Mitokyne: A Ratiometric Raman Probe for Mitochondrial pH

Azo-Enhanced Raman Scattering Probing Proton Transfer between Water and Nanoscale Zero-valent Iron

The interaction between a solid and water at their interface, especially proton transfer, impacts molecular-scale catalysis, macroscopic environmental science, and geoscience. Although being highly desired, directly probing proton transfer between a solid and water is a great challenge, given the subnanometer to nanometer scale of the interface. The fundamental challenge lies in the lack of a measurement tool to sensitively observe local proton concentration without introducing an exogenous electrode or nanoparticle with a minimum size of tens of nanometers. Here, we demonstrate an azo-enhanced Raman scattering strategy to design a 2 nm long small-molecule pH probe with a chelating group anchoring to the solid surface. Empowered by the intramolecular Raman enhancing sensitivity, the probe directly observes proton transfer between water and nanoscale zero-valent iron (nZVI), a famous environmental material for pollution control. This molecular-scale interfacial probing methodology offers a powerful tool to pave the way for advanced environmental and geochemical discernment and management.

Advances in Super-resolution Stimulated Raman Scattering Microscopy

Super-resolution optical imaging overcomes the diffraction limit in light microscopy to enable the visualization of previously invisible molecular details within a sample. The realization of super-resolution imaging based on stimulated Raman scattering (SRS) microscopy represents a recent area of fruitful development that has been used to visualize cellular structures in three dimensions, with multiple spectroscopic colors at the nanometer scale. Several fundamental approaches to achieving super-resolution SRS imaging have been reported, including optical engineering strategies, expansion microscopy, deconvolution image analysis, and photoswitchable SRS reporters as methods to break the diffraction limit. These approaches have enabled the visualization of biological structures, cellular interactions, and dynamics with unprecedented detail. In this Perspective, an overview of the current strategies and capabilities for achieving super-resolution SRS imaging will be highlighted together with an outlook on potential directions of this rapidly evolving field.

A mitochondria-targeted fluorescent sensor for imaging endogenous peroxynitrite changes in acute lung injury

Acute lung injury (ALI) is a serious pulmonary inflammatory disease resulting from excessive reactive oxygen species (ROS) which could cause the damage of the alveolar epithelial cells and capillary endothelial cells. Peroxynitrite, as one of short-lived reactive oxygen species, is closely related to the process of ALI. Thus, it is important to monitor the fluctuation of peroxynitrite in living system for understanding the process of ALI. Herein, the novel mitochondria-targeted fluorescent probe BHMT was designed to respond to peroxynitrite and pH with distinct fluorescence properties respectively. The absorption spectrum of the probe BHMT exhibited a notable red shift as the pH value declined from 8.8 to 2.6. Upon reaction with peroxynitrite, BHMT had a significant increase of fluorescence intensity (63-fold) with maintaining a detection limit of only 43.7 nM. Furthermore, BHMT could detect the levels of endogenous peroxynitrite and image the intracellular pH in ratiometric channels utilizing cell imaging. In addition, BHMT was successfully applied to revealing the relationship between the peroxynitrite and the extent of ALI. Thus, these results indicated the probe BHMT could be a potential tool for diagnosing the early stage of ALI and revealed the peroxynitrite was likely to be a crucial therapeutic target in ALI treatment.

Heterometallic Eu/Zn-MOF-based ratiometric sensing platform: Highly sensitive fluorescence / second-order scattering identification of tetracycline analogs and its molecular informatization applications

The traditional preparation method of ratiometric probes faces challenges such as cumbersome preparation and low sensitivity. Thus, there is an urgent need to provide a simple method of preparing a highly sensitive ratiometric probe. Here, Eu3+-doped zinc-based organic framework (Eu/Zn-MOF) was prepared through hydrothermal method for the detection of tetracycline analogs (TCs). Under the same excitation conditions, the probe can simultaneously display valuable fluorescence and second-order scattering signals. The developed probe enabled specific identification and fast detection (1 min) of TCs, including tetracycline, oxytetracycline, doxycycline, and chlortetracycline. The linear detection ranges of tetracycline, oxytetracycline, doxycycline and chlortetracycline were respectively 100 nM - 200 μM, 100 nM - 200 μM, 98 nM - 195 μM, and 97 nM - 291 μM, and the corresponding detection limits were respectively 15.79 nM, 20.83 nM, 15.31 nM, and 28.30 nM. The developed sensor was successfully applied to detect TCs in real samples, and the recovery rate was from 92.54 % to 109.69 % and the relative standard deviation was from 0.04 % to 2.97 %. Moreover, the heterometallic Eu/Zn-MOF was designed as a ratiometric neuron for Boolean logic computing and information encryption based on the specific identification of TCs. As a proof of concept, molecular steganography was successfully employed to encode, store, and conceal information by transforming the specific identification patterns of Eu/Zn-MOF into binary strings. This study is anticipated to advance the application of metal-organic frameworks in logic detection and information security, and bridging the gap between molecular sensors and the realm of information.

