Imaging of EdU, an alkyne-tagged cell proliferation probe, by Raman microscopy

Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe

Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.

Flexible microfluidic co-recognition coupled with magnetic enrichment and silent SERS sensing for simultaneous analysis of bacteria in food

Food safety represents a critical global public health issue, with safety challenges posed by foodborne pathogens garnering extensive attention. Therefore, we introduce a co-recognition, enrichment and sensing (CES) all-in-one strategy for analysis of bacteria with low background and high specificity. This method employs antimicrobial peptide (AMP) functionalized magnetic nanoparticles (MNPs) to enrich bacteria and uses aptamer@Au@PBA (KxMFe(CN)6 (M = Pb and Ni)) NPs as silent SERS tags. When both S. aureus and E. coli O157:H7 are present, the silent SERS probes could specifically label the target bacteria, forming a sandwich-like structure. This binding induces silent Raman shifts (2139 cm-1 and 2197 cm-1), enabling quantification of two bacteria. Coupling with the modular flexible microfluidics and magnetic control slider device, this platform facilitates rapid switching between magnetic loading and elution. The CES SERS method demonstrated linear relationships for both S. aureus and E. coli O157:H7 at 50-1600 cfu mL-1, with detection limits of 14 and 18 cfu mL-1, respectively. The method achieved recovery rates of 85.6-112% and relative standard deviations of 1.5-8.6%. Validation using the ELISA method revealed relative errors between -7.5 and 4.3%. The CES approach has potential applications in food safety, environmental monitoring, and biomedical diagnosis.

Cyano-Hydrol green derivatives: Expanding the 9-cyanopyronin-based resonance Raman vibrational palette

9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging.

Unveiling brain disorders using liquid biopsy and Raman spectroscopy

Brain disorders, including neurodegenerative diseases (NDs) and traumatic brain injury (TBI), present significant challenges in early diagnosis and intervention. Conventional imaging modalities, while valuable, lack the molecular specificity necessary for precise disease characterization. Compared to the study of conventional brain tissues, liquid biopsy, which focuses on blood, tear, saliva, and cerebrospinal fluid (CSF), also unveils a myriad of underlying molecular processes, providing abundant predictive clinical information. In addition, liquid biopsy is minimally- to non-invasive, and highly repeatable, offering the potential for continuous monitoring. Raman spectroscopy (RS), with its ability to provide rich molecular information and cost-effectiveness, holds great potential for transformative advancements in early detection and understanding the biochemical changes associated with NDs and TBI. Recent developments in Raman enhancement technologies and advanced data analysis methods have enhanced the applicability of RS in probing the intricate molecular signatures within biological fluids, offering new insights into disease pathology. This review explores the growing role of RS as a promising and emerging tool for disease diagnosis in brain disorders, particularly through the analysis of liquid biopsy. It discusses the current landscape and future prospects of RS in the diagnosis of brain disorders, highlighting its potential as a non-invasive and molecularly specific diagnostic tool.

Statistical approaches to Raman imaging: principal component score mapping

In this research, Raman imaging was employed to map various samples, and the resulting data were analyzed using a suite of automated tools to extract critical information, including intensity and signal-to-noise ratio. The acquired spectra were further processed to identify similarities and investigate patterns using principal component analysis. The objective of this study was to establish guidelines for investigating Raman imaging results, particularly when dealing with large datasets comprising thousands of relatively low-intensity spectra. The overall quality of the results was assessed, and representative locations were determined based on the main Raman bands. While automated software solutions are insufficient for removing baselines and fitting the data, statistical analysis proved to be a powerful tool for extracting valuable information directly from the raw spectral data. This approach enables the extraction of as much information as possible from large arrays of spectral data, even in complex cases where automated software may fall short. The findings of this study contribute to enhancing the analysis and interpretation of Raman imaging results, providing researchers with a robust methodology for extracting meaningful insights from complex datasets, reducing the amount of effort required during data interpretation and analysis.

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.

