Single-Nanoparticle ICP-MS for Sensitive Detection of Uracil-DNA Glycosylase Activity

Fluorescent metal nanoclusters: From luminescence mechanism to applications in enzyme activity assays

Metal nanoclusters (MNCs) have outstanding fluorescence property and biocompatibility, which show widespread applications in biological analysis. Particularly, evaluation of enzyme activity with the fluorescent MNCs has been developed rapidly within the past several years. In this review, we first introduced the fluorescent mechanism of mono- and bi-metallic nanoclusters, respectively, whose interesting luminescence properties are mainly resulted from electron transfer between the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels. Meanwhile, the charge migration within the structure occurs through ligand-metal charge transfer (LMCT) or ligand-metal-metal charge transfer (LMMCT). On such foundation, diverse enzyme activities were rigorously evaluated, including three transferases and nine hydrolases, in turn harvesting rapid research progresses within past 5 years. Finally, we summarized the design strategies for evaluating enzyme activity with the MNCs, presented the major issues and challenges remained in the relevant research, coupled by showing some improvement measures. This review will attract researchers dedicated to the studies of the MNCs and provide some constructive insights for their further applications in enzyme analysis.

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.

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.

Ultrasensitive and Wash-Free Detection of Tumor Extracellular Vesicles by Aptamer-Proximity-Ligation-Activated Rolling Circle Amplification Coupled to Single Particle ICP-MS

Tumor-derived extracellular vesicles (TEVs) are rich in cellular information and hold great promise as a biomarker for noninvasive cancer diagnosis. However, accurate measurement of TEVs presents challenges due to their low abundance and potential interference from a high number of EVs derived from normal cells. Herein, an aptamer-proximity-ligation-activated rolling circle amplification (RCA) method for EV membrane recognition, coupled with single particle inductively coupled plasma mass spectrometry (sp-ICP-MS) for the quantification of TEVs, is developed. When DNA-labeled ultrasmall gold nanoparticle (AuNP) probes bind to the long chains formed by RCA, they aggregate to form large particles. Notably, small AuNPs scarcely produce pulse signals in sp-ICP-MS, thereby detecting TEVs in a wash-free manner. By leveraging the strong binding affinity of aptamers, dual aptamers for EpCAM and PD-L1 recognition, and the sp-ICP-MS technique, this method offers remarkable sensitivity and selectivity in tracing TEVs. Under optimized conditions, the present method shows a favorable linear relationship between the pulse signal frequency of sp-ICP-MS and TEV concentration within the range of 105-107 particles/mL, along with a detection limit of 1.1 × 104 particles/mL. The pulse signals from sp-ICP-MS combined with machine learning algorithms are used to discriminate cancer patients from healthy donors with 100% accuracy. Due to its simple and fast operation and excellent sensitivity and accuracy, this approach holds significant potential for diverse applications in life sciences and personalized medicine.

Photoelectrochemical polarity-switching-mode and split-type biosensor based on SQ-COFs/BiOBr heterostructure for the detection of uracil-DNA glycosylase

Here, we constructed a split-type and photocurrent polarity switching photoelectrochemical (PEC) biosensor for ultrasensitive detection of Uracil-DNA glycosylase (UDG, abnormal UDG activity is correlated with human immunodeficiency, cancers, bloom syndrome, neurodegenerative diseases and so on) based on SQ-COFs/BiOBr heterostructure, as the photoactive materials, methylene blue (MB) as the signal sensitizer, and catalytic hairpin assembly (CHA) for signal amplification. Specifically, the photocurrent intensity generated by SQ-COFs/BiOBr was about 2 and 6.4 times of that of BiOBr and SQ-COFs alone, which could be responsible for the detection sensitivity for the proposed biosensor. In addition, it is not common to construct heterojunctions between covalent organic skeletons and inorganic nanomaterials. In UDG recognition tube, the plenty of COP probes loaded methylene blue (MB) were obtained by magnetic separation with the help of the simple chain displacement reaction of CHA. MB, as a responsive substance, can efficiently switched the photocurrent polarity of the SQ-COFs/BiOBr electrode from cathode to anode, which reduce the background signal, further improve the sensitivity of the biosensor. Based on the above, the linear detection range of our designed biosensor is 0.001-3 U mL^-1, and the detection limit (LODs) is as low as 4.07 × 10^-6 U mL^-1. Furthermore, the biosensor can still maintain good analytical performance for UDG in real sample, which means that it has broad application prospects in the field of biomedicine.

Study on the detection of anthrax by ICP-MS based on gold nanoparticle labeling

BACKGROUND

In recent years, inductively coupled plasma mass spectrometry (ICP-MS) has been widely used in the field of molecular biology because of its unique advantages. Anthrax is a widespread and long-standing infectious disease, which affects and restricts people's work and life seriously.

OBJECTIVE

The study goal is to develop a new method for the detection of anthrax.

METHODS

A rapid, sensitive and accurate method for the detection of anthrax characteristic DNA was proposed by combing gold nanoparticles (AuNPs) and inductively coupled plasma mass spectrometry.

RESULTS

The linear range of this method is 100-2500 pmol/L and the limit of detection of 16.61 pmol/L.

CONCLUSION

The proposed method has numerous advantages, including simplicity of operation, high sensitivity, and specificity, which provides a new idea for the detection of anthrax. Importantly, this methodology has good potential for the detection of other biological substances such as bacteria and viruses by changing the modification sequence on the nanoparticle probe.

