Duplex-Specific Nuclease-Mediated Amplification Strategy for Mass Spectrometry Quantification of MiRNA-200c in Breast Cancer Stem Cells

Molecular beacon-peptide probe based double recycling amplification for multiplexed detection of serum exosomal microRNAs

Exosomal microRNAs (exomiRs) have been shown to play crucial roles as biomarkers for early detection and prognosis of cancer. However, simultaneous quantification of multiplex exomiRs is hindered by methods that require additional steps, such as labeling with fluorophores or gel visualization, which are susceptible to various factors. Herein, we developed a mass spectrometry-detectable and target-triggered method for multiplexed exomiR detection using three enzyme-based double recycling amplification in combination with well-designed molecular beacon-peptide (MBP) probes, called molecular beacon-peptide probe-based double recycling amplification (MBPDRA). MBP probes mediated the double recycling amplification reaction and were released as mass-detectable reporter peptides. In particular, the hybridization of the target microRNAs (miRNAs) with the stem-loop of the probe triggers two consecutive processes. The first cycle involved polymerase strand displacement amplification, leading to the production of complementary DNA (cycle I), and the second cycle encompassed the recycling exonuclease cleavage of the MBP probe (cycle II). Subsequently, excess probes were removed by interaction with streptavidin beads via biotin-streptavidin binding. The reporter peptides were released using trypsin and subsequently detected by mass spectrometry. Our method enables quantitative detection of multiple exomiRs with a dynamic range from 0.1 fM to 10 pM and a limit of quantification of 0.1 fM. Moreover, the proposed assay was successfully employed for quantification of three exomiRs, exmiR-21, exmiR-191, and exmiR-451a, in the sera of patients with pancreatic cancer. Based on these findings, we believe that the MBPDRA assay holds significant promise as a reliable method for quantifying multiple miRNAs in biomedical research and clinical diagnostics.

Single Particle Analysis-Enhanced DNA Walking Machine for Sensitive miRNA Detection

DNA walking machines have achieved significant breakthroughs in areas such as biosensing, bioimaging, and early cancer diagnosis, facilitated by the self-assembly of DNA or its combination with other materials, such as magnetic beads and metal nanoparticles. However, current DNA walking machine strategies are constantly challenged by inadequate analytical sensitivity, while sophisticated signal amplification procedures are often indispensable. Single-particle inductively coupled plasma mass spectrometry (SP-ICPMS) provides superior sensitivity and can effectively discriminate between background noise and detected signals due to the large number of metal atoms in a nanoparticle and the concentrating effect of single nanoparticle detection. In this study, we present a novel approach utilizing single nanoparticle counting and duplex-specific nuclease (DSN)-assisted signal amplification to construct a 3D DNA walking machine for detecting the aggressive prostate cancer (PCa) biomarker miRNA-200c. The proposed strategy showed an improvement in sensitivity with a detection limit (LOD) of 0.93 pM (28 amol) and was successfully applied in human serum samples. To the best of our knowledge, this is the first report of the DNA walking machine with single nanoparticle counting study.

Integrating aptasensor with an explosive mass-tag signal amplification strategy for ultrasensitive and multiplexed analysis using a miniature mass spectrometer