Substituent effects on the selectivity of ambimodal [6+4]/[4+2] cycloaddition

In this work, we report a density functional theory (DFT) study and a dynamical trajectory study of substituent effects on the ambimodal [6+4]/[4+2] cycloaddition proposed for 1,3,5,10,12-cycloheptadecapentaene, referred to as cycloheptadecapentaene. The proposed cycloaddition proceeds through an ambimodal transition state, which results in both a [6+4] adduct a [4+2] adduct directly. The [6+4] adduct can be readily converted to the [4+2] adduct via a Cope rearrangement. We study the selectivity of the reaction with regard to the position of substituents, steric effects of substituents, and electronic effects of substituents. In the dynamical trajectory study, we find that nitro-substituted reactants lead to a new product from the ambimodal transition state via the hetero Diels-Alder reaction, and this new product can then be converted to a [4+2] adduct by a hetero [3, 3]-sigmatropic rearrangement. These results may provide insights for designing more bridged heterocyclic compounds.

Background-Free SERS Nanosensor for Endogenous Hydrogen Sulfide Detection Based on Prussian Blue-Coated Gold Nanobipyramids

Surface-enhanced Raman scattering (SERS) has great potential in biological analysis due to its specificity, sensitivity, and non-invasive nature. However, effectively extracting Raman information and avoiding spectral overlapping from biological background interference remain major challenges. In this study, we developed a background-free SERS nanosensor consisting of gold nanobipyramids (Au NBPs) core-Prussian blue (PB) shell (Au NBPs@PB), for endogenous H2S detection. The PB shell degraded quickly upon contact with endogenous H2S, generating a unique Raman signal response in the Raman silent region (1800-2800 cm-1). By taking advantage of the high SERS-activity of Au NBPs and H2S-triggered spectral changes of PB, these SERS nanosensors effectively minimize potential biological interferences. The nanosensor exhibits a detection range of 2.0 μM to 250 μM and a limit of detection (LOD) of 0.34 μM, with good reproducibility and minimal interference. We successfully applied this background-free SERS platform to monitor endogenous H2S concentrations in human serum samples with satisfied results.

Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe

Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.

Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences

Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.

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.

An intelligent alkyne-tag for Raman imaging of living cells: graphdiyne-encapsulated Au nanospheres

A new graphdiyne-encapsulated Au nanosphere (Au@GDY) material was fabricated, which possessed an amplified Raman signal of acetylene linkage and produced bright, stable, and distinct signals in the cellular Raman-silent region. Its signal repeatability is far superior to that of alkyne-containing molecules. This work provides promise as an alkyne-tag for Raman imaging of living cells.

"Photochemical Surgery" of 1D Metal-Organic Frameworks with a Site-Selective Solubilization/Crystallization Strategy

One-dimensional (1D) hybrid MOFs are attractive if they consist of different MOF blocks with interconnected channels. However, the precision synthesis of such 1D multiblock MOFs with the desired block lengths and sequences remains a formidable challenge. Herein we propose the "photochemical surgery" method, which combines top-down and bottom-up approaches to enable the site-selective solubilization (removal)/crystallization (reconstruction) of 1D MOFs. We employed photoreactive MOFs, which were prepared by complexing either Cd2+ or Zn2+ with a mixture containing a photochromic bispyridyl ligand (PyDTEopen or PyDTZEopen) and an isophthalate (5-nitroisophthalate (nip2-) or 5-bromoisophthalate (bip2-)). These MOFs were obtained as high-aspect-ratio, needlelike, colorless crystals that bore 1D channels oriented parallel to the long needle axis. When photoreactive DTECdMOFNO2 ([Cd(nip)(PyDTEopen)(H2O)]n), for example, was immobilized at both ends with a metal alloy on a glass substrate and exposed to UV light through a photomask for 60 min in N,N-dimethylformamide/methanol (DMF/MeOH), the unmasked part was removed via solubilization to produce a 50 μm gap. The resulting specimen was immersed for 24 h at 25 °C in DMF/MeOH containing the necessary components for the construction of DTZECdMOFNO2 ([Cd(nip)(PyDTZEopen)(H2O)]n). Eventually, the gap was filled with DTZECdMOFNO2 to produce a triblock hybrid MOF (DTECdMOFNO2-DTZECdMOFNO2-DTECdMOFNO2). The result of a guest diffusion experiment confirmed that the newly formed DTZECdMOFNO2 block shared its 1D channels with the host DTECdMOFNO2 blocks. "Photochemical surgery" can be applied to synthesize 1D hybrid MOFs bearing unconventional sequences and morphologies, e.g., honeycomb- and inverted-honeycomb-patterned hybrids.

