NIR-to-Vis Handheld Platforms for Detecting miRNA Level and Mutation Based on Sub-10 nm Sulfide Nanodots and HCR Amplification

Insight into Cys and its derivatives metabolism in living system with 3D-printed portable smartphone platform via multifunctional fluorescent probe

Cysteine (Cys) is a crucial biological thiol that facilitates broad range of biological circumstances and health conditions. Especially the aberrant Cys level in human serum is an independent risk factor for cardiovascular diseases. What more, Cys metabolism (Cys to SO2) is typically connected with illnesses such as lung cancer, and are recognized as biomarker. Herein, an innovative multifunctional fluorescent probe was rudimentarily designed and utilized, not only for realizing real-time visualization of the metabolism of Cys to SO2 in tumors through two self-sufficient channels without spectral cross-interference, but also for sensitive, real-time, on-site, and quantitative visual recognition of Cys in human serum through 3D-printed smartphone sensing platform. In addition, the probe's unique response to Cys/HSO3- in distinct spectral behaviors, which have been characterized theoretically using UV-Vis, fluorescence, DFT calculations, and 1H NMR. More importantly, the methodology reported herein enables an available pathway for real-time/on-site and visual determination of Cys in human serum and is expected to extend the use of potential cardiovascular disease biomarker studies for initial monitoring and clinical diagnosis.

Smartphones as a platform for molecular analysis: concepts, methods, devices and future potential

Over the past 15 years, smartphones have had a transformative effect on everyday life. These devices also have the potential to transform molecular analysis over the next 15 years. The cameras of a smartphone, and its many additional onboard features, support optical detection and other aspects of engineering an analytical device. This article reviews the development of smartphones as platforms for portable chemical and biological analysis. It is equal parts conceptual overview, technical tutorial, critical summary of the state of the art, and outlook on how to advance smartphones as a tool for analysis. It further discusses the motivations for adopting smartphones as a portable platform, summarizes their enabling features and relevant optical detection methods, then highlights complementary technologies and materials such as 3D printing, microfluidics, optoelectronics, microelectronics, and nanoparticles. The broad scope of research and key advances from the past 7 years are reviewed as a prelude to a perspective on the challenges and opportunities for translating smartphone-based lab-on-a-chip devices from prototypes to authentic applications in health, food and water safety, environmental monitoring, and beyond. The convergence of smartphones with smart assays and smart apps powered by machine learning and artificial intelligence holds immense promise for realizing a future for molecular analysis that is powerful, versatile, democratized, and no longer just the stuff of science fiction.

A universal fluorescence biosensor based on rolling circle amplification and locking probe for DNA detection

A stable DNA signal amplification sensor was developed on account of rolling circle amplification (RCA). This sensor includes target DNA-controlled rolling circle amplification technology and locking probe DNA replacement technology, which can be used to detect DNA fragments with genetic information, thus constructing a biosensor for universal detection of DNA. This study takes the homologous DNA of human immunodeficiency virus (HIV) and let-7a as examples to describe this biosensor. The padlock probe is first cyclized by T4 DNA ligase in response to the target's reaction with it. Then, rolling cycle amplification is initiated by Phi29 DNA polymerase, resulting in the formation of a lengthy chain with several triggers. These triggers can open the locked probe LP1 with the fluorescence signal turned off, so that it can continue to react with H2 to form a stable H1-H2 double strand. This regulates the distance between B-DNA modified by the quenching group and H1 modified by fluorescent group, and the fluorescence signal is recovered.

Programmable Entropy-Driven Circuit-Cascaded Self-Feedback DNAzyme Network for Ultra-Sensitive Fluorescence and Photoelectrochemical Dual-Mode Biosensing

Inspired by natural DNA networks, programmable artificial DNA networks have become an attractive tool for developing high-performance biosensors. However, there is still a lot of room for expansion in terms of sensitivity, atom economy, and result self-validation for current microRNA sensors. In this protocol, miRNA-122 as a target model, an ultrasensitive fluorescence (FL) and photoelectrochemical (PEC) dual-mode biosensing platform is developed using a programmable entropy-driven circuit (EDC) cascaded self-feedback DNAzyme network. The well-designed EDC realizes full utilization of the DNA strands and improves the atomic economy of the signal amplification system. The unique and rational design of the double-CdSe quantum-dot-released EDC substrate and the cascaded self-feedback DNAzyme amplification network significantly avoids high background signals and enhances sensitivity and specificity. Also, the enzyme-free, programmable EDC cascaded DNAzyme network effectively avoids the risk of signal leakage and enhances the accuracy of the sensor. Moreover, the introduction of superparamagnetic Fe3O4@SiO2-cDNA accelerates the rapid extraction of E2-CdSe QDs and E3-CdSe QDs, which greatly improves the timeliness of sensor signal reading. In addition to the strengths of linear range (6 orders of magnitude) and stability, the biosensor design with dual signal reading makes the test results self-confirming.

Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro

Single-nucleotide variants (SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.

Endogenous mRNA-Powered and Spatial Confinement-Derived DNA Nanomachines for Ultrarapid and Sensitive Imaging of Let-7a

DNA nanostructure-based signal amplifiers offer new tools for imaging intracellular miRNA. However, the inadequate kinetics and susceptibility to enzymatic hydrolysis of these amplifiers, combined with a deficient cofactor concentration within the intracellular environment, significantly undermine their operational efficiency. In this study, we address these challenges by encapsulating a localized target strand displacement assembly (L-SD) and a toehold-exchange endogenous-powered component (R-mRNA) within a framework nucleic acid (FNA) structure─20 bp cubic DNA nanocage (termed RL-cube). This design enables the construction of an endogenous-powered and spatial-confinement DNA nanomachine for ratiometric fluorescence imaging of intracellular miRNA Let-7a. The R-mRNA is designed to be specifically triggered by glyceraldehyde 3-phosphate dehydrogenase (GAPDH), an abundant cellular enzyme, and concurrently releases a component that can recycle the target Let-7a. Meanwhile, L-SD reacts with Let-7a to release a stem-loop beacon, generating a FRET signal. The spatial confinement provided by the framework, combined with the ample intracellular supply of GAPDH, imparts remarkable sensitivity (7.57 pM), selectivity, stability, biocompatibility, and attractive dynamic performance (2240-fold local concentration, approximately four times reaction rate, and a response time of approximately 7 min) to the nanomachine-based biosensor. Consequently, this study introduces a potent sensing approach for detecting nucleic acid biomarkers with significant potential for application in clinical diagnostics and therapeutics.

A Self-Assembled G-Quadruplex/Hemin DNAzyme-Driven DNA Walker Strategy for Sensitive and Rapid Detection of Lead Ions Based on Rolling Circle Amplification

Herein, a sensitive biosensor is constructed based on a novel rolling circle amplification (RCA) for colorimetric quantification of lead ion (Pb2+). At the detection system, GR5 DNAzymes are modified on the surface of an immunomagnetic bead, and Pb2+ is captured by the aptamer, inducing the disintegration of the GR5 DNAzyme and the release of the DNA walker. After the introduction of the template DNA, T4 DNA ligase, and phi29 DNA polymerase, an RCA is initiated for the sensitivity improvement of this method. Moreover, a G4-hemin DNAzyme is formed as a colorimetric signal, owing to its peroxide-like activity to catalyze the TMB-H2O2 substrate. Under the optimized conditions, the limit of detection (LOD) of this fabricated biosensor could reach 3.3 pM for Pb2+ with a concentration in the range of 0.01-1000 nM. Furthermore, the results of real samples analysis demonstrate its satisfactory accuracy, implying its great potential in the rapid detection of heavy metals in the environment.

Advances in Point-of-Care Testing of microRNAs Based on Portable Instruments and Visual Detection

MicroRNAs (miRNAs) are a class of small noncoding RNAs that are approximately 22 nt in length and regulate gene expression post-transcriptionally. miRNAs play a vital role in both physiological and pathological processes and are regarded as promising biomarkers for cancer, cardiovascular diseases, neurodegenerative diseases, and so on. Accurate detection of miRNA expression level in clinical samples is important for miRNA-guided diagnostics. However, the common miRNA detection approaches like RNA sequencing, qRT-PCR, and miRNA microarray are performed in a professional laboratory with complex intermediate steps and are time-consuming and costly, challenging the miRNA-guided diagnostics. Hence, sensitive, highly specific, rapid, and easy-to-use detection of miRNAs is crucial for clinical diagnosis based on miRNAs. With the advantages of being specific, sensitive, efficient, cost-saving, and easy to operate, point-of-care testing (POCT) has been widely used in the detection of miRNAs. For the first time, we mainly focus on summarizing the research progress in POCT of miRNAs based on portable instruments and visual readout methods. As widely available pocket-size portable instruments and visual detection play important roles in POCT, we provide an all-sided discussion of the principles of these methods and their main limitations and challenges, in order to provide a guide for the development of more accurate, specific, and sensitive POCT methods for miRNA detection.