Mass probes attached with aptamers and mass tags offer excellent specificity and sensitivity for multiplexed detection, wherein the dissociation of mass tags from the mass probes is as important as their labeling. Herein, aggregation-induced emission luminogen (AIEgen)-tagged mass probes (AIEMPs) were established to analyze estrogens, which integrated aptasensor with an explosive mass-tag signal amplification strategy via a simple ultrasound-assisted emulsification of nanoliposomes. The AIEMPs were assembled by the hybridization of aptamer-modified Fe3O4 nanoparticles (Fe NPs@Apt) and nanoliposomes loaded with massive AIEgen mass tags and partially complementary DNA strands (AIE NLs@cDNA). The aptamer was preferentially and specifically bound to estrogen, resulting in the detachment of AIE NLs from AIEMPs. Subsequently, the AIEMPs were deposited with electrospray solvents for explosive release of mass tags. Using nanoelectrospray ionization mass spectrometry (nanoESI-MS), the AIEMP-based aptasensor achieved ultrasensitive analysis of estrogens with limits of detection of 0.168-0.543 pg/mL and accuracies in the range of 87.9-114.0%. Compared to direct nanoESI-MS detection, the AIEMP-based aptasensor provides a signal amplification of four orders of magnitude. Furthermore, the utilization of different AIEMPs enables multiplexed detection of three estrogens with a miniature mass spectrometer, showing promising potential for on-site detection. This work expands the diversity of mass-tagging strategy and provides a versatile mass probe-based aptasensor platform for routine MS detection of trace analytes.

Signal differentiation models for multiple microRNA detection: a critical review

MicroRNAs (miRNAs) are a class of small, single-stranded non-coding RNAs which have critical functions in various biological processes. Increasing evidence suggested that abnormal miRNA expression was closely related to many human diseases, and they are projected to be very promising biomarkers for non-invasive diagnosis. Multiplex detection of aberrant miRNAs has great advantages including improved detection efficiency and enhanced diagnostic precision. Traditional miRNA detection methods do not meet the requirements of high sensitivity or multiplexing. Some new techniques have opened novel paths to solve analytical challenges of multiple miRNA detection. Herein, we give a critical overview of the current multiplex strategies for the simultaneous detection of miRNAs from the perspective of two different signal differentiation models, including label differentiation and space differentiation. Meanwhile, recent advances of signal amplification strategies integrated into multiplex miRNA methods are also discussed. We hope this review provides the reader with future perspectives on multiplex miRNA strategies in biochemical research and clinical diagnostics.

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 duplex-specific nuclease (DSN) and catalytic hairpin assembly (CHA)-mediated dual amplification method for miR-146b detection

A novel method for detecting miRNA has been developed using a combination of duplex-specific nuclease signal amplification (DSNSA) and a catalytic hairpin assembly (CHA). In this work, a biotinylated trigger release (BTR) probe with a biotin group at the 3'-end and a CHA reaction sequence trigger as an initiator (catalyst I) at the 5'-end was designed to hybridize target miRNA. The DSN enzyme was introduced to initiate the DSNSA. The miRNA was released to consume more BTR probes and amplify the signals. Subsequently, streptavidin-coated magnetic beads (SA-MBs) were added to the DSNSA reaction solution to remove excess BTR probes that did not hybridize with miRNA, which would then separate BTR probes and catalyst-I, to ensure detection with high selectivity and sensitivity. The catalyst-I remaining in the solution could trigger the CHA reaction to enable signal amplification in the second step. The developed method exhibits a sensitive detection limit and excellent selectivity in identifying a high sequence homology among family members.

State-of-the-Art Fluorescent Probes: Duplex-Specific Nuclease-Based Strategies for Early Disease Diagnostics

Precision healthcare aims to improve patient health by integrating prevention measures with early disease detection for prompt treatments. For the delivery of preventive healthcare, cutting-edge diagnostics that enable early disease detection must be clinically adopted. Duplex-specific nuclease (DSN) is a useful tool for bioanalysis since it can precisely digest DNA contained in duplexes. DSN is commonly used in biomedical and life science applications, including the construction of cDNA libraries, detection of microRNA, and single-nucleotide polymorphism (SNP) recognition. Herein, following the comprehensive introduction to the field, we highlight the clinical applicability, multi-analyte miRNA, and SNP clinical assays for disease diagnosis through large-cohort studies using DSN-based fluorescent methods. In fluorescent platforms, the signal is produced based on the probe (dyes, TaqMan, or molecular beacon) properties in proportion to the target concentration. We outline the reported fluorescent biosensors for SNP detection in the next section. This review aims to capture current knowledge of the overlapping miRNAs and SNPs' detection that have been widely associated with the pathophysiology of cancer, cardiovascular, neural, and viral diseases. We further highlight the proficiency of DSN-based approaches in complex biological matrices or those constructed on novel nano-architectures. The outlooks on the progress in this field are discussed.

