Supermultiplexed optical imaging and barcoding with engineered polyynes

Bead-based spontaneous Raman codes for multiplex immunoassay

In the immunoassay process, for fulfilling the need to identify multiple analytes in a small amount of complex sample matrix, it is desirable to develop highly efficient and specific multiplex suspension array technology. Raman coding strategy offers an attractive solution to code the suspension arrays by simply combing narrow spectral bands with stable signal intensities through solid-phase synthesis on the resin beads. Based on this strategy, we report the bead-based spontaneous Raman codes for multiplex immunoassay. The study resulted in superior selectivity of the Raman-encoded beads for binding with single and multiple analytes, respectively. With the use of mixed types of Raman-encoded immunoassay beads, multiple targets in small amounts of samples were identified rapidly and accurately. By confirming the feasibility of bead-based spontaneous Raman codes for multiplex immunoassay, we anticipate this novel technology to be widely applied in the near future.

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.

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.

A detection system using sensing motif-tethered oligodeoxynucleotides for multiplex biomolecular analysis

We developed a system to detect multiple target biomolecules through sensing motif-tethered oligodeoxynucleotides. DNA-based molecular probes gave the primary amine motif upon reaction with the target biomolecules, glutathione (GSH) and H2O2. After labelling with biotin, the product DNAs were selectively collected to be quantified by qPCR.

A Visual Raman Nano-Delivery System Based on Thiophene Polymer for Microtumor Detection

A visual Raman nano-delivery system (NS) is a widely used technique for the visualization and diagnosis of tumors and various biological processes. Thiophene-based organic polymers exhibit excellent biocompatibility, making them promising candidates for development as a visual Raman NS. However, materials based on thiophene face limitations due to their absorption spectra not matching with NIR (near-infrared) excitation light, which makes it difficult to achieve enhanced Raman properties and also introduces potential fluorescence interference. In this study, we introduce a donor-acceptor (D-A)-structured thiophene-based polymer, PBDB-T. Due to the D-A molecular modulation, PBDB-T exhibits a narrow bandgap of Eg = 2.63 eV and a red-shifted absorption spectrum, with the absorption edge extending into the NIR region. Upon optimal excitation with 785 nm light, it achieves ultra-strong pre-resonant Raman enhancement while avoiding fluorescence interference. As an intrinsically sensitive visual Raman NS for in vivo imaging, the PBDB-T NS enables the diagnosis of microtumor regions with dimensions of 0.5 mm × 0.9 mm, and also successfully diagnoses deeper tumor tissues, with an in vivo circulation half-life of 14.5 h. This research unveils the potential application of PBDB-T as a NIR excited visual Raman NS for microtumor diagnosis, introducing a new platform for the advancement of "Visualized Drug Delivery Systems". Moreover, the aforementioned platform enables the development of a more diverse range of targeted visual drug delivery methods, which can be tailored to specific regions.

Visualization of Modified Bisarylbutadiyne-Tagged Small Molecules in Live-Cell Nuclei by Stimulated Raman Scattering Microscopy

Visualizing the distribution of small-molecule drugs in living cells is an important strategy for developing specific, effective, and minimally toxic drugs. As an alternative to fluorescence imaging using bulky fluorophores or cell fixation, stimulated Raman scattering (SRS) imaging combined with bisarylbutadiyne (BADY) tagging enables the observation of small molecules closer to their native intracellular state. However, there is evidence that the physicochemical properties of BADY-tagged analogues of small-molecule drugs differ significantly from those of their parent drugs, potentially affecting their intracellular distribution. Herein, we developed a modified BADY to reduce deviations in physicochemical properties (in particular, lipophilicity and membrane permeability) between tagged and parent drugs, while maintaining high Raman activity in live-cell SRS imaging. We highlight the practical application of this approach by revealing the nuclear distribution of a modified BADY-tagged analogue of JQ1, a bromodomain and extra-terminal motif inhibitor with applications in targeted cancer therapy, in living HeLa cells. The modified BADY, methoxypyridazyl pyrimidyl butadiyne (MPDY), revealed intranuclear JQ1, while BADY-tagged JQ1 did not show a clear nuclear signal. We anticipate that the present approach combining MPDY tagging with live-cell SRS imaging provides important insight into the behavior of intracellular drugs and represents a promising avenue for improving drug development.

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.

