improved the detection sensitivity for both Hg2+ and AA. Under optimal conditions, the limit of detection (LOD) of AA is as low as 19 nM with a relative standard deviation (RSD, n = 5) of 0.7 %.

SIGNIFICANCE

The developed novel analytical strategy obviously broadens the application of microplasma-based AES, and it is well demonstrated by the determination of AA in several traditional Chinese medicines (TCMs), offering a higher level of sensitivity compared to current AA detection techniques. It has potential for future application in point-of-care testing (POCT) assays.

Hairpin DNA-based electrochemical amplification strategy for miRNA sensing by using single gold nanoelectrodes

A new sensor has been developed to detect miRNA-15 using nanoelectrodes and a hairpin DNA-based electrochemical amplification technique. By utilizing a complex DNA cylinder connected with hairpin DNA1, the sensor is able to absorb more methylene blue (MB) than simple double-stranded DNA. Another hairpin DNA2 is modified on an Au nanoelectrode surface and, when miRNA-15 is introduced, it triggers a chain reaction. This reaction unlocks two hairpins alternatively to polymerize into a complex structure that attaches more MB. The miRNA-15 is then replaced by DNA1 due to strand displacement reactions and continues to react with the next DNA2 to achieve circular amplification. The electrochemical signal from MB oxidation has a linear relationship with the miRNA-15 concentrations, making it possible to detect miRNA-15. Moreover, this method can be readily adapted for the detection of various other miRNA species. The newly devised nanosensor holds promising applications for the in vivo detection of miRNA-15 within biological systems, which is achieved by leveraging the advantageous characteristics of nanoelectrodes, including their low resistance-capacitance time constant, rapid mass transfer kinetics, and small diameter.

High-fidelity imaging of intracellular microRNA via a bioorthogonal nanoprobe

The spatiotemporal visualization of intracellular microRNA (miRNA) plays a critical role in the diagnosis and treatment of malignant disease. Although DNAzyme-based biosensing has been regarded as the most promising candidate, inefficient analytical resolution is frequently encountered. Here, we propose a bioorthogonal approach toward high-fidelity imaging of intracellular miRNA by designing a multifunctional nanoprobe that integrates MnO₂ nanosheet-mediated intracellular delivery and activation by a fat mass and obesity-associated protein (FTO)-switched positive feedback. MnO₂ nanosheets facilitate nanoprobe delivery and intracellular DNAzyme cofactors are released upon glutathione-triggered reduction. Meanwhile, an m6A-caged DNAzyme probe could be bioorthogonally activated by intracellular FTO to eliminate potential off-target activation. Therefore, the activated DNAzyme probe and substrate probe could recognize miRNA to perform cascade signal amplification in the initiation of the release of Mn²⁺ from MnO₂ nanosheets. This strategy realized high-fidelity imaging of intracellular aberrant miRNA within tumor cells with a satisfactory detection limit of 9.7 pM, paving the way to facilitate clinical tumor diagnosis and prognosis monitoring.

Mass Nanotags Mediate Parallel Amplifications on Nanointerfaces for Multiplexed Profiling of RNAs

Multiplexed profiling of RNAs aids in a comprehensive understanding of multiparameter-defined cellular processes and pathological states. We herein present a mass nanotags-enabled interfacial assembly system (MNTs-AS) with parallel amplification motors for simultaneous assaying of multiple RNAs in biosystems by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Four kinds of MNTs encoding corresponding RNA can be cyclically assembled on magnetic beads by target-triggered catalytic hairpin assembly (CHA) machineries on nanointerfaces, generating multiplexed and amplified characteristic ion signals assigned to target RNAs upon MALDI MS interrogation. By virtue of high sensitivity and multiplexing capability, the MNTs-AS-based MS assay allows precision subtyping of diverse breast cancer cells and their exosomes by multiplexed profiling of miRNA-21, miRNA-373, miRNA-155, and manganese superoxide dismutase mRNA via a single MS inquiry. This method provides a promising tool for unraveling multiple RNA-involved biological events in fundamental research and distinguishing different cancer subtypes in clinical practice.

A renewable platform based on the entropy-driven catalytic amplification and element labeling inductively coupled plasma mass spectrometry for microRNA analysis

The element labeling inductively coupled plasma mass spectrometry (ICP-MS) strategy has been increasingly applied to the bioanalysis for various bio-targets. Herein, a renewable analysis platform with element labeling ICP-MS was firstly proposed for microRNA (miRNA) analysis. The analysis platform was established on the magnetic bead (MB) with entropy-driven catalytic (EDC) amplification. When the EDC reaction was initiated by target miRNA, numerous strands labeled with Ho element were released from MBs, and ¹⁶⁵Ho in the supernatant detected by ICP-MS could reflect the amount of target miRNA. After detection, the platform was easily regenerated by adding strands to reassemble EDC complex on MBs. This MB platform could be used four times, and the limit of detection for miRNA-155 was 8.4 pmol L^-1. Moreover, the developed regeneration strategy based on EDC reaction can be easily expanded to other renewable analysis platforms, such as, the renewable platform involving EDC and rolling circle amplification technology. Overall, this work proposed a novel regenerated bioanalysis strategy to reduce the consumption of reagent and time for probe preparation, profiting the development of bioassay based on element labeling ICP-MS strategy.

Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules

Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.

A General Signal Amplifier of Self-Assembled DNA Micelles for Sensitive Quantification of Biomarkers

Owing to the excellent structural rigidity and programmable reaction sites, DNA nanostructures are more and more widely used, but they are limited by high cost, strict sequence requirements, and time-consuming preparation. Herein, a general signal amplifier based on a micelle-supported entropy-driven circuit (MEDC) was designed and prepared for sensitive quantification of biomarkers. By modifying a hydrophobic cholesterol molecule onto a hydrophilic DNA strand, the amphiphilic DNA strand was first prepared and then self-assembled into DNA micelles (DMs) driven by hydrophobic effects. The as-developed DM showed unique advantages of sequence-independence, easy preparation, and low cost. Subsequently, amplifier units DMF and DMTD were successfully fabricated by connecting fuel strands and three-strand duplexes (TDs) to DMs, respectively. Finally, the MEDC was triggered by microRNA-155 (miR-155), which herein acted as a model analyte, resulting in dynamic self-assembly of poly-DNA micelles (PDMs) and causing the recovery of cyanine 3 (Cy3) fluorescence as the DMTD dissociated. Benefiting from the "diffusion effect", the MEDC herein had a nearly 2.9-fold increase in sensitivity and a nearly 97-fold reduction in detection limit compared to conventional EDC. This amplifier exhibited excellent sensitivity of microRNAs, such as miR-155 detection in a dynamic range from 0.05 to 4 nM with a detection limit of 3.1 pM, and demonstrated outstanding selectivity with the distinguishing ability of a single-base mismatched sequence of microRNAs. Overall, the proposed strategy demonstrated that this sequence-independent DNA nanostructure improved the performance of traditional DNA probes and provided a versatile method for the development of DNA nanotechnology in biosensing.