Ultrasensitive detection of β-lactamase-associated drug-resistant bacteria using a novel mass-tagged probe-mediated cascaded signal amplification strategy

The emergence and spread of drug-resistant bacteria (DRB) is a global health threat. Early and accurate detection of DRB is a critical step in the treatment of DRB infection. However, traditional assays for DRB detection are time-consuming and have inferior analytical sensitivity and quantification capability. Herein, a mass-tagged probe (MP-CMSA)-mediated enzyme- and light-assisted cascaded signal amplification strategy was developed for the ultrasensitive detection of β-lactamase (BLA), an enzyme closely associated with most DRB. Each MP-CMSA probe contained multiple poly(amidoamine) (PAMAM) dendrimer molecules immobilized on a streptavidin agarose bead via a BLA-cleavable linker, and each dendrimer was modified with multiple mass tags via a photo-cleavable linker. In BLA detection, BLA could cleave the BLA-cleavable linker, leading to dendrimers shedding from the MP-CMSA probe to achieve enzyme-assisted signal amplification. Then, each dendrimer can further release mass tags under UV light to achieve light-assisted signal amplification. After this cascaded signal amplification, the released mass tags were ultimately quantified by mass spectrometry. Consequently, the sensitivity of BLA detection can be significantly enhanced by four orders of magnitude with a detection limit of 50.0 fM. Finally, this approach was applied to the blood samples from patients with DRB. This platform provides a potential strategy for the sensitive, rapid and quantitative detection of DRB infection.

Construction of a Recyclable DNAzyme Motor for MUC1-Specific Glycoform In Situ Quantification

Changes in the glycosylation content, especially in specific proteins, are of great importance for interpreting the mechanisms and development of certain diseases. However, current detection techniques are limited by the weak ionization efficiency of glycosyls and poor anti-interference of fluorescence signals. Herein, we present a general in situ quantification strategy for protein-specific glycoforms by constructing a recyclable DNAzyme motor for mass spectrometric detection using MUC1-specific sialic acid (Sia) as a model. This approach relies on a DNAzyme-based recycling strategy and two well-designed probes: a protein and a glycan probe. The protein probe consists of an aptamer and a DNAzyme. The glycan probe contains three functional domains: a DNAzyme complementary sequence, a substrate peptide segment, and a dibenzocyclooctyne tag. First, these two probes bind to their corresponding targets and trigger hybridization between adjacent probes on the same protein. With the help of the metal cofactor, the DNAzyme of the protein probe hydrolyzes the double-stranded glycan probe. The protein probe then reverts to a single-stranded state and remains intact for the next round of hybridization and cleavage. In this way, the recyclable DNAzyme motor can hydrolyze all glycan probes bound to the target protein. Finally, the reporter peptide released from the hydrolyzed glycan probes can be quantified by mass spectrometry, thereby converting the signal of the protein-specific glycoform to that of mass spectrometry. This strategy has been successfully used for in situ quantification of MUC1-specific Sia in different breast cancer cell lines. It provides a promising platform for protein-specific glycoform quantification.

A glucose/O2 biofuel cell integrated with an exonuclease-powered DNA walker for self-powered sensing of microRNA

With the aid of an exonuclease-powered DNA walker, the amount of glucose oxidase immobilized on the bioanode can be facilely tailored by varying the concentration of microRNA-141, so a glucose/O₂ biofuel cell is employed as a self-powered sensor for sensitive and selective detection of microRNA-141.