Impact of Halogen Termination and Chain Length on π-Electron Conjugation and Vibrational Properties of Halogen-Terminated Polyynes

We explored the optoelectronic and vibrational properties of a new class of halogen-terminated carbon atomic wires in the form of polyynes using UV-vis, infrared absorption, Raman spectroscopy, X-ray single-crystal diffraction, and DFT calculations. These polyynes terminate on one side with a cyanophenyl group and on the other side, with a halogen atom X (X = Cl, Br, I). We focus on the effect of different halogen terminations and increasing lengths (i.e., 4, 6, and 8 sp-carbon atoms) on the π-electron conjugation and the electronic structure of these systems. The variation in the sp-carbon chain length is more effective in tuning these features than changing the halogen end group, which instead leads to a variety of solid-state architectures. Shifts between the vibrational frequencies of samples in crystalline powders and in solution reflect intermolecular interactions. In particular, the presence of head-to-tail dimers in the crystals is responsible for the modulation of the charge density associated with the π-electron system, and this phenomenon is particularly important when strong I··· N halogen bonds occur.

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.

Biomimetic NIR-II fluorescent proteins created from chemogenic protein-seeking dyes for multicolor deep-tissue bioimaging

Near-infrared-I/II fluorescent proteins (NIR-I/II FPs) are crucial for in vivo imaging, yet the current NIR-I/II FPs face challenges including scarcity, the requirement for chromophore maturation, and limited emission wavelengths (typically < 800 nm). Here, we utilize synthetic protein-seeking NIR-II dyes as chromophores, which covalently bind to tag proteins (e.g., human serum albumin, HSA) through a site-specific nucleophilic substitution reaction, thereby creating proof-of-concept biomimetic NIR-II FPs. This chemogenic protein-seeking strategy can be accomplished under gentle physiological conditions without catalysis. Proteomics analysis identifies specific binding site (Cys 477 on DIII). NIR-II FPs significantly enhance chromophore brightness and photostability, while improving biocompatibility, allowing for high-performance NIR-II lymphography and angiography. This strategy is universal and applicable in creating a wide range of spectrally separated NIR-I/II FPs for real-time visualization of multiple biological events. Overall, this straightforward biomimetic approach holds the potential to transform fluorescent protein-based bioimaging and enables in-situ albumin targeting to create NIR-I/II FPs for deep-tissue imaging in live organisms.

Raman Flow Cytometry and Its Biomedical Applications

Raman flow cytometry (RFC) uniquely integrates the "label-free" capability of Raman spectroscopy with the "high-throughput" attribute of traditional flow cytometry (FCM), offering exceptional performance in cell characterization and sorting. Unlike conventional FCM, RFC stands out for its elimination of the dependency on fluorescent labels, thereby reducing interference with the natural state of cells. Furthermore, it significantly enhances the detection information, providing a more comprehensive chemical fingerprint of cells. This review thoroughly discusses the fundamental principles and technological advantages of RFC and elaborates on its various applications in the biomedical field, from identifying and characterizing cancer cells for in vivo cancer detection and surveillance to sorting stem cells, paving the way for cell therapy, and identifying metabolic products of microbial cells, enabling the differentiation of microbial subgroups. Moreover, we delve into the current challenges and future directions regarding the improvement in sensitivity and throughput. This holds significant implications for the field of cell analysis, especially for the advancement of metabolomics.

Photoswitchable polyynes for multiplexed stimulated Raman scattering microscopy with reversible light control

Optical imaging with photo-controllable probes has greatly advanced biological research. With superb chemical specificity of vibrational spectroscopy, stimulated Raman scattering (SRS) microscopy is particularly promising for super-multiplexed optical imaging with rich chemical information. Functional SRS imaging in response to light has been recently demonstrated, but multiplexed SRS imaging with reversible photocontrol remains unaccomplished. Here, we create a multiplexing palette of photoswitchable polyynes with 16 Raman frequencies by coupling asymmetric diarylethene with super-multiplexed Carbow (Carbow-switch). Through optimization of both electronic and vibrational spectroscopy, Carbow-switch displays excellent photoswitching properties under visible light control and SRS response with large frequency change and signal enhancement. Reversible and spatial-selective multiplexed SRS imaging of different organelles are demonstrated in living cells. We further achieve photo-selective time-lapse imaging of organelle dynamics during oxidative stress and protein phase separation. The development of Carbow-switch for photoswitchable SRS microscopy will open up new avenues to study complex interactions and dynamics in living cells with high spatiotemporal precision and multiplexing capability.