Multifocal Raman Spectrophotometer for Examining Drug-Induced and Chemical-Induced Cellular Changes in 3D Cell Spheroids

Cell spheroids offer alternative in vitro cell models to monolayer cultured cells because they express complexities similar to those of in vivo tissues, such as cellular responses to drugs and chemicals. Raman spectroscopy emerged as a powerful analytical tool for detecting chemical changes in living cells because it nondestructively provides vibrational information regarding a target. Although multiple iterations are required in drug screening to determine drugs to treat cell spheroids and assess the inter-spheroid heterogeneity, current Raman applications used in spheroids analysis allow the observation of only a few spheroids owing to the low throughput of Raman spectroscopy. In this study, we developed a multifocal Raman spectrophotometer that enables simultaneous analysis of multiple spheroids in separate wells of a regular 96-well plate. By utilizing 96 focal spots excitation and parallel signal collection, our system can improve the throughput by approximately 2 orders of magnitude compared to a conventional single-focus Raman microscope. The Raman spectra of HeLa cell spheroids treated with anticancer drugs and HepG2 cell spheroids treated with free fatty acids were measured simultaneously, and concentration-dependent cellular responses were observed in both studies. Using the multifocal Raman spectrophotometer, we rapidly observed chemical changes in spheroids, and thus, this system can facilitate the application of Raman spectroscopy in analyzing the cellular responses of spheroids.

Boosting the Brightness of Raman Tags Using Cyanostar Macrocycles

Raman probes have received growing attention for their potential use in super-multiplex biological imaging and flow cytometry applications that cannot be achieved using fluorescent probes. However, obtaining strong Raman scattering signals from small Raman probes has posed a challenge that holds back their practical implementation. Here, we present new types of Raman-active nanoparticles (Rdots) that incorporate ionophore macrocycles, known as cyanostars, to act as ion-driven and structure-directing spacers to address this problem. These macrocycle-enhanced Rdots (MERdots) exhibit sharper and higher electronic absorption peaks than Rdots. When combined with resonant broadband time-domain Raman spectroscopy, these MERdots show a ∼3-fold increase in Raman intensity compared to conventional Rdots under the same particle concentration. Additionally, the detection limit on the concentration of MERdots is improved by a factor of 2.5 compared to that of Rdots and a factor of 430 compared to that of Raman dye molecules in solution. The compact size of MERdots (26 nm in diameter) and their increased Raman signal intensity, along with the broadband capabilities of time-domain resonant Raman spectroscopy, make them promising candidates for a wide range of biological applications.

Alkyne-tethered oligodeoxynucleotides that allow simultaneous detection of multiple DNA/RNA targets using Raman spectroscopy

Detection of multiple DNA/RNA targets is essential for understanding cellular function. Herein, we propose a general method for the simultaneous detection of plural nucleic acids based on surface-enhanced Raman scattering (SERS) using gold nanoparticles bearing functional oligodeoxynucleotides (ODNs) on their surface. Modified ODNs bearing an acetylene tag hybridized with their complementary ODNs on the surface of the gold nanoparticles, inducing a strong SERS signal of the acetylene tag. The addition of the target nucleic acid to the system resulted in a spontaneous displacement of the strand on the particle and dissociation of the alkyne-tagged ODN from the particle, resulting in a dramatic decrease in signal intensity. By using an alkyne tag for each of the multiple target nucleic acids, each target could be detected simultaneously. In addition, we successfully detected cellular microRNA. Different targets showed changes with different wavenumbers in the Raman spectra, allowing for the detection of multiple nucleic acids.

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.

Protocol to image deuterated propofol in living rat neurons using multimodal stimulated Raman scattering microscopy

Propofol is a widely used anesthetic important in clinics, but like many other bioactive molecules, it is too small to be tagged and visualized by fluorescent dyes. Here, we present a protocol to visualize deuterated propofol in living rat neurons using stimulated Raman scattering (SRS) microscopy with carbon-deuterium bonds serving as a Raman tag. We describe the preparation and culture of rat neurons, followed by optimization of the SRS system. We then detail neuron loading and real-time imaging of anesthesia dynamics. For complete details on the use and execution of this protocol, please refer to Oda et al.¹.