Alkyne-tagged imidazolium-based membrane cholesterol analogs for Raman imaging applications

Cholesterol is an important lipid playing a crucial role in mediating essential cellular processes as well as maintaining the basic structural integrity of biological membranes. Given its vast biological importance, there is an unabated need for sophisticated strategies to investigate cholesterol-mediated biological processes. Raman-tagged sterol analogs offer the advantage of being visualizable without the need for a bulky dye that potentially affects natural membrane integration and cellular interactions as it is the case for many conventionally used fluorescent analogs. Herein, we report a series of alkyne-tagged imidazolium-based cholesterol analogs (CHIMs) with large Raman scattering cross-sections that readily integrate into HEK cells and primary monocyte-derived macrophages and allow (multiplexed) cellular Raman imaging. We envision Raman-tagged CHIM analogs to be a powerful platform for the investigation of cholesterol-mediated cellular processes complementary to other established methods, such as the use of fluorescent analogs.

Viewing 3D spatial biology with highly-multiplexed Raman imaging: from spectroscopy to biotechnology

Understansding complex biological systems requires the simultaneous characterization of a large number of interacting components in their native 3D environment with high spatial resolution. Highly-multiplexed Raman imaging is an emerging general strategy for detecting biomarkers with scalable multiplexity and ultra-sensitivity based on a series of stimulated Raman scattering (SRS) techniques. Here we review recent advances in highly-multiplexed Raman imaging and how they contribute to the technological revolution in 3D spatial biology, focusing on the developmental pathway from spectroscopy study to biotechnology invention. We envision highly-multiplexed Raman imaging is taking off, which will greatly facilitate our understanding in biological and medical research fields.

Label-Free Screening of Drug-Induced Liver Injury Using Stimulated Raman Scattering Microscopy and Spectral Phasor Analysis

Hepatic toxicity is a leading cause of the termination of clinical trials and the withdrawal of therapeutics following regulatory approval. The detection of drug-induced liver injury (DILI) is therefore of importance to ensure patient safety and the effectiveness of novel small molecules and drugs. DILI encompasses drug-induced steatosis (DIS) and drug-induced phospholipidosis (DIPL) which involve the accumulation of excess intracellular lipids. Here, we develop hyperspectral stimulated Raman scattering (SRS) microscopy as a label-free methodology for discriminating DIS and DIPL in mammalian cell culture. We demonstrate that hyperspectral SRS imaging in tandem with spectral phasor analysis is capable of discriminating DIS and DIPL based on the nature and distribution of intracellular lipids resulting from each process. To demonstrate the practical application of this methodology, we develop a panel of alkyne-tagged propranolol analogues that display varying DILI effects. Using hyperspectral SRS imaging together with spectral phasor analysis, our label-free methodology corroborated the standard fluorescence-based assay for DILI. As a label-free screening method, it offers a convenient and expedient methodology for visualizing hepatotoxicity in cell cultures which could be integrated into the early stages of the drug development process for screening new chemical entities for DILI.

Raman micro-spectroscopy reveals the spatial distribution of fumarate in cells and tissues

Aberrantly accumulated metabolites elicit intra- and inter-cellular pro-oncogenic cascades, yet current measurement methods require sample perturbation/disruption and lack spatio-temporal resolution, limiting our ability to fully characterize their function and distribution. Here, we show that Raman spectroscopy (RS) can directly detect fumarate in living cells in vivo and animal tissues ex vivo, and that RS can distinguish between Fumarate hydratase (Fh1)-deficient and Fh1-proficient cells based on fumarate concentration. Moreover, RS reveals the spatial compartmentalization of fumarate within cellular organelles in Fh1-deficient cells: consistent with disruptive methods, we observe the highest fumarate concentration (37 ± 19 mM) in mitochondria, where the TCA cycle operates, followed by the cytoplasm (24 ± 13 mM) and then the nucleus (9 ± 6 mM). Finally, we apply RS to tissues from an inducible mouse model of FH loss in the kidney, demonstrating RS can classify FH status. These results suggest RS could be adopted as a valuable tool for small molecule metabolic imaging, enabling in situ non-destructive evaluation of fumarate compartmentalization.

Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level

This outlook explores how two different molecular imaging approaches might be combined to gain insight into dynamic, subcellular metabolic processes. Specifically, we discuss how matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and stimulated Raman scattering (SRS) microscopy, which have significantly pushed the boundaries of imaging metabolic and metabolomic analyses in their own right, could be combined to create comprehensive molecular images. We first briefly summarize the recent advances for each technique. We then explore how one might overcome the inherent limitations of each individual method, by envisioning orthogonal and interchangeable workflows. Additionally, we delve into the potential benefits of adopting a complementary approach that combines both MSI and SRS spectro-microscopy for informing on specific chemical structures through functional-group-specific targets. Ultimately, by integrating the strengths of both imaging modalities, researchers can achieve a more comprehensive understanding of biological and chemical systems, enabling precise metabolic investigations. This synergistic approach holds substantial promise to expand our toolkit for studying metabolites in complex environments.

Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window

Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.

Spectral fingerprinting of cellular lipid droplets using stimulated Raman scattering microscopy and chemometric analysis

Hyperspectral stimulated Raman scattering (SRS) microscopy is a powerful method for direct visualisation and compositional analysis of cellular lipid droplets. Here we report the application of spectral phasor analysis as a convenient method for the segmentation of lipid droplets using the hyperspectral SRS spectrum in the high wavenumber and fingerprint region of the spectrum. Spectral phasor analysis was shown to discriminate six fatty acids based on vibrational spectroscopic features in solution. The methodology was then applied to studying fatty acid metabolism and storage in a mammalian cancer cell model and during drug-induced steatosis in a hepatocellular carcinoma cell model. The accumulation of fatty acids into cellular lipid droplets was shown to vary as a function of the degree of unsaturation, whilst in a model of drug-induced steatosis, the detection of increased saturated fatty acid esters was observed. Taking advantage of the fingerprint and high wavenumber regions of the SRS spectrum has yielded a greater insight into lipid droplet composition in a cellular context. This approach will find application in the label-free profiling of intracellular lipids in complex disease models.

Ratiometric analysis of reversible thia-Michael reactions using nitrile-tagged molecules by Raman microscopy

Ratiometric Raman analysis of reversible thia-Michael reactions was achieved using α-cyanoacrylic acid (αCNA) derivatives. Among αCNAs, the smallest derivative, ThioRas (molecular weight: 167 g mol-1), and its glutathione adduct were simultaneously detected in various subcellular locations using Raman microscopy.

Expanding the Range of Bioorthogonal Tags for Multiplex Stimulated Raman Scattering Microscopy

Multiplex optical detection in live cells is challenging due to overlapping signals and poor signal-to-noise associated with some chemical reporters. To address this, the application of spectral phasor analysis to stimulated Raman scattering (SRS) microscopy for unmixing three bioorthogonal Raman probes within cells is reported. Triplex detection of a metallacarborane using the B-H stretch at 2480-2650 cm-1 , together with a bis-alkyne and deuterated fatty acid can be achieved within the cell-silent region of the Raman spectrum. When coupled to imaging in the high-wavenumber region of the cellular Raman spectrum, nine discrete regions of interest can be spectrally unmixed from the hyperspectral SRS dataset, demonstrating a new capability in the toolkit of multiplexed Raman imaging of live cells.

Recent advances in the design of intracellular pH sensing nanoprobes based on organic and inorganic materials