Encoding fluorescence intensity with tetrahedron DNA nanostructure based FRET effect for bio-detection

Biocoding technology constructed by readable tags with distinct signatures is a brand-new bioanalysis method to realize multiplexed identification and bio-information decoding. In this study, a novel fluorescence intensity coding technology termed Tetra-FICT was reported based on tetrahedron DNA nanostructure (TDN) carrier and Főrster Resonance Energy Transfer (FRET) effect. By modulating numbers and distances of Cy3 and Cy5 at four vertexes of TDN, different fluorescence intensities of twenty-six samples were produced at ∼565.0 nm (FICy3) and ∼665.0 nm (FICy5) by detecting fluorescence spectra. By developing an error correction mechanism, eleven codes were established based on divided intensity ranges of the final FICy3 together with FICy5 (Final-FICy3&FICy5). These resulting codes were used to construct barcode probes, with three miRNA biomarkers (miRNA-210, miRNA-199a and miRNA-21) as cases for multiplexed bio-assay. The high specificity and sensitivity were also demonstrated for the detection of miRNA-210. Overall, the proposed Tetra-FICT enriched the toolbox of fluorescence coding, which could be applied to multiplexing biomarkers detection.

Force-Encoding DNA Nanomachines for Simultaneous and Direct Detection of Multiple Pathogenic Bacteria in Blood

Pathogen detection is growing in importance in the early stages of bacterial infection and treatment due to the significant morbidity and mortality associated with bloodstream infections. Although various diagnostic approaches for pathogen detection have been proposed, most of them are time-consuming, with insufficient sensitivity and limited specificity and multiplexing capability for clinical use. Here, we report a force-encoding DNA nanomachine for simultaneous and high-throughput detection of multiple pathogens in blood through force-induced remnant magnetization spectroscopy (FIRMS). The force-encoding DNA nanomachines coupled with DNA walkers enable analytical sensitivity down to a single bacterium via a cascade signal amplification strategy. More importantly, it allows for rapid and specific profiling of various pathogens directly in blood samples, without being affected by factors such as light color and solution properties. We expect that this magnetic sensing platform holds great promise for various applications in biomedical research and clinical diagnostics.

Transient stimulated Raman scattering spectroscopy and imaging

Stimulated Raman scattering (SRS) has been developed as an essential quantitative contrast for chemical imaging in recent years. However, while spectral lines near the natural linewidth limit can be routinely achieved by state-of-the-art spontaneous Raman microscopes, spectral broadening is inevitable for current mainstream SRS imaging methods. This is because those SRS signals are all measured in the frequency domain. There is a compromise between sensitivity and spectral resolution: as the nonlinear process benefits from pulsed excitations, the fundamental time-energy uncertainty limits the spectral resolution. Besides, the spectral range and acquisition speed are mutually restricted. Here we report transient stimulated Raman scattering (T-SRS), an alternative time-domain strategy that bypasses all these fundamental conjugations. T-SRS is achieved by quantum coherence manipulation: we encode the vibrational oscillations in the stimulated Raman loss (SRL) signal by femtosecond pulse-pair sequence excited vibrational wave packet interference. The Raman spectrum was then achieved by Fourier transform of the time-domain SRL signal. Since all Raman modes are impulsively and simultaneously excited, T-SRS features the natural-linewidth-limit spectral line shapes, laser-bandwidth-determined spectral range, and improved sensitivity. With ~150-fs laser pulses, we boost the sensitivity of typical Raman modes to the sub-mM level. With all-plane-mirror high-speed time-delay scanning, we further demonstrated hyperspectral SRS imaging of live-cell metabolism and high-density multiplexed imaging with the natural-linewidth-limit spectral resolution. T-SRS shall find valuable applications for advanced Raman imaging.

New Highly Sensitive and Specific Raman Probe for Live Cell Imaging of Mitochondrial Function

For Raman hyperspectral detection and imaging in live cells, it is very desirable to create novel probes with strong and unique Raman vibrations in the biological silent region (1800-2800 cm-1). The use of molecular probes in Raman imaging is a relatively new technique in subcellular research; however, it is developing very rapidly. Compared with the label-free method, it allows for a more sensitive and selective visualization of organelles within a single cell. Biological systems are incredibly complex and heterogeneous. Directly visualizing biological structures and activities at the cellular and subcellular levels remains by far one of the most intuitive and powerful ways to study biological problems. Each organelle plays a specific and essential role in cellular processes, but importantly for cells to survive, mitochondrial function must be reliable. Motivated by earlier attempts and successes of biorthogonal chemical imaging, we develop a tool supporting Raman imaging of cells to track biochemical changes associated with mitochondrial function at the cellular level in an in vitro model. In this work, we present a newly synthesized highly sensitive RAR-BR Raman probe for the selective imaging of mitochondria in live endothelial cells.