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.

Resonant Raman-Active Polymer Dot Barcodes for Multiplex Cell Mapping

Resonance Raman spectroscopy is an efficient tool for multiplex imaging because of the narrow bandwidth of the electronically enhanced vibrational signals. However, Raman signals are often overwhelmed by concurrent fluorescence. In this study, we synthesized a series of truxene-based conjugated Raman probes to show structure-specific Raman fingerprint patterns with a common 532 nm light source. The subsequent polymer dot (Pdot) formation of the Raman probes efficiently suppressed fluorescence via aggregation-induced quenching and improved the dispersion stability of particles without leakage of Raman probes or particle agglomeration for more than 1 year. Additionally, the Raman signal amplified by electronic resonance and increased probe concentration exhibited over 10³ times higher relative Raman intensities versus 5-ethynyl-2'-deoxyuridine, enabling successful Raman imaging. Finally, multiplex Raman mapping was demonstrated with a single 532 nm laser using six Raman-active and biocompatible Pdots as barcodes for live cells. Resonant Raman-active Pdots may suggest a simple, robust, and efficient way for multiplex Raman imaging using a standard Raman spectrometer, suggesting the broad applicability of our strategy.

Enhancing Alkyne-Based Raman Tags with a Sulfur Linker

Alkyne-based Raman tags have proven their utility for biological imaging. Although the alkynyl stretching mode is a relatively strong Raman scatterer, the detection sensitivity of alkyne-tagged compounds is ultimately limited by the magnitude of the probe's Raman response. In order to improve the performance of alkyne-based Raman probes, we have designed several tags that benefit from π-π conjugation as well as from additional n-π conjugation with a sulfur linker. We show that the sulfur linker provides additional enhancement and line width narrowing, offering a simple yet effective strategy for improving alkyne-based Raman tags. We validate the utility of various sulfur-linked alkyne tags for cellular imaging through stimulated Raman scattering microscopy.

High-throughput line-illumination Raman microscopy with multislit detection

Raman microscopy is an emerging tool for molecular imaging and analysis of living samples. Use of Raman microscopy in life sciences is, however, still limited because of its slow measurement speed for spectral imaging and analysis. We developed a multiline-illumination Raman microscope to achieve ultrafast Raman spectral imaging. A spectrophotometer equipped with a periodic array of confocal slits detects Raman spectra from a sample irradiated by multiple line illuminations. A comb-like Raman hyperspectral image is formed on a two-dimensional detector in the spectrophotometer, and a hyperspectral Raman image is acquired by scanning the sample with multiline illumination array. By irradiating a sample with 21 simultaneous illumination lines, we achieved high-throughput Raman hyperspectral imaging of mouse brain tissue, acquiring 1108800 spectra in 11.4 min. We also measured mouse kidney and liver tissue as well as conducted label-free live-cell molecular imaging. The ultrafast Raman hyperspectral imaging enabled by the presented technique will expand the possible applications of Raman microscopy in biological and medical fields.

Synthesis and evaluation of a deltic guanidinium analogue of a cyclic RGD peptide

A guanidine group is abundantly found in natural products and drugs. Guanidine has the highest basicity among many common functional groups in nature. Because of its high basicity, it generally exists as a protonated guanidinium and functions as a cationic hydrogen bond donor. Finding an appropriate bioisostere of guanidinium is challenging because of its high basicity and unique trigonal planar shape. In this study, we explored the possibility of "deltic guanidinium" as a bioisostere of guanidinium using a cyclic arginine-glycine-aspartic acid (RGD) peptide as a parent compound. We synthesized c(deltic RGDyK), in which a guanidinium group of an arginine residue in c(RGDyK) is replaced with deltic guanidinium. A target binding assay, biodistribution study, and metabolic stability assay were conducted with c(deltic RGDyK) and its radioiodinated variant. The deltic guanidinium analog peptides exhibited similar biological properties to the parent peptides and improved in vivo stability, indicating that deltic guanidinium could work as a unique bioisostere of guanidinium.