In the biological system, the intracellular pH (pHi) plays an important role in regulating diverse physiological activities, including enzymatic action, ion transport, cell proliferation, metabolism, and programmed cell death. The monitoring of pH inside living cells is also crucial for studying cellular events such as phagocytosis, endocytosis, and receptor-ligand internalization. Furthermore, some organelles, viz., endosomes and lysosomes, have intracompartmental pH, which is critical for maintaining the stability of protein structure and function. The dysfunction and abnormal pH regulation can result in terminal diseases such as cancer, Alzheimer, and so forth. Therefore, the accuracy of intracellular pH measurement is always the top priority and demands cutting-edge research and analysis. Such techniques, such as Raman spectroscopy and fluorescence imaging, preferably use nanotechnology due to their remarkable advantages, such as a non-invasive approach and providing accuracy, repeatability, and reproducibility. In the past decades, there have been numerous attempts to design and construct non-invasive organic and inorganic materials-based nanoprobes for pHi sensing. For Raman-based techniques, metal nanostructures such as Au/Ag/Cu nanoparticles are utilized to enhance the signal intensity. As for the fluorescence-based studies, the organic-based small molecules, such as dyes, show higher sensitivity toward pH. However, they possess several drawbacks, including high photobleaching rate, and autofluorescence background signals. To this end, there are alternative nanomaterials proposed, including semiconductor quantum dots (QDs), carbon QDs, upconversion nanoparticles, and so forth. Moreover, the fluorescence technique allows for ratiometric measurement of pHi, which as a result, offers a reliable calibration curve. This timely review will critically examine the current progression in the existing nanoprobes. In addition, based on our knowledge and available research findings, we provide a brief future outlook that may advance the state-of-the-art methodologies for pHi sensing.

Stretching the Bisalkyne Raman Spectral Palette Reveals a New Electrophilic Covalent Motif

Small heteroaryl-diyne (Het-DY) tags with distinct vibrational frequencies, and physiologically relevant cLog P were designed for multiplexed bioorthogonal Raman imaging. Pd-Cu catalyzed coupling, combined with the use of Lei ligand, was shown to improve overall yields of the desired heterocoupled Het-DY tags, minimizing the production of homocoupled side-products. Spectral data were in agreement with the trends predicted by DFT calculations and systematic introduction of electron- rich/poor rings stretched the frequency limit of aryl-capped diynes (2209-2243 cm-1 ). The improved Log P of these Het-DY tags was evident from their diffuse distribution in cellular uptake studies and functionalizing tags with organelle markers allowed the acquisition of location-specific biological images. LC-MS- and NMR-based assays showed that some heteroaryl-capped internal alkynes are potential nucleophile traps with structure-dependent reactivity. These biocompatible Het-DY tags, equipped with covalent reactivity, open up new avenues for Raman bioorthogonal imaging.

Determination of Intracellular Esterase Activity Using Ratiometric Raman Sensing and Spectral Phasor Analysis

Carboxylesterases (CEs) are a class of enzymes that catalyze the hydrolysis of esters in a variety of endogenous and exogenous molecules. CEs play an important role in drug metabolism, in the onset and progression of disease, and can be harnessed for prodrug activation strategies. As such, the regulation of CEs is an important clinical and pharmaceutical consideration. Here, we report the first ratiometric sensor for CE activity using Raman spectroscopy based on a bisarylbutadiyne scaffold. The sensor was shown to be highly sensitive and specific for CE detection and had low cellular cytotoxicity. In hepatocyte cells, the ratiometric detection of esterase activity was possible, and the result was validated by multimodal imaging with standard viability stains used for fluorescence microscopy within the same cell population. In addition, we show that the detection of localized ultraviolet damage in a mixed cell population was possible using stimulated Raman scattering microscopy coupled with spectral phasor analysis. This sensor demonstrates the practical advantages of low molecular weight sensors that are detected using ratiometric Raman imaging and will have applications in drug discovery and biomedical research.

Raman Spectroscopy for Chemical Biology Research

In chemical biology research, various fluorescent probes have been developed and used to visualize target proteins or molecules in living cells and tissues, yet there are limitations to this technology, such as the limited number of colors that can be detected simultaneously. Recently, Raman spectroscopy has been applied in chemical biology to overcome such limitations. Raman spectroscopy detects the molecular vibrations reflecting the structures and chemical conditions of molecules in a sample and was originally used to directly visualize the chemical responses of endogenous molecules. However, our initial research to develop "Raman tags" opens a new avenue for the application of Raman spectroscopy in chemical biology. In this Perspective, we first introduce the label-free Raman imaging of biomolecules, illustrating the biological applications of Raman spectroscopy. Next, we highlight the application of Raman imaging of small molecules using Raman tags for chemical biology research. Finally, we discuss the development and potential of Raman probes, which represent the next-generation probes in chemical biology.