Extension of duplex specific nuclease sensing application with RNA aptamer

Duplex specific nuclease (DSN) that can precisely cleave DNA portion in double-stranded DNA or DNA-RNA hybrid has engrossed immense attention owing to its great potential in emerging bioanalytical applications. Here, we present a novel approach to extend DSN sensing application by coupling RNA aptamer. Specially designed RNA ligand sequences are used to capture the target and simultaneously provide complementary sequences of DNA for DSN aided fluorescent signal enhancement. A clotting enzyme, thrombin, has been used as a model analyte. One RNA aptamer combined with the target molecule can generate fluorescent signals through cleavage of hybridized TaqMan DNA probe (P2) by DSN. The proposed assay has achieved the lowest detection limit of 0.039 pM. The assay has been applied for real-time detection of thrombin release from live cells and other biotic media for early disease diagnosis. The developed method is versatile and can detect various other targets by choosing the relevant aptamer and probe sequences. This method is promising to be applied to medical diagnosis, biosensing, food safety, environmental monitoring, and other fields.

A mismatch-suppressed, duplex-specific nuclease powered nanowalker for multiplexed sensing of microRNA

DNA molecular machines have attracted immense interest for their potential in biosensing, drug delivery, and cellular imaging. Herein, we report a duplex-specific nuclease (DSN) powered nanowalker that can autonomously and progressively move on a spherical three-dimensional track, which is constructed by functionalizing a 13 nm diameter gold nanoparticle (AuNP) with densely mismatched DNA duplexes. The motion is initiated by an RNA walking strand, and in its absence, the walker is suppressed because the DSN is inactive toward the mismatched DNA duplexes. Once the walking strand is added, perfectly matched DNA-RNA hybrid is formed via a toehold-mediated displacement reaction between the walking strand and mismatched duplex. Thereafter, the DNA-RNA hybrid is simultaneously cleaved by DSN, by releasing the walking strand, which autonomously moves on the track with the aid of DSN. The present study provides a novel energy input and power mechanism for the operation of 3-D nanowalker with high efficiency. Moreover, the proposed nanowalker can be designed in a target microRNA (miRNA)-specific manner by altering the mismatched duplexes, and it exhibits femtomole level sensitivity in both singleplexed and multiplexed sensing of three miRNA targets. In addition, multiplexed quantification of the three miRNAs in biological samples is achieved, further suggesting that the proposed nanowalker has immense potential in biomedical research and early diagnosis of clinical disorders.

Peptide and protein assays using customizable bio-affinity arrays combined with ambient ionization mass spectrometry

High-throughput identification and quantification of protein/peptide biomarkers from biofluids in a label-free manner is achieved by interfacing bio-affinity arrays (BAAs) with nano-electrospray desorption electrospray ionization mass spectrometry (nano-DESI-MS). A wide spectrum of proteins and peptides ranging from phosphopeptides to cis-diol biomolecules as well as thrombin can be rapidly extracted via arbitrarily predefined affinity interactions including coordination chemistry, covalent bonding, and biological recognition. An integrated MS platform allows continuous interrogation. Profiling and quantitation of dysregulated phosphopeptides from small-volume (∼5 μL) serum samples has been successfully demonstrated. As a front-end device adapted to any mass spectrometer, this MS platform might hold much promise in protein/peptide analysis in point-of-care (POC) diagnostics and clinical applications.

Customizable bio-affinity arrays were interfaced with ambient ionization mass spectrometry for high-throughput assays of protein/peptide biomarkers in biofluids.