Changes in the mitochondrial membrane potential in endothelial cells can be detected by Raman microscopy

The role of mitochondria goes beyond their capacity to create molecular fuel and includes e.g. the production of reactive oxygen species and the regulation of cell death. In endothelial cells, mitochondria have a significant impact on cellular function under both healthy and pathological conditions. Endothelial dysfunction contributes to the development of various lifestyle diseases and the key players in their pathogenesis are among others vascular inflammation and oxidative stress. The latter is very closely related to mitochondrial dysfunction; however, it is not straightforward. First, because mitochondria are small cellular structures, and second, it requires a sensitive method to follow the subtle biochemical changes. For this purpose, Raman microscopy (RM) was used here, which is considered a high-resolution method and can be applied in situ, usually as a non-labeled technique. In this work, we show that RM can not only locate mitochondria in the cell but also track their functional changes. Moreover, we test if labeling cells with Raman probes (Rp) can improve the specificity and sensitivity of RM (compared to conventional labeled techniques such as fluorescence, and the non-labeled Raman technique). MitoBADY Rp was used to detect changes in mitochondrial membrane potential as an indicator of mitochondrial activity, e.g. hyperpolarization or distortion of the proton gradient in the intermembrane space (depolarization). Thus, we show and compare RM, in the form of a label and non-labeled, to such a subtle cellular analysis.

Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases

The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.

9-Cyano-10-telluriumpyronin Derivatives as Red-light-activatable Raman Probes

Photoactivatable fluorescence probes can track the dynamics of specific cells or biomolecules with high spatiotemporal resolution, but their broad absorption and emission peaks limit the number of wavelength windows that can be employed simultaneously. In contrast, the narrower peak width of Raman signals offers more scope for simultaneous discrimination of multiple targets, and therefore a palette of photoactivatable Raman probes would enable more comprehensive investigation of biological phenomena. Herein we report 9-cyano-10-telluriumpyronin (9CN-TeP) derivatives as photoactivatable Raman probes whose stimulated Raman scattering (SRS) intensity is enhanced by photooxidation of the tellurium atom. Modification to increase the stability of the oxidation product led to a julolidine-like derivative, 9CN-diMeJTeP, which is photo-oxidized at the tellurium atom by red light irradiation to afford a sufficiently stable oxidation product with strong electronic pre-resonance, resulting in a bathochromic shift of the absorption spectrum and increased SRS intensity.

Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments

The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.

Raman Signal Enhancement by DABCYL-Substitution on DNA Aptamer for Identification of Cellular ATP

Raman probes have attracted widespread attention for the visualization and identification of biomolecules, because they can be applied to identify detailed chemical structures, detect multiple molecules simultaneously, and visualize cellular functional molecules. However, the biological application of Raman probes is still limited because of their weak signal intensity. Herein, we present a molecular system that shows an enhanced Raman signal using a nonfluorescent dye. We introduced a DABCYL molecule bearing an acetylene unit into thymidine at the 5-position. The resulting modified nucleobase, d^DAU, showed a robust signal around 2200 cm^-1, which was attributed to the acetylene unit, due to resonance Raman induced by the DABCYL group. We further prepared a DNA aptamer modified with d^DAU, and characterized the change of the Raman spectra. Combination with gold nanoparticles, which enhanced the Raman signal by surface-enhanced Raman scattering (SERS), allowed sensitive detection of cellular adenosine derivatives including ATP. Thus, the present system is a promising tool for the detection of biological materials by Raman spectroscopy.

Direct imaging of intracellular RNA, DNA, and liquid-liquid phase separated membraneless organelles with Raman microspectroscopy

Methodologies for direct intracellular imaging of RNA and DNA are necessary for the advancement of bioimaging. Here we show direct label-free imaging of RNA and DNA in single cells by isolating their accurate Raman spectra. Raman images of DNA from interphase cells show intact nucleus, while those from mitotic cells reveal condensed chromosome. The condensed chromosome images are accurate enough to assign the stage of mitotic cell division (e.g., metaphase). Raman spectral features indicate B-DNA double helical conformational form in all the cell lines investigated here. The Raman images of RNAs, on the other hand, reveal liquid-liquid phase separated (LLPS) membraneless organelles in interphase cells, which disappears during mitosis. Further, the Raman spectrum of proteins from the intracellular LLPS organelles indicates slight enrichment of amyloid-like secondary structural features. Vibrational imaging of intracellular DNA and RNA simultaneously would open myriad of opportunities for examining functional biochemical aspects of cells and organelles.

