Algorithm-Assisted Detection and Imaging of microRNAs in Living Cancer Cells via the Disassembly of Plasmonic Core-Satellite Probes Coupled with Strand Displacement Amplification

Highly sensitive and specific detection of human papillomavirus type 16 using CRISPR/Cas12a assay coupled with an enhanced single nanoparticle dark-field microscopy imaging technique

Human papillomavirus (HPV) is a prevalent sexually transmitted pathogen associated with cervical cancer. Detecting high-risk HPV (hr-HPV) infections is crucial for cervical cancer prevention, particularly in resource-limited settings. Here, we present a highly sensitive and specific sensor for HPV-16 detection based on CRISPR/Cas12a coupled with enhanced single nanoparticle dark-field microscopy (DFM) imaging techniques. Ag-Au satellites were assembled through the hybridization of AgNPs-based spherical nucleic acid (Ag-SNA) and AuNPs-based spherical nucleic acid (Au-SNA), and their disassembly upon target-mediated cleavage by the Cas12a protein was monitored using DFM for HPV-16 quantification. To enhance the cleavage efficiency and detection sensitivity, the composition of the ssDNA sequences on Ag-SNA and Au-SNA was optimized. Additionally, we explored using the SynSed technique (synergistic sedimentation of Brownian motion suppression and dehydration transfer) as an alternative particle transfer method in DFM imaging to traditional electrostatic deposition. This addresses the issue of inconsistent deposition efficiency of Ag-Au satellites and their disassembly due to their size and charge differences. The sensor achieved a remarkable limit of detection (LOD) of 10 fM, lowered by 9-fold compared to traditional electrostatic deposition methods. Clinical testing in DNA extractions from 10 human cervical swabs demonstrated significant response differences between the positive and negative samples. Our sensor offers a promising solution for sensitive and specific HPV-16 detection, with implications for cancer screening and management.

Dark-field imaging and fluorescence dual-mode detection of microRNA-21 in living cells by core-satellite plasmonic nanoprobes

The in situ precise quantification and simultaneous imaging of low abundance microRNAs (miRNAs) within living cells is critical for cancer diagnosis, yet it remains a significant challenge. Leveraging the excellent sensitivity and spatiotemporal resolution of dark-field microscopy (DFM) and fluorescence imaging, we have successfully devised a novel detection approach using dual-signal reporter probes (DSRPs). These probes allow for highly sensitive detection of miRNA-21 in living cells via toehold-mediated strand displacement cascades. The DSRPs were constructed by Au nanoparticles and Ag nanoclusters core-satellite nanostructures. After the recognition of miRNA-21, the strand displacement cascades were triggered, inducing the disassembly of the Au/Ag core-satellite nanostructure with apparent scattering intensity decrease and peak wavelength shifts. Additionally, the fluorescence of Ag clusters could be recovered and further enhanced when in close proximity to specific guanine-rich strands. The dual-signal response capability enables the accurate detection of miRNA-21 from 1 fM to 1 nM, with a limit of detection reached 0.75 fM. DFM and fluorescent imaging of living cells efficiently confirms the applicable detection of miRNA-21 in complex detection media. The biosensor based on DSRPs represents a promising nanoplatform for visual monitoring and imaging of biomolecules in living cells, even at the single particle level.

Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review

Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.

Single-Particle Optical Imaging for Ultrasensitive Bioanalysis

The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.

Toehold-mediated strand displacement coupled with single nanoparticle dark-field microscopy imaging for ultrasensitive biosensing

