Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification

Ultra-stable and highly-bright CsPbBr3 perovskite/silica nanocomposites for miRNA detection based on digital single-nanoparticle counting

Single-nanoparticle counting (SNPC) based on fluorescent tag (FT) stands out for its capacity to achieve amplification-free and sensitive detection of biomarkers. The stability and luminescence of FT are important to the sensitivity and reliability of SPNC. In this work, we developed novel perovskite/silica nanocomposites by in-situ nanoconfined growth of CsPbBr3 nanocrystals inside mesoporous structure of silica nanoparticles. PbBr(OH) was formed in an alkaline-assisted reaction triggered by water on the surface of CsPbBr3 nanocrystals. The as-obtained nanocomposites, featuring dual protection from silica matrix and PbBr(OH), exhibited high absolute photoluminescence quantum yield (PLQY) of 86.5% and demonstrated outstanding PL stability confronting with water, heat, ultrasound and UV-irradiation, which is desired by SNPC-based biosensor. Thereafter, these nanocomposites were used to construct an operationally friendly SNPC assay for the amplification-free quantification of cancer-associated miRNA. Quantitative detection of miRNA could be accomplished by directly counting the number of nanocomposites using a flow cytometer in this assay. This strategy did not ask for multiple washing steps and demonstrated specific and sensitive detection of miRNA 21, which exhibited a dynamic range of 1-1000 pM and limit of detection of 79 amol. The employment of highly stable perovskite/silica nanocomposites improved the test reliability and stability of SNPC, revealing the vast potential of perovskites in biosensing.

Amplification-free microRNA profiling with femtomolar sensitivity on a plasmonic enhanced fluorescence nano-chip

MicroRNAs (miRNAs) are a class of small, non-coding RNA molecules involved in the regulation of gene expression, thus considered as promising biomarkers for cancer, cardiovascular diseases, neurodegenerative diseases, etc. However, quantitative analysis of miRNAs faces challenges owing to their high homology, small size & ultra-low abundance, and disease occurrence is often related to abnormal expression of multiple miRNAs where method for parallel miRNAs analysis is required. In this work, multiplexed analysis of miRNAs was established on a plasmonic nano-chip capable of fluorescence enhancement in the near-infrared region. Combined with polyadenylation at the hydroxyl terminate of target miRNA to afford abundant sites for fluorophore labeling, our assay achieved amplification-free detection of miRNAs from nM to fM with the limit of detection down to ca. 5 fM. A miRNA panel was constructed to detect 10 miRNAs differentially expressed in MCF-7 and A549 cell lines and validated with qRT-PCR, demonstrating the practical application of this method. This scalable platform can be customized for different miRNA panels, facilitating multiple miRNA profiling for various diseases.

Microparticle-Based Detection of Viruses

Surveillance of viral pathogens in both point-of-care and clinical settings is imperative to preventing the widespread propagation of disease-undetected viral outbreaks can pose dire health risks on a large scale. Thus, portable, accessible, and reliable biosensors are necessary for proactive measures. Polymeric microparticles have recently gained popularity for their size, surface area, and versatility, which make them ideal biosensing tools. This review cataloged recent investigations on polymeric microparticle-based detection platforms across eight virus families. These microparticles were used as labels for detection (often with fluorescent microparticles) and for capturing viruses for isolation or purification (often with magnetic microparticles). We also categorized all methods by the characteristics, materials, conjugated receptors, and size of microparticles. Current approaches were compared, addressing strengths and weaknesses in the context of virus detection. In-depth analyses were conducted for each virus family, categorizing whether the polymeric microparticles were used as labels, for capturing, or both. We also summarized the types of receptors conjugated to polymeric microparticles for each virus family.

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.

Amplification-free smartphone-based attomolar HBV detection

Classical gold standard HBV detection relies on expensive devices and complicated procedures, thus is always restricted in large-scale hospitals and centers for disease control and prevention. To extend HBV detection to primary clinics especially in underdeveloped areas, we design amplification-free smartphone-based attomolar HBV detecting technique based on single molecule sensing. Verified by synthesized HBV target DNA, this technique reaches a detection limit at attomolar concentration (100 aM); and verified by 110 clinical samples, it also reaches a rather high sensitivity of 10⁴ copy/mL (≈2000 IU/mL) with a high accuracy of 93.64% certificated by gold standard HBV detecting devices. Besides, this technique can quantify HBV viral load in 70 min only using portable and inexpensive devices as well as simple operations. Because of its cost-effective, field-portable and operable design, highly sensitive and selective detecting capability and wireless data connectivity, this technique can be potentially used in mobile HBV diagnoses and share HBV epidemic information especially in resource limited situations.

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.

Low-Numerical Aperture Microscope Objective Boosted by Liquid-Immersed Dielectric Microspheres for Quantum Dot-Based Digital Immunoassays

Quantum dot (QD)-based digital immunoassays play an important role in ultrasensitive biomarker detection. However, the requirement of an objective with a high numerical aperture (NA) limits the application of this immunoassay. Here, high-quality imaging of massive single-QDs was achieved by the combination of an air objective (20×/0.4 NA) and liquid-immersed microspheres (150 μm, n = 2.2). The signal-to-noise ratio was comparable to that of a 100×/1.4 NA oil objective. Digital analysis of prostate-specific antigen (PSA) was performed within the dynamic range of 0-50 ng/mL and a limit of detection of 0.17 ng/mL. The measured serum data from the PSA were close to the values provided by a hospital. Using a low-magnification and low-NA objective may reduce the barrier of microscopy miniaturization and is beneficial to popularize biomolecular digital analysis.