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.

Correlating the orbital overlap area and vibrational frequency shift of an isocyanide moiety adsorbed on Pt and Pd covered Au(111) surfaces

Orbital interactions between adsorbed molecules and the underlying metal surfaces play critical roles in a wide range of surface and interfacial processes. Establishing a correlation between an experimental observable (e.g., vibrational frequency shift of the adsorbed molecule) and the orbital interactions is of vital importance. Herein, theoretical calculations are used to investigate the vibrational frequency shift of phenyl isocyanide molecules as a probe molecule adsorbed on mono- and bi-layer Pt and Pd covered Au(111) surfaces and Pd₂Au₄ and Pt₂Au₄ clusters. By analyzing the density of states (DOS) of the adsorption system, we show that the orbital overlap area of d electronic DOS with a molecular σ or π* orbital, particularly their ratio (R_d-σ/d-π*), can be a meaningful descriptor to explain the frequency shift of the CN moiety. This hypothesis has been verified by simulations for phenyl isocyanide with electron donating NH₂- and withdrawing CF₃- substituent groups, formonitrile and carbon monoxide. Quasi-linear dependence of the frequency shift on R_d-σ/d-π* is observed for both the red and blue shift regions. Our findings build up on previous notions of electronic interactions, which will provide a more quantitative and solid footing to understand and analyze the frequency shift of adsorbed molecules on metal surfaces and the related electronic interactions and catalytic properties.

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.

Dealkenylative Alkynylation Using Catalytic FeII and Vitamin C

In this paper, we report the synthesis of alkyl-tethered alkynes through ozone-mediated and FeII-catalyzed dealkenylative alkynylation of unactivated alkenes in the presence of alkynyl sulfones. This one-pot reaction, which employs a combination of a catalytic FeII salt and l-ascorbic acid, proceeds under mild conditions with good efficiency, high stereoselectivity, and broad functional group compatibility. In contrast to our previous FeII-mediated reductive fragmentation of α-methoxyhydroperoxides, the FeII-catalyzed process was devised through a thorough kinetic analysis of the multiple competing radical (redox) pathways. We highlight the potential of this dealkenylative alkynylation through multiple post-synthetic transformations and late-stage diversifications of complex molecules, including natural products and pharmaceuticals.

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.

EdU sensing: The Raman way of following endothelial cell proliferation in vitro and ex vivo

Endothelial cells line the lumen of all vessels in the body and maintain vascular homeostasis. In particular, endothelial cell regeneration in response to insult sustain functional endothelial layer. EdU (5-ethynyl-2'-deoxyuridine) is an alkyne-tagged proliferation probe that incorporates into newly synthesized DNA and is used for fluorescence imaging of cell proliferation with the use of "click chemistry" reaction with a fluorescent azide. Here, we utilized EdU as a click-free Raman probe for tracking endothelial cell proliferation. Raman imaging of EdU was performed in live endothelial cells, showing an advantage over fluorescence imaging of EdU, as this technique did not require sample fixation and permeabilization. To validate Raman-based imaging of EdU to study endothelial cell proliferation, we showed that when endothelial cells were treated with cycloheximide or doxorubicin to impair the proliferation of endothelial cells, the Raman-based signal of EdU was diminished. Furthermore, endothelial cells proliferation detected using EdU-labelled Raman imaging was compared with fluorescence imaging. Finally, the method of Raman-based EdU imaging was used in the isolated murine aorta ex vivo. Altogether, our results show that Raman-based imaging of EdU provides a novel alternative for fluorescence-based assay to assess endothelial proliferation and regeneration.