2D Hierarchical Microbarcodes with Expanded Storage Capacity for Optical Multiplex and Information Encryption

The design of nanosegregated fluorescent tags/barcodes by geometrical patterning with precise dimensions and hierarchies could integrate multilevel optical information within one carrier and enhance microsized barcoding techniques for ultrahigh-density optical data storage and encryption. However, precise control of the spatial distribution in micro/nanosized matrices intrinsically limits the accessible barcoding applications in terms of material design and construction. Here, crystallization forces are leveraged to enable a rapid, programmable molecular packing and rapid epitaxial growth of fluorescent units in 2D via crystallization-driven self-assembly. The fluorescence encoding density, scalability, information storage capacity, and decoding techniques of the robust 2D polymeric barcoding platform are explored systematically. These results provide both a theoretical and an experimental foundation for expanding the fluorescence storage capacity, which is a longstanding challenge in state-of-the-art microbarcoding techniques and establish a generalized and adaptable coding platform for high-throughput analysis and optical multiplexing.

Quality Control of Mass-Encoded Nanodevices by Compartmented DNA Origami Frames for Precision Information Coding and Logic Mapping

Encoded nanostructures afford an ideal platform carrying multi-channel signal components for multiplexed assay and information security. However, with the demand on exclusivity and reproducibility of coding signals, precise control on the structure and composition of nanomaterials featuring fully distinguishable signals remains challenging. By using the multiplexing capability of mass spectrometry (MS) and spatial addressability of DNA origami nanostructures, we herein propose a quality control methodology for constructing mass-encoded nanodevices (namely MNTs-TDOFs) in the scaffold of compartmented tetrahedral DNA origami frames (TDOFs), in which the arrangement and stoichiometry of four types of mass nanotags (MNTs) can be finely regulated and customized to generate characteristic MS patterns. The programmability of combinatorial MNTs and orthogonality of individual compartments allows further evolution of MNTs-TDOFs to static tagging agents and dynamic nanoprobes for labeling and sensing of multiple targets. More importantly, structure control at single TDOF level ensures the constancy of prescribed MS outputs, by which a high-capacity coding system was established for secure information encryption and decryption. In addition to the multiplexed outputs in parallel, the nanodevices could also map logic circuits with interconnected complexity and logic events of c-Met recognition and dimerization on cell surface for signaling regulation by MS interrogation.

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.

Temporally multiplexed imaging of dynamic signaling networks in living cells

Molecular signals interact in networks to mediate biological processes. To analyze these networks, it would be useful to image many signals at once, in the same living cell, using standard microscopes and genetically encoded fluorescent reporters. Here, we report temporally multiplexed imaging (TMI), which uses genetically encoded fluorescent proteins with different clocklike properties-such as reversibly photoswitchable fluorescent proteins with different switching kinetics-to represent different cellular signals. We linearly decompose a brief (few-second-long) trace of the fluorescence fluctuations, at each point in a cell, into a weighted sum of the traces exhibited by each fluorophore expressed in the cell. The weights then represent the signal amplitudes. We use TMI to analyze relationships between different kinase activities in individual cells, as well as between different cell-cycle signals, pointing toward broad utility throughout biology in the analysis of signal transduction cascades in living systems.

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.

Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level

As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.

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.

Non-Mass Spectrometric Targeted Single-Cell Metabolomics

Metabolic assays serve as pivotal tools in biomedical research, offering keen insights into cellular physiological and pathological states. While mass spectrometry (MS)-based metabolomics remains the gold standard for comprehensive, multiplexed analyses of cellular metabolites, innovative technologies are now emerging for the targeted, quantitative scrutiny of metabolites and metabolic pathways at the single-cell level. In this review, we elucidate an array of these advanced methodologies, spanning synthetic and surface chemistry techniques, imaging-based methods, and electrochemical approaches. We summarize the rationale, design principles, and practical applications for each method, and underscore the synergistic benefits of integrating single-cell metabolomics (scMet) with other single-cell omics technologies. Concluding, we identify prevailing challenges in the targeted scMet arena and offer a forward-looking commentary on future avenues and opportunities in this rapidly evolving field.