Duplex-Specific Nuclease-Assisted CRISPR-Cas12a Strategy for MicroRNA Detection Using a Personal Glucose Meter

A CRISPR-Cas system holds great promise as a next-generation biosensing technology for molecular diagnostics. Nevertheless, the current CRISPR-Cas12a-based detection strategies always need bulky instruments or auxiliary devices to obtain a quantitative signal output, which restrains its point-of-care testing application. Herein, we proposed a duplex-specific nuclease-assisted CRISPR-Cas12a strategy to detect microRNA (miRNA) with a personal glucose meter. The target miRNA was first converted into an amplified initiator DNA via duplex-specific nuclease. Afterward, the initiator DNA activated the collateral cleavage activity of CRISPR-Cas12a to cleave the single-strand DNA (ssDNA) linker on sucrase-ssDNA-modified magnetic beads, which led to the release of sucrase. The released sucrase was collected and then utilized to catalyze sucrose to glucose, which could be quantitatively detected by a personal glucose meter. The change in the glucose signal directly reflected the concentration of miRNA, which avoided expensive equipment for signal quantification. Two different miRNAs (miRNA21 and miRNA205) could be detected by simply changing the sequence of the template strand (H strand). The developed strategy showed high sensitivity with a limit of detection (LOD) of 2.4 and 1.1 pM for miRNA21 and miRNA205, respectively. In addition, good selectivity and anti-interference ability were achieved using this method, which enabled it promising for miRNA detection at the point-of-care.

Surface plasmon resonance biosensor for the detection of miRNAs by combining the advantages of homogeneous reaction and heterogeneous detection

The hybridization and enzymolysis reactions for nucleic acid detection were carried out on the chip surface in the traditional surface plasmon resonance (SPR) biosensors. Herein, we proposed an innovative method for microRNA (miRNA) detection in which the hybridization-enzymolysis recycling reactions were performed in solution. Duplex-specific nuclease (DSN) and streptavidin-modified gold nanoparticles (SA-AuNPs) were employed for enhancing the assay sensitivity. In the absence of miRNA, the biotinylated DNA probe (bio-DNA-bio, biotin tags at both the 3' and 5' termini of DNA) was attached to the SA-modified chip through the SA-biotin binding, allowing the capture of SA-AuNPs with the same interaction. As a result, a larger SPR signal was attained. However, in the presence of miRNA, bio-DNA-bio hybridized with miRNA was digested by DSN. In this process, the miRNA strand remained intact and participated in the next hybridization-enzymolysis recycling process. Thus, one miRNA could promote the hydrolysis of many bio-DNA-bio probes and allow the generation of numerous bio-DNA fragments. Meanwhile, the produced bio-DNA competed with the undigested bio-DNA-bio to bind SA on the chip surface. The digestion of bio-DNA-bio and the competitive binding between bio-DNA-bio and bio-DNA led to the attachment of fewer SA-AuNPs and then smaller SPR signals. The change in SPR signal at the concentration as low as 1 fM miRNA has been readily determined. The strategy possessed the advantageous properties of simple operation, fast response, high sensitivity and excellent specificity, serving as a viable means for the fabrication of novel sensing platforms.

Integrated nicking enzyme-powered numerous-legged DNA walker prepared by rolling circle amplification for fluorescence detection of microRNA

MicroRNAs (miRNAs) have been accepted as promising non-invasive biomarkers for cancer early diagnosis. Developing amplified sensing strategies for detecting ultralow concentration of miRNAs in clinical samples still requires much effort. Herein, an integrated fluorescence biosensor using nicking enzyme-powered numerous-feet DNA walking machine was developed for ultrasensitive detection of miRNA. A long numerous-feet walker produced by target-triggered rolling circle amplification autonomously moves along the defined DNA tracks on gold nanorods (AuNRs) with the help of nicking enzyme, leading to the recovery of fluorescence. This results in an amplified fluorescence signal, typically measured at 518 nm emission wavelength. Benefiting from the long walker that dramatically improves movement range, the homogenous and one-step strategy realizes ultrahigh sensitivity with a limit of detection of 0.8 fM. Furthermore, this walking machine has been successfully used to quantification of miRNA in clinical serum samples. The consistency of the gained results between of the developed strategy and reverse transcription quantitative polymerase chain reaction (RT-qPCR) shows that the sensing method has great promise for tumor diagnostics based on nucleic acid. Schematic representation of the fluorescent biosensing strategy, numerous-legged DNA walker prepared by rolling circle amplification on gold nanorods (AuNRs) for microRNA analysis, which can be applied in real samples with good results.

