Rolling circle amplification combined with gold nanoparticles-tag for ultra sensitive and specific quantification of DNA by inductively coupled plasma mass spectrometry

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.

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.

Fast detection of bacterial gut pathogens on miniaturized devices: an overview

INTRODUCTION

Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation.

AREAS COVERED

Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges.

EXPERT OPINION

Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.

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.

Electrochemiluminescence biosensor based on molybdenum disulfide-graphene quantum dots nanocomposites and DNA walker signal amplification for DNA detection

Based on the prominent electrochemiluminescence (ECL) performances of molybdenum disulfide-graphene quantum dots (MoS2-GQDs) nanocomposite and combined with enzyme-assisted recycling DNA walker signal amplification, an "on-off" switch ECL biosensor was proposed for sensitive assay of specific DNA sequences. Noticeably, MoS2 with two-dimensional nanosheet structure increased the loading capacity of GQDs to support abundant hairpin DNA (H). The composites of MoS2 and GQDs facilitated the charge transfer in ECL process, which significantly improved the ECL signal to achieve an "on" state. Then, the DNA walker cyclic amplification was performed by adding the target DNA and exonuclease III (Exo III). Finally, the DNA2-Fc-DNA1 was introduced into the system as ECL signal quencher, turning the ECL signal into an "off" state. The sensitive assay of ultra-low concentration specific DNA sequences was realized according to the variation of ECL signal strength before and after the existence of target DNA. The proposed ECL biosensor showed a good linear relationship ranging from 1 nM to 100 aM with a detection limit of 25.1 aM, providing a powerful strategy for biomedical research and clinical analysis.

Elemental Mass Spectrometry and Fluorescence Dual-Mode Strategy for Ultrasensitive Label-Free Detection of HBV DNA

This work reported a simple and ultrasensitive label-free method for the detection of hepatitis B virus (HBV) DNA by combining hyperbranched rolling circle amplification (HRCA) with dual-mode detection by inductively coupled plasma mass spectrometry (ICP-MS) and fluorescence using ruthenium complex [Ru(bpy)₂dppz]²⁺ (bpy = 2,2'-bipyridine, dppz = dipyrido [3,2-a:2',3'-c] phenazine) as a dual functional probe. An HBV DNA-initiated HRCA system was designed to realize the highly efficient amplification of HBV DNA with the generation of a mass of dsDNA. Also, the [Ru(bpy)₂dppz]²⁺ probe was then added to intercalate into the dsDNA products, resulting in strong fluorescence recovery of the probe for fluorescence detection. Meanwhile, using a biotin-modified primer in HRCA, the dsDNA-[Ru(bpy)₂dppz]²⁺ complexes could be captured by the avidin-coated 96-well plates, and the captured [Ru(bpy)₂dppz]²⁺ probe was later desorbed by acid for ICP-MS detection. The linear range of the proposed method was 3.5-200 amol L^-1 and the limit of detection (LOD) was 1 amol L^-1 for ICP-MS detection, while the linear range was 20-500 amol L^-1 and the LOD was 9.6 amol L^-1 for fluorescence detection. The developed method was applied to human serum sample analysis, and the analytical results coincided very well with those obtained by the real-time polymerase chain reaction (PCR) method. The developed dual-mode label-free detection method was ultrasensitive, simple, and accurate, showing great potential for therapeutic monitoring of HBV infection.

DNA Transformations for Diagnosis and Therapy

Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.

Signal amplification strategies for clinical biomarker quantification using elemental mass spectrometry

The current trends in modern medicine towards early diagnosis, or even prognosis, of different diseases have brought about the need for the corresponding biomarker detection at ever lower levels in really complex matrices. To do so, it is necessary to use proper extremely sensitive detection techniques such as elemental mass spectrometry. However, target labelling with metals for subsequent sensitive ICP-MS detection falls short nowadays even if resorting to inorganic nanoparticles containing a high number of detectable elements. Thus, new amplification strategies are being proposed to face this analytical challenge that will be critically discussed in this paper. Fundamentals of different novel strategies developed to achieve signal amplification and sensitive elemental mass spectrometry detection are here discussed. Some representative examples of relevant clinical applications are highlighted, along with future prospects and challenges.