Continuous-Wave Raman Lasing from Metal-Linked Organic Dimer Microcrystals

Stimulated Raman scattering offers an alternative strategy to explore continuous-wave (c.w.) organic lasers, which, however, still suffers from the limitation of inadequate Raman gain in organic material systems. Here we propose a metal-linking approach to enhance the Raman gain of organic molecules. Self-assembled microcrystals of the metal linked organic dimers exhibit large Raman gain, therefore allowing for c.w. Raman lasing. Furthermore, broadband tunable Raman lasing is achieved in the organic dimer microcrystals by adjusting excitation wavelengths. This work advances the understanding of Raman gain in organic molecules, paving a way for the design of c.w. organic lasers.

Plasmon-Induced Charge Transfer-Enhanced Raman Scattering on a Semiconductor: Toward Amplification-Free Quantification of SARS-CoV-2

Semiconductors demonstrate great potentials as chemical mechanism-based surface-enhanced Raman scattering (SERS) substrates in determination of biological species in complex living systems with high selectivity. However, low sensitivity is the bottleneck for their practical applications, compared with that of noble metal-based Raman enhancement ascribed to electromagnetic mechanism. Herein, a novel Cu2 O nanoarray with free carrier density of 1.78×1021  cm-3 comparable to that of noble metals was self-assembled, creating a record in enhancement factor (EF) of 3.19×1010 among semiconductor substrates. The significant EF was mainly attributed to plasmon-induced hot electron transfer (PIHET) in semiconductor which was never reported before. This Cu2 O nanoarray was subsequently developed as a highly sensitive and selective SERS chip for non-enzyme and amplification-free SARS-CoV-2 RNA quantification with a detection limit down to 60 copies/mL within 5 min. This unique Cu2 O nanoarray demonstrated the significant Raman enhancement through PIHET process, enabling rapid and sensitive point-of-care testing of emerging virus variants.

Cycloaddition-Retro-Electrocyclization Click Reaction of Amine End-Capped Oligoynes with Tetracyanoethylene

This study shows the first example of cycloaddition-retro-electrocyclization (CA-RE) click reaction involving nitrogen end-capped push-pull oligoynes. The reported CA-RE reaction with TCNE (tetracyanoethylene) is fully regioselective and leads exclusively to the unprecedented TCBD (tetracyanobuta-1,3-diene-2,3-diyl) end-capped carbon rods. The molecular structure of the products was unambiguously confirmed using X-ray single crystal diffraction and their optical and electronic properties were investigated experimentally and rationalized using DFT (density functional theory) calculations.

Disclosing Early Excited State Relaxation Events in Prototypical Linear Carbon Chains

One-dimensional (1D) linear nanostructures comprising sp-hybridized carbon atoms, as derivatives of the prototypical allotrope known as carbyne, are predicted to possess outstanding mechanical, thermal, and electronic properties. Despite recent advances in their synthesis, their chemical and physical properties are still poorly understood. Here, we investigate the photophysics of a prototypical polyyne (i.e., 1D chain with alternating single and triple carbon bonds) as the simplest model of finite carbon wire and as a prototype of sp-carbon-based chains. We perform transient absorption experiments with high temporal resolution (<30 fs) on monodispersed hydrogen-capped hexayne H─(C≡C)6─H synthesized by laser ablation in liquid. With the support of computational studies based on ground state density functional theory (DFT) and excited state time-dependent (TD)-DFT calculations, we provide a comprehensive description of the excited state relaxation processes at early times following photoexcitation. We show that the internal conversion from a bright high-energy singlet excited state to a low-lying singlet dark state is ultrafast and takes place with a 200 fs time constant, followed by thermalization on the picosecond time scale and decay of the low-energy singlet state with hundreds of picoseconds time constant. We also show that the time scale of these processes does not depend on the end groups capping the sp-carbon chain. The understanding of the primary photoinduced events in polyynes is of key importance both for fundamental knowledge and for potential optoelectronic and light-harvesting applications of low-dimensional nanostructured carbon-based materials.

Co-multiplexing spectral and temporal dimensions based on luminescent materials

Optical multiplexing is a pivotal technique for augmenting the capacity of optical data storage (ODS) and increasing the security of anti-counterfeiting. However, due to the dearth of appropriate storage media, optical multiplexing is generally restricted to a single dimension, thus curtailing the encoding capacity. Herein, the co-multiplexing spectral and temporal dimensions are proposed for optical encoding based on photoluminescence (PL) and persistent-luminescence (PersL) at four different wavelengths. Each emission color comprises four luminescence modes. The further multiplexing of four wavelengths leads to the maximum encoding capacity of 8 bits at each pixel. The wavelength difference between adjacent peaks is larger than 50 nm. The well-separated emission wavelengths significantly lower the requirements for high-resolution spectrometers. Moreover, the information is unable to be decoded until both PL and PersL spectra are collected, suggesting a substantial improvement in information security and the security level of anti-counterfeiting.