Mass Spectrometric Multiplex Detection of MicroRNA and Protein Biomarkers for Liver Cancer

The occurrence of cancers is often accompanied by the abnormal expression of several sorts of biomarkers (e.g., nucleic acids and proteins). The multiplex assessment of them would substantially aid in the early detection and precise diagnosis, which is often hampered by their different detection schemes, different reaction matrix and reagents, and spectral overlapping. Herein, we propose a simple and sensitive mass spectrometric method for the multiplex detection of nucleic acid and protein, in which liver cancer-related biomarkers miRNA 223 and alpha-fetoprotein (AFP) were selected as model analytes. The self-amplification effect of metal atom-based nanoparticle probes can provide high sensitivity in complex serum samples without any additional amplification procedure. The detection limits for the simultaneous detection of miRNA 223 and AFP were 103 (2.1 pM) and 219 amol (0.15 ng/mL), respectively, with high specificity and selectivity. The proposed method is potentially useful for the rapid screening of cancers.

Single Particle Inductively Coupled Plasma Mass Spectrometry-Based Homogeneous Detection of HBV DNA with Rolling Circle Amplification-Induced Gold Nanoparticle Agglomeration

A highly sensitive and simple method based on rolling circle amplification (RCA) and single particle inductively coupled plasma mass spectrometry (spICP-MS) was proposed for the homogeneous detection of hepatitis B virus (HBV) deoxyribonucleic acid (DNA). In the presence of target DNA, long ssDNA possessing a large number of repeating sequence units was generated by RCA. DNA-labeled AuNP probes assembled into long chains based on complementary base pairing, further aggregating into large particles. Small Au NPs hardly produced pulse signals in spICP-MS; obvious pulse signals appeared in spICP-MS after the agglomeration of Au NPs caused by the addition of RCA products and spermidine. On the basis of this, the homogeneous detection of target DNA was realized by spICP-MS with high sensitivity. Under optimal conditions, the proposed method exhibited a good linear relationship between the frequency of the pulse signal of Au in spICP-MS and the concentration of target HBV DNA in the range of 10-2000 fmol L^-1 (R = 0.997), the limit of detection was 5.1 fmol L^-1, and the relative standard deviation was 3.7-6.8%. Recoveries of 94.2-108% were obtained for target DNA in spiked serum samples, demonstrating a good matrix tolerance ability for the method.

Ultrasensitive DNA Methylation Ratio Detection Based on the Target-Induced Nanoparticle-Coupling and Site-Specific Base Oxidation Damage for Colorectal Cancer

DNA methylation analysis holds great promise in the whole process management of cancer early screening, diagnosis, and prognosis monitoring. Nevertheless, accurate detection of target methylated DNA, especially its methylation ratio in the genome, remains challenging. Herein, we report for the first time an integrated strategy of target-induced nanoparticle-coupling and site-specific base oxidation damage for DNA methylation analysis with the assistance of well-designed nanosensors. The ultrahigh sensitivity for detecting target methylated DNA as low as 32 × 10^-17 M and high specificity for distinguishing 0.001% methylation ratio are achieved by this proposed strategy without amplification operations. Notably, the precise quantification of target DNA methylation ratio has been achieved for the first time. Through quantitative detection of target methylated DNA and methylation ratio, this proposed strategy could reliably diagnose and monitor cancer progression and treatment responses for colorectal cancer, which is superior to the clinical Septin 9 kit. It is anticipated that the proposed strategy has attractive application prospects in early diagnosis and monitoring for colorectal cancer and other various diseases.

Recent advances in biosensor for DNA glycosylase activity detection

Base excision repair (BER) is vital for maintaining the integrity of the genome under oxidative damage. DNA glycosylase initiates the BER pathway recognizes and excises the mismatched substrate base leading to the apurinic/apyrimidinic site generation, and simultaneously breaks the single-strand DNA. As the aberrant activity of DNA glycosylase is associated with numerous diseases, including cancer, immunodeficiency, and atherosclerosis, the detection of DNA glycosylase is significant from bench to bedside. In this review, we summarized novel DNA strategies in the past five years for DNA glycosylase activity detection, which are classified into fluorescence, colorimetric, electrochemical strategies, etc. We also highlight the current limitations and look into the future of DNA glycosylase activity monitoring.

Development of a single quantum dot-mediated FRET biosensor for amplification-free detection of ten-eleven translocation 2

Ten-eleven translocation (TET) family proteins play key roles in multiple cellular processes by mediating the oxidation of 5-methylcytosine to directly participate in DNA demethylation, and often aberrantly expressed in various diseases. In this research, we develop a single-quantum-dot (QD)-mediated fluorescence resonance energy transfer (FRET) biosensor for amplification-free measurement of ten-eleven translocation 2 (TET2). When TET2 is present, it catalyzes the oxidation of 5-vinylcytosine in dsDNA to 5-formylmethylcytosine, and the subsequent labeling of dsDNA with Cy5 generates a biotinylated Cy5-dsDNA complex. Biotinylated Cy5-dsDNA complexes are conjugated to the streptavidin-coated 605QDs to obtain a Cy5-dsDNA-605QD nanostructures, inducing FRET from 605QD to Cy5. FRET signal can be simply measured by single-molecule counting. This biosensor enables homogeneous detection of TET2 with a limit of detection (LOD) of 0.042 ng/μL, and it can accurately measure cellular TET2 down to 1 cell. Moreover, this biosensor can be used to screen TET2 inhibitors, offering a new platform for TET2-related medical research and clinical diagnostics.

Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules

Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.