Sensitive Immunoassay Detection of Plasmodium Lactate Dehydrogenase by Inductively Coupled Plasma Mass Spectrometry

Rapid, reliable, and sensitive detection of Plasmodium infection is central to malaria control and elimination. Many Malaria Rapid Diagnostic Tests (RDTs) developed for this purpose depend upon immunoassays that can be improved by advances in bound antibody sensor technology. In a previous study, immuno-polymerase chain reaction (PCR) was shown to provide highly sensitive detection of Plasmodium falciparum lactate dehydrogenase (PfLDH) in monoclonal antibody (mAb) sandwich assays. Here, we show comparably high immunoassay sensitivity by inductively coupled plasma mass spectrometry (ICP-MS) detection of gold nanoparticles (AuNPs). Following capture of PfLDH with the primary mAb and binding of the AuNP-labeled detection mAb, ICP-MS signals from the AuNPs provided quantitative measures of recombinant PfLDH test dilutions and P. falciparum-infected erythrocytes. A detection limit of 1.5 pg/mL was achieved with the PfLDH protein. Parasitemia in cultures of P. falciparum-infected erythrocytes could be detected to a lower limit of 1.6 parasite/μl (p/μl) for early ring-stage forms and 0.3 p/μl for mixed stages including mature trophozoites and schizont-stages. These results show that ICP-MS detection of AuNPs can support highly sensitive and accurate detection of Plasmodium infection.

Selective recognition of CdTe QDs and strand displacement signal amplification-assisted label-free and homogeneous fluorescence assay of nucleic acid and protein

Due to their simplicity of design and operation, homogeneous bioassays have been of great interest to researchers. Herein, a label-free and free separation fluorescence sensing platform was constructed for the determination of nucleic acid and prostate specific antigen (PSA) using CdTe QDs as the signal molecule. In our previous work, we surprisingly found that the CdTe QDs can selectively distinguish Ag+ and the C-Ag+-C complex, which was the basis of the sensor. On the basis of the selective cation exchange reaction (CER), combined with the signal amplification of the strand displacement reaction (SDR), this work was first applied for the sensitive analysis of DNA. There are two types of hairpin structures in this sensing system, including the recognition probe (HP) and Ag+, which formed the C-Ag+-C structure, and the hairpin structure formed by the helper DNA itself. In this work, target DNA can trigger the SDR that generates lots of HP-helper double-stranded DNA (dsDNA) and recycles the target DNA while releasing a large amount of Ag+, thus quenching the fluorescence signal of CdTe QDs to achieve the highly sensitive detection of DNA. In order to verify the versatility of this system using DNA as a bridge and aptamers as recognition probes, we extended the system to the detection of PSA. After examining its experimental performance, it was determined that this method displayed good analytical capability for DNA in the range of 10-13-10-10 M and PSA in the range of 10-13-10-10 g mL-1 with low 25 fM and 30 fg mL-1 limits of detection (LODs), respectively; high selectivity for both the target sequence and protein was shown. In addition, this platform was successfully used for the analysis of PSA in serum samples.

A unique FRET approach toward detection of single-base mismatch DNA in BRCA1 gene

Early detection of mutation carriers in predisposing genes such as BRCA1 plays an important role in disease prevention. This work developed a quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) technique for the detection of single-base mismatch DNA in BRCA1 gene. The FRET between QDs as the donor and silver nanocluster (AgNCs) as the acceptor was designed by the strong interaction between CdTe QDs with appropriate size and dsDNA through binding to its major groove. The dsDNA was formed by the hybridization of ssDNA labeled to AgNCs with target DNA, which introduced CdTe QDs into the major grooves to place the AgNCs in close proximity to the QDs. The complementary and single-base mismatch DNA led to obviously different FRET signals. The FRET signal linearly correlated to the concentration of single-base mismatch DNA in the range of 1.5 × 10^-10-1.0 × 10^-6 mol L^-1. The proposed method showed a detection limit of 80 pmol L^-1 and the sensitivity comparable to the previously reported assays, indicating promising potential for single nucleotide polymorphisms diagnosis in clinical application.

Visual/CVG-AFS/ICP-MS multi-mode and label-free detection of target nucleic acids based on a selective cation exchange reaction and enzyme-free strand displacement amplification

Visual/CVG-AFS/ICP-MS three-mode detection of DNA based on the selective cation exchange reaction and enzyme-free strand displacement amplification.