Label-Free Monitoring of Drug-Induced Cytotoxicity and Its Molecular Fingerprint by Live-Cell Raman and Autofluorescence Imaging

Simultaneous observation of drug distribution at the effector site and subsequent cell response are essential in the drug development process. However, few studies have visualized the drug itself and biomolecular interactions in living cells. Here, we used label-free Raman microscopy to investigate drug-induced cytotoxicity and visualize drug uptake and subcellular localization by its specific molecular fingerprint. A redox-sensitive Raman microscope detected the decrease of reduced cytochrome c (cyt c) after Actinomycin D (ActD) treatment in a time-dependent and dose-dependent format. Immunofluorescence staining of cyt c suggested that the release of cyt c was not the major cause. Combining Raman microscopy with conventional biological methods, we reported that the oxidization of cyt c is an early cytotoxicity marker prior to the release of cyt c. Moreover, as the spectral properties of ActD are sensitive to the surrounding environment, subcellular localization of ActD was visualized sensitively by the weak autofluorescence, and the intercalation of ActD into DNA was detected by shifted Raman peaks, allowing for parallel observation of drug uptake and the mechanism of action. In this research, we achieved simultaneous observation of cytotoxicity and cellular drug uptake by Raman microscopy, which could facilitate a precise understanding of pharmacological effects and predict potential drug toxicity in the future.

Bessel-beam illumination Raman microscopy

We demonstrate the use of Bessel beams for side illumination slit-scanning Raman imaging for label-free and hyperspectral analysis of cell spheroids. The background elimination by the side illumination and the aberration-resistant Bessel beam drastically improves the image contrast in Raman observation, allowing label-free investigation of intracellular molecules in thick biological samples. Live cell spheroids were observed to confirm the improvement in image contrast and background reduction with Bessel illumination compared to conventional epi-line illumination.

Pharmaceutical applications of a nanospectroscopic technique: Surface-enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) is a very sensitive technique offering unique opportunities for detection and identification of molecules and molecular structures at extremely low concentrations even in complex sample matrixes. Since a nanostructured noble metal surface is required for the enhancement of Raman scattering, the acquired spectral information naturally originates from nanometer size domains making it a nanospectroscopic technique by breaking the diffraction limit of light. In this review, first Raman spectroscopy, its comparison to other related techniques, its modes and instrumentation are briefly introduced. Then, the SERS mechanism, substrates and the parameters influencing a SERS experiment are discussed. Finally, its applications in pharmaceuticals including drug discovery, drug metabolism, multifunctional chemo-photothermal-therapy-delivery-release-imaging, drug stability and drug/metabolite detection in complex biological samples are summarized and elaborated.

Super-multiplexed vibrational probes: Being colorful makes a difference

Biological systems with intrinsic complexity require multiplexing techniques to comprehensively describe the phenotype, interaction, and heterogeneity. Recent years have witnessed the development of super-multiplexed vibrational microscopy, overcoming the 'color barrier' of fluorescence-based optical techniques. Here, we will review the recent progress in the design and applications of super-multiplexed vibrational probes. We hope to illustrate how rainbow-like vibrational colors can be generated from systematic studies on structure-spectroscopy relationships and how being colorful makes a difference to various biomedical applications.

Non-enzymatic catalytic asymmetric cyanation of acylsilanes

The asymmetric cyanation of acylsilanes affords densely functionalized tetrasubstituted chiral carbon centers bearing silyl, cyano, and hydroxy groups, which are of particular interest in synthetic and medicinal chemistry. However, this method has been limited to a few enzymatic approaches, which employ only one substrate because of substrate specificity. Here we show the non-enzymatic catalytic asymmetric cyanation of acylsilanes using a chiral Lewis base as an enantioselective catalyst, trimethylsilyl cyanide as a cyanating reagent, and isopropyl alcohol as an additive to drive catalyst turnover. High enantio- and site-selectivities are achieved in a catalytic manner, and a variety of functional groups are installed in optically active acylsilane cyanohydrins, thus overcoming the limitations imposed by substrate specificity in conventional enzymatic methods. A handle for the synthetic application of the products is also established through the development of a catalyst for protecting acylsilane cyanohydrins, which are unstable and difficult to protect alcohols.

Design and evaluation of Raman reporters for the Raman-silent region

Rationale: Surface enhanced Raman scattering (SERS) is proving to be a useful tool for biomedical imaging. However, this imaging technique can suffer from poor signal-to-noise ratio, as the complexity of biological tissues can lead to overlapping of Raman bands from tissues and the Raman reporter molecule utilized. Methods: Herein we describe the synthesis of triple bond containing Raman reporters that scatter light in the biological silent window, between 1750 cm^-1 and 2750 cm^-1. Results: Our SERS nanoprobes are comprised of uniquely designed Raman reporters containing either alkyne- or cyano-functional groups, enabling them to be readily distinguished from background biological tissue. Conclusion: We identify promising candidates that eventually can be moved forward as Raman reporters in SERS nanoparticles for highly specific contrast-enhanced Raman-based disease or analyte detection in biological applications.