Highly Sensitive and Specific Mass Spectrometric Platform for miRNA Detection Based on the Multiple-Metal-Nanoparticle Tagging Strategy

The multiple-metal-nanoparticle tagging strategy has generally been applied to the multiplexed detection of multiple analytes of interest such as microRNAs (miRNAs). Herein, it was used for the first time to improve both the specificity and sensitivity of a novel mass spectroscopic platform for miRNA detection. The mass spectroscopic platform was developed through the integration of the ligation reaction, hybridization chain reaction amplification, multiple-metal-nanoparticle tagging, and inductively coupled plasma mass spectrometry. The high specificity resulted from the adoption of the ligation reaction is further enhanced by the multiple-metal-nanoparticle tagging strategy. The combination of hybridization chain reaction amplification and metal nanoparticle tagging endows the proposed platform with the feature of high sensitivity. The proposed mass spectrometric platform achieved quite satisfactory quantitative results for Let-7a in real-world cell line samples with accuracy comparable to that of the real-time quantitative reverse-transcriptase polymerase chain reaction method. Its limit of detection and limit of quantification for Let-7a were experimentally determined to be about 0.5 and 10 fM, respectively. Furthermore, due to the unique way of utilizing the multiple-metal-nanoparticle tagging strategy, the proposed platform can unambiguously discriminate between the target miRNA and nontarget ones with single-nucleotide polymorphisms based on their response patterns defined by the relative mass spectral intensities among the multiple tagged metal elements and can also provide location information of the mismatched bases. Its unique advantages over conventional miRNA detection methods make the proposed platform a promising and alternative tool in the fields of clinical diagnosis and biomedical research.

Duplex-specific nuclease signal amplification-based fluorescent lateral flow assay for the point-of-care detection of microRNAs

MiRNAs play important regulatory roles in numerous biological processes and serve as significant biomarkers for the development and prognosis of several diseases. Their unique characteristics, such as short size, high sequence homology among family members, low abundance, and easy degradability, have hindered their specific and highly sensitive detection. Herein, a duplex-specific nuclease (DSN)-assisted target recycling signal amplification-based fluorescent lateral flow assay was demonstrated for the point-of-care detection of cancer-related miRNA-21. In this assay, digoxin/biotin-labeled DNA probes were selectively cleaved by the DSN enzyme in the rounds of hybridization with the miRNA-21 target and cleavage cycle. Subsequently, the resulting mixture, containing the miRNA-21 target and intact and cleaved DNA probes, was loaded onto the lateral flow strip with digoxin antibody-conjugated quantum dot nanobeads and the streptavidin-coated test line. The increase in the proportion of cleaved DNA probes can induce a weakened response signal, which is directly associated with the amount of the miRNA target. Thus, highly sensitive quantification of miRNA-21 was achieved at a low limit of detection of 0.16 pM within 2 h of assay time. Assay specificity toward miRNA-21 was validated by testing several other miRNAs, including let-7b, let-7d, miRNA-141, and miRNA-200a. Moreover, the assay can quantify miRNA-21 spiked in human serum samples with acceptable recovery values, thus indicating its considerable clinical feasibility.

Nanoscale assembly line composed of dual DNA-machines enabling sensitive microRNA detection using upconversion nanoparticles probes