Ni(II) Ions May Target the Entire Melatonin Biosynthesis Pathway—A Plausible Mechanism of Nickel Toxicity

Nickel is toxic to humans. Its compounds are carcinogenic. Furthermore, nickel allergy is a severe health problem that affects approximately 10–20% of humans. The mechanism by which these conditions develop remains unclear, but it may involve the cleavage of specific proteins by nickel ions. Ni(II) ions cleave the peptide bond preceding the Ser/Thr-Xaa-His sequence. Such sequences are present in all four enzymes of the melatonin biosynthesis pathway, i.e., tryptophan 5-hydroxylase 1, aromatic-l-amino-acid decarboxylase, serotonin N-acetyltransferase, and acetylserotonin O-methyltransferase. Moreover, fragments prone to Ni(II) are exposed on surfaces of these proteins. Our results indicate that all four studied fragments undergo cleavage within tens of hours at pH 8.2 and 37 °C, corresponding with the conditions in the mitochondrial matrix. Since melatonin, a potent antioxidant and anti-inflammatory agent, is synthesized within the mitochondria of virtually all human cells, depleting its supply may be detrimental, e.g., by raising the oxidative stress level. Intriguingly, Ni(II) ions have been shown to mimic hypoxia through the stabilization of HIF-1α protein, but melatonin prevents the action of HIF-1α. Considering all this, the enzymes of the melatonin biosynthesis pathway seem to be a toxicological target for Ni(II) ions.

Miniaturized Chemical Tags for Optical Imaging

Recent advances in optical bioimaging have prompted the need for minimal chemical reporters that can retain the molecular recognition properties and activity profiles of biomolecules. As a result, several methodologies to reduce the size of fluorescent and Raman labels to a few atoms (e.g., single aryl fluorophores, Raman-active triple bonds and isotopes) and embed them into building blocks (e.g., amino acids, nucleobases, sugars) to construct native-like supramolecular structures have been described. The integration of small optical reporters into biomolecules has also led to smart molecular entities that were previously inaccessible in an expedite manner. In this article, we review recent chemical approaches to synthesize miniaturized optical tags as well as some of their multiple applications in biological imaging.

High-Resolution Low-Power Hyperspectral Line-Scan Imaging of Fast Cellular Dynamics Using Azo-Enhanced Raman Scattering Probes

Small-molecule Raman probes for cellular imaging have attracted great attention owing to their sharp peaks that are sensitive to environmental changes. The small cross section of molecular Raman scattering limits dynamic cellular Raman imaging to expensive and complex coherent approaches that acquire single-channel images and lose hyperspectral Raman information. We introduce a new method, dynamic azo-enhanced Raman imaging (DAERI), to couple the new class of azo-enhanced Raman probes with a high-speed line-scan Raman imaging system. DAERI achieved high-resolution low-power imaging of fast cellular dynamics resolved at ∼270 nm along the confocal direction, 75 μW/μm² and 3.5 s/frame. Based on the azo-enhanced Raman probes with characteristic signals 10²-10⁴ stronger than classic Raman labels, DAERI was not restricted to the cellular Raman-silent region as in prior work and enabled multiplex visualization of organelle motions and interactions. We anticipate DAERI to be a powerful tool for future studies in biophysics and cell biology.

Quantitative Stimulated Raman Scattering Microscopy: Promises and Pitfalls

Since its first demonstration, stimulated Raman scattering (SRS) microscopy has become a powerful chemical imaging tool that shows promise in numerous biological and biomedical applications. The spectroscopic capability of SRS enables identification and tracking of specific molecules or classes of molecules, often without labeling. SRS microscopy also has the hallmark advantage of signal strength that is directly proportional to molecular concentration, allowing for in situ quantitative analysis of chemical composition of heterogeneous samples with submicron spatial resolution and subminute temporal resolution. However, it is important to recognize that quantification through SRS microscopy requires assumptions regarding both system and sample. Such assumptions are often taken axiomatically, which may lead to erroneous conclusions without proper validation. In this review, we focus on the tacitly accepted, yet complex, quantitative aspect of SRS microscopy. We discuss the various approaches to quantitative analysis, examples of such approaches, challenges in different systems, and potential solutions. Through our examination of published literature, we conclude that a scrupulous approach to experimental design can further expand the powerful and incisive quantitative capabilities of SRS microscopy.

Upconversion fluorescent nanoprobe based on 4-NP reversible structure for a wide range of pH determination

Accurate detection of pH value has received more and more attention in various fields. However, most reported probes show pH values in the acidic or alkaline range and work within...