CSDR Coupling with Exo III for Ultrasensitive Electrochemistry Determination of miR-145

Recently, miRNAs have become a promising biomarker for disease diagnostics. miRNA-145 is closely related to strokes. The accuracy determination of miRNA-145 (miR-145) in stroke patients still remains challenging due to its heterogeneity and low abundance, as well as the complexity of the blood matrix. In this work, we developed a novel electrochemical miRNA-145 biosensor via subtly coupling the cascade strand displacement reaction (CSDR), exonuclease III (Exo III), and magnetic nanoparticles (MNPs). The developed electrochemical biosensor can quantitatively detect miRNA-145 ranging from 1 × 10² to 1 × 10⁶ aM with a detection limit as low down as 100 aM. This biosensor also exhibits excellent specificity to distinguish similar miRNA sequences even with single-base differences. It has been successfully applied to distinguish healthy people from stroke patients. The results of this biosensor are consistent with the results of the reverse transcription quantitative polymerase chain reaction (RT-qPCR). The proposed electrochemical biosensor has great potential applications for biomedical research on and clinical diagnosis of strokes.

CRISPR/Cas12a Coupling with Magnetic Nanoparticles and Cascaded Strand Displacement Reaction for Ultrasensitive Fluorescence Determination of Exosomal miR-21

Exosomal MicroRNA-21 (miRNA-21, miR-21) is significantly up-regulated in blood samples of patients with lung cancer. Exosomal-derived miR-21 can be used as a promising biomarker for the early diagnosis of lung cancer. This paper develops a fluorescent biosensor based on the combination of magnetic nanoparticles (MNPs), cascade strand displacement reaction (CSDR) and CRISPR/Cas12a to detect the exosomal miR-21 from lung cancer. The powerful separation performance of MNPs can eliminate the potential interference of matrix and reduce the background signal, which is very beneficial for the improvement of specificity and sensitivity. The CSDR can specifically transform one miR-21 into plenty of DNA which can specifically trigger the trans-cleavage nuclease activity of Cas12a, resulting in the cleavage of ssDNA bi-labeled with fluorescent and a quencher. Under the optimized experimental conditions, the developed fluorescence biosensor exhibited high sensitivity and specificity towards the determination of exosomal-derived miR-21 with a linear range from 10 to 1 × 10⁵ fM and a low detection limit of about 0.89 fM. Most importantly, this method can be successfully applied to distinguish the exosomal miR-21 from the lung cancer patients and the healthy people.

Double Signal Amplification Strategy for Dual-Analyte Fluorescent Aptasensors for Visualizing Cancer Biomarker Proteins

The simultaneous analysis of diversified biomarkers with high sensitivity and in a point-of-care (POC) manner is of great significance for facile and early cancer diagnosis. Herein, we develop a target amplification-assisted ratiometric fluorescence assay (TARFA) platform integrating the dual-amplification strategy and colorimetric readout technology for sensitive and specific detection of two malignancy-associated biomarkers. Meanwhile, the NIR-excited alkaline-earth sulfide nanodots (ASNDs) with an ultrasmall (<10 nm) diameter and tunable emission wavelength are employed to replace commonly UV/visible light-excited fluorescent labels to minimize background interference from the sample matrix. Unique advantages of the ASNDs, together with superiority of consecutive signal amplification of enzymatic target recycling (ETR) and hybridization chain reaction (HCR), realize the pg/mL-range detection limit in specifically recognizing the vascular endothelial growth factor (VEGF) and soluble interleukin-6 receptors (sIL-6R). The combination detection of the dual analyte exhibits an improved sensitivity for cancer diagnosis. The addition of the target biomarkers leads to an increasingly ratiometric RGB signal, and quantification based on the ratio-dependent signal is more reliable rather than measuring the absolute RGB signals. Moreover, perceptible color transformation makes the TARFA platform competent for visual analysis of the target analytes as convenient as reading the pH indicator strip, and hue-based image analysis also improves the method with fine precision by quantitatively identifying the visual color. This work provides a new kind of NIR-excited aptasensing platform with a low detection limit, high throughput, and great portability, which also highlights the potential of the ASNDs in biomolecular fluorescent labeling.