Dual-Modal Apoptosis Assay Enabling Dynamic Visualization of ATP and Reactive Oxygen Species in Living Cells

High-Resolution and Dynamic Visualization of Intracellular Redox Potential Using a Metal-Organic Framework-Functionalized Nanopotentiometer

Redox potential plays a key role in regulating intracellular signaling pathways, with its quantitative analysis in individual cells benefiting our understanding of the underlying mechanism in the pathophysiological events. Here, a metal organic framework (MOF)-functionalized SERS nanopotentiometer has been developed for the dynamic monitoring of intracellular redox potential. The approach is based on the encapsulation of zirconium-based MOF (Uio-66-F4) on a surface of gold-silver nanorods (Au-Ag NRs) that is modified with the newly synthesized redox-sensitive probe ortho-mercaptohydroquinone (HQ). Thanks to size exclusion of MOF as the chemical protector, the nanopotentiometer can be adapted to long-term use and possess high anti-interference ability toward nonredox species. Combining the superior fingerprint identification of SERS with the electrochemical activity of the quinone/hydroquinone, the nanopotentiometer shows a reversible redox responsivity and can quantify redox potential with a relatively wide range of -250-100 mV. Furthermore, the nanopotentiometer allows for dynamic visualization of intracellular redox potential changes induced by drugs' stimulation in a high-resolution manner. The developed approach would be promising for offering new insights into the correlation between redox potential and tumor proliferation-involved processes such as oxidative stress and hypoxia.

Application of Aptamer-SERS Nanotags for Unveiling the PD-L1 Immunomarker Progression Correlated to the Cell Metabolic Bioprocess

In recent years, the expression and progression of programmed cell death ligand 1 (PD-L1) as an immunomarker in the context of a cell metabolic environment has gained significant attention in cancer research. However, intercellular bioprocesses that control the dynamics of PD-L1 have been largely unexplored. This study aimed to explore the cell metabolic states and conditions that govern dynamic variations of PD-L1 within the cell metabolic environment using an aptamer-based surface-enhanced Raman scattering (SERS) approach. The aptamer-SERS technique offers a sensitive, rapid, and powerful analytical tool for targeted and nondestructive detection of an immunomarker with high sensitivity and specificity. By combining aptamer-SERS with cell state profiling, we investigated the modulation in PD-L1 expression under different metabolic states, including glucose deprivation, metabolic coenzyme activity, and altered time/concentration-based cytokine availability. The most intriguing features in our findings include the cell-specific responses, cell differentiation by revealing distinct patterns, and dynamics of PD-L1 in different cell lines. Additionally, the time-dependent variations in PD-L1 expression, coupled with the dose-dependent relationship between glucose concentration and PD-L1 levels, underscore the complex interplay between immune checkpoint regulation and cellular metabolism. Therefore, this work demonstrates the advantages of using highly-sensitive and specific aptamer-SERS nanotags for investigating the immune checkpoint dynamics and related metabolic bioprocess.

Engineered aptamers for molecular imaging

Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.

Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids

Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.

Universal Near-Infrared Fluorescent Nanoprobes for Detection and Real-Time Imaging of ATP in Real Food Samples, Living Cells, and Bacteria

Adenosine triphosphate (ATP), an essential metabolite for active microorganisms to maintain life activities, has been widely regarded as a marker of cell activity and an indicator of microbial contamination. Herein, we designed two near-infrared (NIR) fluorescent nanoprobes named CYA@ZIF-90 and CYQ@ZIF-90 by encapsulating the NIR dye CYA/CYQ in ZIF-90 for the rapid detection of ATP. Between them, nanoprobe CYA@ZIF-90 can achieve higher NIR emission (702 nm) and rapid detection (2 min). Based on the superior spatiotemporal resolution imaging of ATP fluctuations in living cells, the applicability of CYA@ZIF-90 for imaging and detection of ATP in living bacteria was explored for the first time. The nanoprobe indirectly realizes the quantitative detection of bacteria, and the detection limit can be as low as 74 CFU mL-1. Therefore, the prepared nanoprobe is expected to become a universal ATP sensing detection tool, which can be further applied to evaluate cell apoptosis, cell proliferation, and food-harmful microbial control.

ATP-triggered highly sensitive probes for super-resolution mitochondrial imaging and low-dose bioimaging

Adenosine triphosphate (ATP), mainly produced in mitochondria, plays an important role in various pathological processes such as inflammation and acute liver injury. Fluorescence imaging is a powerful tool for imaging tissue structure and function in vivo. To date, the lack of biocompatible ATP probes with bright fluorescence emission has hindered their application in basic research and clinical trials. Here, we report a method for preparing ATP probes using a ZIF-90 potting dye, which produces bright ATP probes by encapsulating a modified high fluorescence quantum yield dye into a ZIF-90 skeleton. The nanoprobe does not fluoresce due to the coating. ATP can cooperate with Zn²⁺ to decompose the nanoprobe structure, release the dye and restore the fluorescence. Both nanoprobes ORhBSO₂@ZIF-90 and SiRhBSO₂@ZIF-90 showed higher sensitivity than the reported ATP nanoprobes with detection limits of 7.56 μM and 6.6 μM, and with lower doses (10 μg mL^-1) of probes for cell imaging. In addition, SiRhBSO₂@ZIF-90 has also been successfully used in the liver injury model. The ZIF-90 encapsulation strategy can retain the high fluorescence quantum yield and improve the biocompatibility of the dye.

Machine Learning-Based Label-Free SERS Profiling of Exosomes for Accurate Fuzzy Diagnosis of Cancer and Dynamic Monitoring of Drug Therapeutic Processes

Exosomes are a class of extracellular vesicles secreted by cells, which can be used as promising noninvasive biomarkers for the early diagnosis and treatment of diseases, especially cancer. However, due to the heterogeneity of exosomes, it remains a grand challenge to distinguish accurately and reliably exosomes from clinical samples. Herein, we achieve accurate fuzzy discrimination of exosomes from human serum samples for accurate diagnosis of breast cancer and cervical cancer through machine learning-based label-free surface-enhanced Raman spectroscopy (SERS), by using "hot spot" rich 3D plasmonic AuNPs nanomembranes as substrates. Due to the existence of some weak distinguishable SERS fingerprint signals and the high sensitivity of the method, the machine learning-based SERS analysis can precisely identify three (normal and cancerous) cell lines, two of which are different types of cancer cells, without specific labeling of biomarkers. The prediction accuracy based on the machine learning algorithm was up to 91.1% for the discrimination of different cell lines (H8, HeLa, and MCF-7 cell)-derived exosomes. Our model trained with SERS spectra of cell-derived exosomes could reach 93.3% prediction accuracy for clinical samples. Furthermore, the action mechanism of the chemotherapeutic process of MCF-7 cells can be revealed by dynamic monitoring of SERS profiling of the exosomes secreted. The method would be useful for noninvasive and accurate diagnosis and postoperative assessment of cancer or other diseases in the future.