Highly sensitive detection of biomarkers is essential for disease prevention and early diagnosis. Herein, a highly sensitive strategy was proposed for microRNA-21 (miRNA-21) detection by the incorporation of programmable toehold-mediated strand displacement (TMSD) and dark-field microscopy imaging. Firstly, efficient and specific TSMD was carried out via hybridization between the substrate strand (Sub) and two short probe strands (P1, P2). Then, miRNA-21 could specifically hybridize with Sub due to the toehold that existed on its tail, which triggered the amplification with the help of the assist strands, and forming a large number of Sub-assist double-stranded DNA (dsDNA). This process realized the targeted highly specific recognition of miRNA-21 and the amplification of the trace target to high-output dsDNA. Additionally, as glucose oxidase (Gox) was modified on the end of the assist strands in advance, hydrogen peroxide was generated after adding glucose to the system, which further etched gold-silver core-shell nanocubes (Au@Ag NCs). As a result, the size of Au@Ag NCs decreased and the scattering intensity reduced simultaneously. The scattering intensity reduction value of Au@Ag NCs has a linear relationship with miRNA-21 concentration in the range of 1.0 to 100.0 fM with a limit of detection of 1.0 fM. Finally, the proposed method has been successfully demonstrated for the determination of miRNA-21 in lung cancer cell A549 lysate.

A designer DNA tetrahedron-based molecular beacon for tumor-related microRNA fluorescence imaging in living cells

A designer nanoprobe of tetrahedral DNA framework (TDF) combined with MB (termed TDFM nanoprobe) for the efficient fluorescence imaging of tumor-related miRNA-214 in living cells.

Electrochemical sensor propelled by exonuclease III for highly efficient microRNA-155 detection

We constructed an electrochemical sensor, propelled by exonuclease III, for highly efficient microRNA-155 detection. The detection performance of the sensor was excellent, with a detection limit as low as 0.035 fM.

An algorithm-assisted automated identification and enumeration system for sensitive hydrogen sulfide sensing under dark field microscopy

A sensitive H2S sensing strategy has been developed based on the automated identification and enumeration algorithm.

Plasmonic biosensor for the highly sensitive detection of microRNA-21 via the chemical etching of gold nanorods under a dark-field microscope

MicroRNAs involved in tumor-related tissues at abnormal expression level present tremendous potential in the early diagnosis of cancers. However, their intrinsic shortcomings, for instance, low abundance and high sequence homology, make it challengeable to quantify them with high sensitivity and selectivity. Herein, a highly sensitive platform with great specificity was developed for microRNA-21 based on the produced-I₂ triggered chemical etching of gold nanorods to a smaller size, resulting in a significant blue shift and a great intensity decrease in the localized surface plasmon resonance (LSPR) scattering. The synergism of strand displacement and enzymatic reaction enabled the proposed strategy with a high sensitivity and selectivity toward microRNA-21 in a dynamic range from 0.1 to 10,000 pM and a low limit of detection of 71.22 fM (3σ/k) by dark-field microscope. Additionally, the remarkable discrimination of single nucleotide difference suggested the superior selectivity towards microRNA-21, which presented a satisfactory recovery in human serum samples. The proposed plasmon platform could also serve as a universal and sensitive detection of cancer biomarkers, presenting the amusing application prospects in the early diagnosis of various cancers by adapting the corresponding nucleic acid sequences.

Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection

Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.

Assembling of anisotropic plasmonic sheet-core-satellites for simultaneous ultrasensitive detection of MC-LR toxin

An anisotropic plasmonic sheet-core-satellite (PSCS) superstructure can be controlled via competitive binding between aptamer/MC-LR conjugation and aptamer-ssDNA hybridization. SERS nanotags can be incorporated into anisotropic plasmonic sheet-cores, e.g., pGO/nanorods, or pGO/hollow AgCl : Au nanoplates so as to fabricate an aptasensor for "ON-OFF" detection of MC-LR toxin. Preparing a PSCS superstructure and detection of toxin can be simultaneously completed so as to simplify the detection procedure of MC-LR toxin. Detection sensitivity of MC-LR toxin can be optimized by controlling aspect ratios or hollow interiors of plasmonic core nanoparticles. Herein, a limit of detection (0.635 pM) with a wide linear range from 1 pM to 10 nM can be obtained via optimized PSCS of pGO/nanorod/dotnanotags. When the aptasensor was tested in real samples, the PSCS shows excellent recoveries from 96.6% to 104.5% with relative standard deviation (RSD) lower than 2.89% in spiked reservoir samples. It can be predicted that a one-step facile nanofabrication/aptasensing approach would be extensively applied for rapid detection of some other environmental contaminants.