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.

Revealing Population Heterogeneity in Vesicle-Based Nanomedicines Using Automated, Single Particle Raman Analysis

The intrinsic heterogeneity of many nanoformulations is currently challenging to characterize on both the single particle and population level. Therefore, there is great opportunity to develop advanced techniques to describe and understand nanomedicine heterogeneity, which will aid translation to the clinic by informing manufacturing quality control, characterization for regulatory bodies, and connecting nanoformulation properties to clinical outcomes to enable rational design. Here, we present an analytical technique to provide such information, while measuring the nanocarrier and cargo simultaneously with label-free, nondestructive single particle automated Raman trapping analysis (SPARTA). We first synthesized a library of model compounds covering a range of hydrophilicities and providing distinct Raman signals. These compounds were then loaded into model nanovesicles (polymersomes) that can load both hydrophobic and hydrophilic cargo into the membrane or core regions, respectively. Using our analytical framework, we characterized the heterogeneity of the population by correlating the signal per particle from the membrane and cargo. We found that core and membrane loading can be distinguished, and we detected subpopulations of highly loaded particles in certain cases. We then confirmed the suitability of our technique in liposomes, another nanovesicle class, including the commercial formulation Doxil. Our label-free analytical technique precisely determines cargo location alongside loading and release heterogeneity in nanomedicines, which could be instrumental for future quality control, regulatory body protocols, and development of structure-function relationships to bring more nanomedicines to the clinic.

Super-resolution vibrational imaging based on photoswitchable Raman probe

Super-resolution vibrational microscopy is promising to increase the degree of multiplexing of nanometer-scale biological imaging because of the narrower spectral linewidth of molecular vibration compared to fluorescence. However, current techniques of super-resolution vibrational microscopy suffer from various limitations including the need for cell fixation, high power loading, or complicated detection schemes. Here, we present reversible saturable optical Raman transitions (RESORT) microscopy, which overcomes these limitations by using photoswitchable stimulated Raman scattering (SRS). We first describe a bright photoswitchable Raman probe (DAE620) and validate its signal activation and depletion characteristics when exposed to low-power (microwatt level) continuous-wave laser light. By harnessing the SRS signal depletion of DAE620 through a donut-shaped beam, we demonstrate super-resolution vibrational imaging of mammalian cells with excellent chemical specificity and spatial resolution beyond the optical diffraction limit. Our results indicate RESORT microscopy to be an effective tool with high potential for multiplexed super-resolution imaging of live cells.

Analytical Techniques for Single-Cell Biochemical Assays of Lipids

Lipids are essential cellular components forming membranes, serving as energy reserves, and acting as chemical messengers. Dysfunction in lipid metabolism and signaling is associated with a wide range of diseases including cancer and autoimmunity. Heterogeneity in cell behavior including lipid signaling is increasingly recognized as a driver of disease and drug resistance. This diversity in cellular responses as well as the roles of lipids in health and disease drive the need to quantify lipids within single cells. Single-cell lipid assays are challenging due to the small size of cells (∼1 pL) and the large numbers of lipid species present at concentrations spanning orders of magnitude. A growing number of methodologies enable assay of large numbers of lipid analytes, perform high-resolution spatial measurements, or permit highly sensitive lipid assays in single cells. Covered in this review are mass spectrometry, Raman imaging, and fluorescence-based assays including microscopy and microseparations.

Visualizing drug-induced lipid accumulation in lysosomes of live cancer cells with stimulated Raman imaging

The low pH of the lysosomal compartment often results in sequestration of chemotherapeutic agents that contain positively charged basic functional groups, leading to anti-cancer drug resistance. To visualize drug localization in lysosomes and its influence on lysosomal functions, we synthesize a group of drug-like compounds that contain both a basic functional group and a bisarylbutadiyne (BADY) group as a Raman probe. With quantitative stimulated Raman scattering (SRS) imaging, we validate that the synthesized lysosomotropic (LT) drug analogs show high lysosomal affinity, which can also serve as a photostable lysosome tracker. We find that long-term retention of the LT compounds in lysosomes leads to the increased amount and colocalization of both lipid droplets (LDs) and lysosomes in SKOV3 cells. With hyperspectral SRS imaging, further studies find that the LDs stuck in lysosomes are more saturated than the LDs staying out of the lysosomes, indicating impaired lysosomal lipid metabolism by the LT compounds. These results demonstrate that SRS imaging of the alkyne-based probes is a promising approach to characterizing the lysosomal sequestration of drugs and its influence on cell functions.