DNA machines are smart artificial devices that perform well-organized DNA hybridization reactions or nanoscale mechanical movements. Herein, a nanoscale assembly line composing of dual DNA machines is meticulously designed by coupling a catalytic hairpin assembly (CHA)-based machine with a 3D DNA walker machine. Equipped with upconversion nanoparticles (UCNPs) as signal tags, the dual DNA machines-based assembly line (DDMAL) can efficiently amplify the fluorescent signal of target recognition event, enabling sensitive detection of microRNA (miRNA). In detail, once activated by target miRNA-21, the CHA machine is initiated to constantly produce a single-stranded DNA (named binding DNA) via the strand displacement reaction. The binding DNA as a trigger factor can initiate the DNA walker machine by linking a walking strand DNA with an anchor strand DNA immobilized on the surface of magnetic beads (MBs). The movement of walking strand on the surface of MBs is then driven by Mn²⁺-dependent DNAzyme formed through the hybridization of walking strand with a UCNPs-linked substrate strand. The DNAzyme-catalyzed cleavage of substrate strand is accompanied by the release of numerous UCNPs from MBs. By measuring the fluorescent signal of released UCNPs after the magnetic separation, target miRNA-21 can be detected by the DDMAL system in a linear range from 1.0 fM to 10 nM, with a limit of detection (LOD) of 0.62 fM (3σ). Moreover, the practicability of DDMAL system was demonstrated by using it to evaluate the expression levels of miRNA-21 in cell lines and assay miRNA-21 in human serum.

A light-up "G-quadruplex nanostring" for label-free and selective detection of miRNA via duplex-specific nuclease mediated tandem rolling circle amplification

MicroRNA (miRNA) has emerged as a promising genetic marker for cancer diagnosis and therapy because its expression level is closely related to the progression of malignant diseases. Herein, a label-free and selective fluorescence platform was proposed for miRNA based on light-up "G-quadruplex nanostring" via duplex-specific nuclease (DSN) mediated tandem rolling circle amplification (RCA). First, a long DNA generated from upstream RCA was designed with the antisense sequences for miR-21 and downstream RCA primer. Upon recognizing miR-21, the resulting DNA-RNA permitted DSN digestion and triggered downstream two-way RCA, and generation of abundant "G-quadruplex nanostring" binding with ZnPPIX for label-free fluorescent responses. In our strategy, the strong preference of DSN for perfectly matched DNA/RNA ensures its excellent selectivity. The developed method generated wide linear response with LOD of 1.019 fM. Additionally, the miR-21 levels in cell extracts have been evaluated, revealing the utility of this tool for biomedical research and clinical diagnosis.

A label-free mass spectrometry detection of microRNA by signal switching from high-molecular-weight polynucleotides to highly sensitive small molecules

MicroRNAs (miRNAs) are associated with various cellular processes and have been recognized as potential biomarkers for many human diseases. The sensitive and accurate determination of miRNA expression levels in biological specimens is highly significant for understanding their biological functions and clinical diagnosis. Mass spectrometry (MS) has shown its potential to study bioactive molecules, however, direct MS analysis of miRNAs is often hampered by limited sensitivity. For sensitive detection of miRNAs, indirect methods are generally employed through the use of DNA probes labeled with peptides or metal elements. In this work, we proposed a novel MS-based label-free strategy for miRNA quantification. A dual-amplification system was developed by using a padlock probe containing the poly(thymine) sequence in combination with rolling circle amplification (RCA). The specific recognition of target miRNA by the padlock probes produced long single-stranded DNAs containing poly (adenine) segments, which guaranteed the specificity of detection and realized primary amplification. Then the RCA products were extracted and treated with acid to release a large number of free adenines as reporter molecules for secondary signal amplification. Overall, the quantification of target miRNA was carried out by signal switching from high-molecular-weight RCA products to highly sensitive small molecule of adenine. The developed method achieved a linear detection range from 200 amol to 100 fmol for miRNA-21 with a limit of detection of 50 amol, and successfully applied to detect endogenous miRNA-21 levels from lung cancer cells. Overall, the present study provides a sensitive, specific MS-based method for miRNA detection and holds great potential for further application of MS technology to detect other biomarkers in biomedical research and early clinical diagnosis.