Applications of Gold Nanoparticles in Non-Optical Biosensors

Due to their unique properties, such as good biocompatibility, excellent conductivity, effective catalysis, high density, and high surface-to-volume ratio, gold nanoparticles (AuNPs) are widely used in the field of bioassay. Mainly, AuNPs used in optical biosensors have been described in some reviews. In this review, we highlight recent advances in AuNP-based non-optical bioassays, including piezoelectric biosensor, electrochemical biosensor, and inductively coupled plasma mass spectrometry (ICP-MS) bio-detection. Some representative examples are presented to illustrate the effect of AuNPs in non-optical bioassay and the mechanisms of AuNPs in improving detection performances are described. Finally, the review summarizes the future prospects of AuNPs in non-optical biosensors.

Detection of nucleic acids via G-quadruplex-controlled l-cysteine oxidation and catalyzed hairpin assembly-assisted signal amplification

A novel homogeneous strategy for detection of DNA via biomimetic synthesis of luminescent QDs coupled with nucleic acid signal amplification.

Evaluation of in vitro cytotoxicity, biocompatibility, and changes in the expression of apoptosis regulatory proteins induced by cerium oxide nanocrystals

Cerium oxide nanocrystals (CeO₂-NCs) exhibit superoxide dismutase and catalase mimetic activities. Based on these catalytic activities, CeO₂-NCs have been suggested to have the potential to treat various diseases. The crystalline size of these materials is an important factor that influences the performance of CeO₂-NCs. Previous reports have shown that several metal-based nanocrystals, including CeO₂-NCs, can induce cytotoxicity in cancer cells. However, the underlying mechanisms have remained unclear. To characterize the anticancer activities of CeO₂-NCs, several assays related to the mechanism of cytotoxicity and induction of apoptosis has been performed. Here, we have carried out a systematic study to characterize CeO₂-NCs phase purity (X-ray diffraction), morphology (electron microscopy), and optical features (optical absorption, Raman scattering, and photoluminescence) to better establish their potential as anticancer drugs. Our study revealed anticancer effects of CeO₂-NCs in HT29 and SW620 colorectal cancer cell lines with half-maximal inhibitory concentration (IC₅₀) values of 2.26 and 121.18 μg ml^-1, respectively. Reductions in cell viability indicated the cytotoxic potential of CeO₂-NCs in HT29 cells based on inverted and florescence microscopy assessments. The mechanism of cytotoxicity confirmed by estimating possible changes in the expression levels of Bcl2, BclxL, Bax, PARP, cytochrome c, and β-actin (control) proteins in HT29 cells. Down-regulation of Bcl2 and BclxL and up-regulation of Bax, PARP, and cytochrome c proteins suggested the significant involvement of CeO₂-NCs exposure in the induction of apoptosis. Furthermore, biocompatibility assay showed minimum effect of CeO₂-NCs on human red blood cells.

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

Gold nanoparticles labeling with hybridization chain reaction amplification strategy for the sensitive detection of HepG2 cells by inductively coupled plasma mass spectrometry

Sensitive detection of circulating tumor cells (CTCs) is of great significance in the early detection of cancer and cancer metastasis. This work reported an efficient, specific, and sensitive immunoassay protocol for detection of tumor cells by using inductively coupled plasma mass spectrometry (ICP-MS) with gold nanoparticles (AuNPs) labeling and hybridization chain reaction (HCR) amplification. In the established approach, antibodies against epithelial cell adhesion molecule (anti-EpCAM) conjugated magnetic beads (MBs) were used for selective capture of tumor cells from peripheral blood, aptamer was applied for the recognition of captured tumor cells, and AuNPs labeled DNA concatamer was used as the signal probe for tumor cell labeling and ICP-MS detection. Due to the dual amplification effect of AuNPs and HCR, the limit of detection of this ICP-MS based method for HepG2 cells was as low as 15 cells, and the linear range was 40-8000 cells with the relative standard deviation for seven replicate detections of 200 HepG2 cells was 8.7%. Furthermore, the applicability of the method for the analysis of peripheral blood samples was demonstrated by the spiking tests. The established method was highly specific and sensitive for the detection of HepG2 cells, and has a good application potential in clinical diagnosis.

A linear DNA probe as an alternative to a molecular beacon for improving the sensitivity of a homogenous fluorescence biosensing platform for DNA detection using target-primed rolling circle amplification

Linear single-labeled DNA probes are used in this RCA-based fluorescence strategy for DNA detection, which could effectively avoid the fluorescence quenching between neighboring signal probes using hairpin probe as signal probe.

A cascade signal amplification strategy for ultrasensitive colorimetric detection of BRCA1 gene

Schematic illustration of a colorimetric biosensor for breast cancer1 gene detection based on DNAzyme assistant DNA recycling and rolling circle amplification.