Comparing Performance of Spectral Image Analysis Approaches for Detection of Cellular Signals in Time-Lapse Hyperspectral Imaging Fluorescence Excitation-Scanning Microscopy

Hyperspectral imaging (HSI) technology has been applied in a range of fields for target detection and mixture analysis. While HSI was originally developed for remote sensing applications, modern uses include agriculture, historical document authentication, and medicine. HSI has also shown great utility in fluorescence microscopy. However, traditional fluorescence microscopy HSI systems have suffered from limited signal strength due to the need to filter or disperse the emitted light across many spectral bands. We have previously demonstrated that sampling the fluorescence excitation spectrum may provide an alternative approach with improved signal strength. Here, we report on the use of excitation-scanning HSI for dynamic cell signaling studies-in this case, the study of the second messenger Ca2+. Time-lapse excitation-scanning HSI data of Ca2+ signals in human airway smooth muscle cells (HASMCs) were acquired and analyzed using four spectral analysis algorithms: linear unmixing (LU), spectral angle mapper (SAM), constrained energy minimization (CEM), and matched filter (MF), and the performances were compared. Results indicate that LU and MF provided similar linear responses to increasing Ca2+ and could both be effectively used for excitation-scanning HSI. A theoretical sensitivity framework was used to enable the filtering of analyzed images to reject pixels with signals below a minimum detectable limit. The results indicated that subtle kinetic features might be revealed through pixel filtering. Overall, the results suggest that excitation-scanning HSI can be employed for kinetic measurements of cell signals or other dynamic cellular events and that the selection of an appropriate analysis algorithm and pixel filtering may aid in the extraction of quantitative signal traces. These approaches may be especially helpful for cases where the signal of interest is masked by strong cellular autofluorescence or other competing signals.

Orthogonal Combinatorial Raman Codes Enable Rapid High-Throughput-Out Library Screening of Cell-Targeting Ligands

High-throughput assays play an important role in the fields of drug discovery, genetic analysis, and clinical diagnostics. Although super-capacity coding strategies may facilitate labeling and detecting large numbers of targets in a single assay, practically, the constructed large-capacity codes have to be decoded with complicated procedures or are lack of survivability under the required reaction conditions. This challenge results in either inaccurate or insufficient decoding outputs. Here, we identified chemical-resistant Raman compounds to build a combinatorial coding system for the high-throughput screening of cell-targeting ligands from a focused 8-mer cyclic peptide library. The accurate in situ decoding results proved the signal, synthetic, and functional orthogonality for this Raman coding strategy. The orthogonal Raman codes allowed for a rapid identification of 63 positive hits at one time, evidencing a high-throughput-out capability in the screening process. We anticipate this orthogonal Raman coding strategy being generalized to enable efficient high-throughput-out screening of more useful ligands for cell targeting and drug discovery.

Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications

Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.

Toward the Next Frontiers of Vibrational Bioimaging

Chemical imaging based on vibrational contrasts can extract molecular information entangled in complex biological systems. To this end, nonlinear Raman scattering microscopy, mid-infrared photothermal (MIP) microscopy, and atomic force microscopy (AFM)-based force-detected photothermal microscopies are emerging with better chemical sensitivity, molecular specificity, and spatial resolution than conventional vibrational methods. Their utilization in bioimaging applications has provided biological knowledge in unprecedented detail. This Perspective outlines key methodological developments, bioimaging applications, and recent technical innovations of the three techniques. Representative biological demonstrations are also highlighted to exemplify the unique advantages of obtaining vibrational contrasts. With years of effort, these three methods compose an expanding vibrational bioimaging toolbox to tackle specific bioimaging needs, benefiting many biological investigations with rich information in both label-free and labeling manners. Each technique will be discussed and compared in the outlook, leading to possible future directions to accommodate growing needs in vibrational bioimaging.