Stimuli-Responsive Autonomous-Motion Molecular Machine for Sensitive Simultaneous Fluorescence Imaging of Intracellular MicroRNAs

DNAzymes with enzymatic activity identified from random DNA pools by in vitro selection have recently attracted considerable attention. In this work, a DNAzyme-based autonomous-motion (AM) molecular machine is demonstrated for sensitive simultaneous imaging of different intracellular microRNAs (miRNAs). The AM molecular machine consists of two basic elements, one of which is a target-analogue-embedded double-stem hairpin substrate (TDHS) and the other is a locking-strand-silenced DNAzyme (LSDz). LSDz can be activated by target miRNA and catalytically cleave TDHS, generating Clv-TDHS and releasing free target analogue capable of triggering the next round of cleavage reaction. As such, the molecular machine can exert sustainable autonomous operation, producing an enhanced signal. Because the active target analogue comes from the machine itself and offers cyclical stimulation in a feedback manner, this target-induced autonomous cleavage circuit is termed a self-feedback circuit (SFC). The SFC-based molecular machine can be used to quantify miRNA-21 down to 10 pM without interference from nontarget miRNAs, indicating a substantial improvement in assay performance compared with its counterpart system without an SFC effect. Moreover, due to the enzyme-free process, the AM molecular machine is suitable for miRNA imaging in living cells, and the quantitative results are consistent with the gold standard PCR assay. More interestingly, the AM molecular machine can be used for the simultaneous fluorescence imaging of several intracellular miRNAs, enabling the accurate discrimination of cancerous cells (e.g., HeLa and MCF-7) from healthy cells. The SFC-based autonomous-motion machine is expected to be a promising tool for the research of molecular biology and early diagnosis of human diseases.

Nonamplification Multiplexed Assay of Endonucleases and DNA Methyltransferases by Colocalized Particle Counting

Restriction endonucleases (ENases) and DNA methyltransferases (MTases) are important enzymes in biological processes, and detection of ENases/MTases activity is significant for biological and pharmaceutical studies. However, available nonamplification methods with a versatile design, desirable sensitivity, and signal production mode of unbiased quantification toward multiple nucleases are rare. By combining deliberately designed hairpin DNA probes with the colocalized particle counting technique, we present a nonamplification, separation-free method for multiplexed detection of ENases and MTases. In the presence of target ENases, the hairpin DNA is cleaved and the resulting DNA sequence forms a sandwich structure to tie two different-colored fluorescent microbeads together to generate a colocalization signal that can be easily detected using a standard fluorescence microscope. The multiplexed assay is realized via different color combinations. For the assay of methyltransferase, methylation by MTases prevents cleavage of the hairpin by the corresponding ENase, leading to decreased colocalization events. Three ENases can be simultaneously detected with high selectivity, minimal cross-talk, and detection limits of (4.1-6.4) × 10^-4 U/mL, and the corresponding MTase activity can be measured without a change of the probe design. The potential for practical application is evaluated with human serum samples and different ENase and MTase inhibitors with satisfactory results. The proposed method is separation-free, unbiased toward multiple targets, and easy to implement, and the strategy has the potential to be extended to other targets.

Single-particle fibrinogen detection using platelet membrane-coated fluorescent polystyrene nanoparticles

Fibrinogen participates in many physiological processes and is a biomarker for a variety of diseases. On this account, the development of a sensitive method for fibrinogen assay is particularly important. Herein, we demonstrate a new color-coded single-particle detection (SPD) method for fibrinogen detection by using platelet membrane-coated fluorescent polystyrene nanoparticles (PNPs) as the probes. Due to the specific interactions between fibrinogen and integrin receptors on platelet membranes, PNPs can form aggregated structures in the presence of fibrinogen. Therefore, colocalization events between green and red PNPs and the corresponding Pearson's correlation coefficient vary with the concentrations of fibrinogen. The sensing ability shows a linear range of 30-300 μg mL^-1 and a limit of detection (LOD) of 3.9 μg mL^-1 (11.3 nM) for fibrinogen detection. Moreover, it has been validated that the proposed biosensor can selectively detect fibrinogen and shows a good performance in real sample applications.

Advances in multiplexed techniques for the detection and quantification of microRNAs

MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.

Nanomaterial-based multiplex optical sensors

The drive for a simultaneous analysis of multiple targets with excellent accuracy and efficiency, which is often required in both basic biomedical research and clinical applications, demands the development of multiplexed bioassays with desired throughput. With the development of nanotechnologies, innovative multiplex optical bioassays have been achieved. Nanomaterials exhibit unique physical and chemical properties such as easily tunable size, large surface-to-volume ratio, excellent catalysis and the desired signal transduction mechanism, which makes them excellent candidates for the fabrication of novel optical nanoprobes. This mini review summarizes nanomaterial-based optical multiplex sensors from the last 5 years. Specific optical techniques covered in this review are fluorescence, surface-enhanced Raman scattering (SERS), localized surface plasmon resonance (LSPR), chemiluminescence (CL), and the multimodality with fundamentals and examples.