Dual-Probe Approach for Mass Spectrometric Quantification of MUC1-Specific Terminal Gal/GalNAc In Situ

Protein glycosylation is a prevalent post-translational modification that mediates a variety of cellular processes. For membrane proteins, glycosylation at their terminal motif is usually more functional. Among the various glycosylation types found in membrane proteins, O-glycosylation is the most common and is closely correlated with a variety of cancer types, including breast cancer. Slightly aberrant expression of certain O-glycans can significantly affect cancer progression, especially at the cancer-related membrane protein level. To collect biological information on protein-specific glycosylation and further explore clinical applications, quantitative detection of glycosylation is essential. However, few assays have been reported for the in situ detection of protein-specific glycosylation to date. Herein, we developed a dual-probe approach for mass spectrometric quantification of protein-specific glycosylation using the terminal galactose/N-acetylgalactosamine (Gal/GalNAc) of MUC1 as a model. The dual-probe (i.e., protein probe and glycan probe) system was first designed and built. The protein probe contained an aptamer for MUC1 protein recognition and a capture DNA sequence. Correspondingly, the glycan probe had a DNA sequence complementary to that of the capture DNA, a substrate peptide containing a reporter peptide, and a tryptic cleavage site, and could be covalently linked with the terminal Gal/GalNAc. Exonuclease III enabled recycling of the hybridization-dehybridization process in a restricted space. Finally, the reporter peptide was tryptically released and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The mass response of the reporter peptide represented the amount of MUC1-specific terminal Gal/GalNAc. This dual-probe approach was applied for in situ detection of MUC1-specific terminal Gal/GalNAc in three human breast cancer cell lines and 32 pairs of matched breast cancer tissue samples. The relationship between MUC1-specific terminal Gal/GalNAc expression and breast cancer diagnosis/prognosis was also assessed.

A photocleavable and mass spectrometric DNA-peptide probe enables fast and specific enzyme-free detection of microRNA

MiRNAs are known to be involved in a series of diseases, including breast cancer, and they have the potential to serve as diagnostic/prognostic markers and therapeutic targets. A prerequisite for miRNAs to be applied in clinical practice is the quantitative profiling of their expression. However, the majority of current assays used in miRNA detection are highly enzyme-dependent. In this study, a novel enzyme-free assay was developed that relies on stacking hybridization and a photocleavable DNA-PL-peptide probe, which contains a reporter peptide (AVLGVDPFR), a photocleavable o-nitrobenzyl derivative linker and a detection DNA sequence that is complementary to a part of the target miRNA (e.g., miR-21, miR-125a or miR-200c). Stacking hybridization enabled the DNA-PL-peptide probe to capture DNA in a contiguous tandem arrangement to generate a long DNA single strand complementary to the target miRNA. Then, photolysis was initiated to rapidly release the reporter peptide, and the reporter peptide was ultimately monitored by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this experiment, the parameters linked with photorelease, binding, conjugation and hybridization were characterized. The results showed that the assay time was significantly shortened, and the detection specificity was improved. After validation of the assay, the target miRNA level was determined in human breast cells and tissue samples. The results demonstrated that photocleavable materials coupled with mass spectrometric detection have great potential in clinical practice.

Applications of Mass Spectrometry for Clinical Diagnostics: The Influence of Turnaround Time

This critical review discusses how the need for reduced clinical turnaround times has influenced chemical instrumentation. We focus on the development of modern mass spectrometry (MS) and its application in clinical diagnosis. With increased functionality that takes advantage of novel front-end modifications and computational capabilities, MS can now be used for non-traditional clinical analyses, including applications in clinical microbiology for bacteria differentiation and in surgical operation rooms. We summarize here recent developments in the field that have enabled such capabilities, which include miniaturization for point-of-care testing, direct complex mixture analysis via ambient ionization, chemical imaging and profiling, and systems integration.

Photo-driven self-powered biosensor for ultrasensitive microRNA detection via DNA conformation-controlled co-sensitization behavior

We developed a photoelectrochemical enzymatic fuel cell-based self-powered biosensing platform for microRNA detection via DNA conformation change-controlled co-sensitization behavior.