Ultrafast Spectral Tuning of a Fiber Laser for Time-Encoded Multiplex Coherent Raman Scattering Microscopy

Coherent Raman scattering microscopy utilizing bioorthogonal tagging approaches like isotope or alkyne labeling allows for a targeted monitoring of spatial distribution and dynamics of small molecules of interest in cells, tissues, and other complex biological matrices. To fully exploit this approach in terms of real-time monitoring of several Raman tags, e.g., to study drug uptake dynamics, extremely fast tunable lasers are needed. Here, we present a laser concept without moving parts and fully electronically controlled for the quasi-simultaneous acquisition of coherent anti-Stokes Raman scattering images at multiple Raman resonances. The laser concept is based on the combination of a low noise and spectrally narrow Fourier domain mode-locked laser seeding a compact four wave mixing-based high-power fiber-based optical parametric amplifier.

Stimulated Raman Scattering Imaging Sheds New Light on Lipid Droplet Biology

A lipid droplet (LD) is a dynamic organelle closely associated with cellular functions and energy homeostasis. Dysregulated LD biology underlies an increasing number of human diseases, including metabolic disease, cancer, and neurodegenerative disorder. Commonly used lipid staining and analytical tools have difficulty providing the information regarding LD distribution and composition at the same time. To address this problem, stimulated Raman scattering (SRS) microscopy uses the intrinsic chemical contrast of biomolecules to achieve both direct visualization of LD dynamics and quantitative analysis of LD composition with high molecular selectivity at the subcellular level. Recent developments of Raman tags have further enhanced sensitivity and specificity of SRS imaging without perturbing molecular activity. With these advantages, SRS microscopy has offered great promise for deciphering LD metabolism in single live cells. This article overviews and discusses the latest applications of SRS microscopy as an emerging platform to dissect LD biology in health and disease.

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.

The complexities of proanthocyanidin biosynthesis and its regulation in plants

Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.

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.

Multiscale microscopy to decipher plant cell structure and dynamics

New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.

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.

Self-Referenced Synthetic Urinary Biomarker for Quantitative Monitoring of Cancer Development

Urinary monitoring of diseases has gained considerable attention due to its simple and non-invasive sampling. However, urinalysis remains limited by the dearth of reliable urinary biomarkers and the intrinsically enormous heterogeneity of urine samples. Herein, we report, to our knowledge, the first renal-clearable Raman probe encoded by an internal standard (IS)-conjugated reporter that acts as a quantifiable urinary biomarker for reliable monitoring of cancer development, simultaneously eliminating the impact of sample heterogeneity. Upon delivery of the probes into tumor microenvironments, the endogenously overexpressed β-glucuronidase (GUSB) can cleave the target-responsive residues of the probes to produce IS-retained gold nanoclusters, which were excreted into host urine and analyzed by Au growth-based surface-enhanced Raman spectroscopy. As a result, the in vivo GUSB activity was transformed into in vitro quantitative urinary signals. Based on this IS-encoded synthetic biomarker, both the cancer progression and therapy efficacy were quantitatively monitored, potentiating clinical implications.

Color-scalable flow cytometry with Raman tags

Flow cytometry is an indispensable tool in biology and medicine for counting and analyzing cells in large heterogeneous populations. It identifies multiple characteristics of every single cell, typically via fluorescent probes that specifically bind to target molecules on the cell surface or within the cell. However, flow cytometry has a critical limitation: the color barrier. The number of chemical traits that can be simultaneously resolved is typically limited to several due to the spectral overlap between fluorescence signals from different fluorescent probes. Here, we present color-scalable flow cytometry based on coherent Raman flow cytometry with Raman tags to break the color barrier. This is made possible by combining a broadband Fourier-transform coherent anti-Stokes Raman scattering (FT-CARS) flow cytometer, resonance-enhanced cyanine-based Raman tags, and Raman-active dots (Rdots). Specifically, we synthesized 20 cyanine-based Raman tags whose Raman spectra are linearly independent in the fingerprint region (400 to 1,600 cm^-1). For highly sensitive detection, we produced Rdots composed of 12 different Raman tags in polymer nanoparticles whose detection limit was as low as 12 nM for a short FT-CARS signal integration time of 420 µs. We performed multiplex flow cytometry of MCF-7 breast cancer cells stained by 12 different Rdots with a high classification accuracy of 98%. Moreover, we demonstrated a large-scale time-course analysis of endocytosis via the multiplex Raman flow cytometer. Our method can theoretically achieve flow cytometry of live cells with >140 colors based on a single excitation laser and a single detector without increasing instrument size, cost, or complexity.