[Application of non-linear Raman scattering microscopy to pharmacology to visualize invisible targets]

Visualization and measurement of drugs themselves as well as biological responses to those drugs are crucial in pharmacological research. To this end, various fluorescent dyes and proteins have been developed. Despite such progresses, there still remains technical difficulties to overcome in bioimaging that keep many pharmacological targets and phenomena invisible. Outside the fields of biology where fluorescence and luminescence prevail, variety of other optical phenomena are well known and utilized. These optical phenomena can shed unique lights on biological phenomena based on their specific physical and chemical properties. Although applications of these optical phenomena to biology are yet to be explored, they have high potentials in realizing visualization and measurement of currently invisible targets and phenomena, and thereby bringing new insights into pharmacological research. Thus, here I will introduce Raman scattering microscopy that visualize vibration of functional groups as an alternative imaging platform to fluorescence and luminescence. Special focus will be put on two recent technical advancements; namely, nonlinear Raman scattering microscopy that utilizes multi-photon effect of highly tissue penetrating near-infrared lights, and Raman-tag that realizes tagging of targets that could not have been labeled, combination of which is expected to pave a way toward imaging previously invisible targets in pharmacology.

Quantitative Analysis of Compatibility and Dispersibility in Nanocellulose-Reinforced Composites: Hansen Solubility and Raman Mapping

Considering its high specific modulus, nanocellulose, including rigid cellulose nanocrystals (CNCs) and semiflexible cellulose nanofibrils (CNFs), is widely used as a nano-reinforcing filler for polymeric-based composites, which is regarded as the most promising application of these biomass nanoparticles. The quantitative evaluation of the compatibility and dispersion/aggregation state of nanocellulose in polymeric matrices is a critical issue, as it conditions the efficient stress transfer from the matrix to the filler and effective mechanical reinforcement effect. This study reports a comprehensive set of theories and methods to directly evaluate the compatibility and dispersibility of CNCs and CNFs in four polymer matrices with different polarities, where the compatibility was assessing by Hansen solubility and dispersibility by Raman mapping and cluster analysis. Triple-bond modification on the surface of nanocellulose is a promising approach for accurate recognition in composites, exhibiting the individual signal located in the Raman-silent regions of various polymeric matrices. Based on the discussion of the quantitative dispersion factor, a multiscale percolation model is proposed to better predict the mechanical properties of nanocellulose-reinforced composites based on Raman mapping results, in order to update traditional percolation models.

Cuprous Cluster-Based Coordination Sheets as Photocatalytic Regulators to Activate Oxygen, Benzoquinone, and Thianthrenium Salts

Cuprous clusters are well known for their important fluorescent properties and tunable redox behavior, but the coordinated protecting groups restrict their application in photocatalysis, in particular, the inner-sphere activation of substrates. By modifying fluorescent cuprous clusters with terminal iodides into two-dimensional coordination sheets, we report a photocatalytic regulator to synergistically combine electron transfer and energy transfer for the oxidative coupling of benzoquinone and terminal alkynes. Under visible light irradiation, the well-modified excited state of the cuprous clusters in the coordination sheets reduces benzoquinones to generate aoxy radicals through electron transfer and activates oxygen through energy transfer. The aoxy radicals interact with copper-coordinated phenylacetylene to form an active intermediate, which is further oxidized by the in situ formed active oxygen species and aryl ketones are obtained. The warranted potential of the excited coordination sheets enables the reductive activation of thianthrenium salts as radical precursors, facilitating radical capture and further C-N coupling via an inner-sphere activation mechanism. The new catalytic approach optimizes the redox properties and excited-state lifetime, shortens the electron transfer steps, and promotes the potential collision of a low concentration of active species in tandem catalytic cycles, thus paving a new way to develop ecologically benign, cost-effective, multipurpose, and flexible catalytic systems.