Multicolor Photoactivatable Raman Probes for Subcellular Imaging and Tracking by Cyclopropenone Caging

Stimuli-responsive 'On-Off' SERS-darkfield bimodal plasmonic nanoprobes for selective cancer cell illumination

Early detection is essential for improving cancer treatment outcomes. Surface-enhanced Raman scattering (SERS) offers high sensitivity and molecular specificity but suffers from slow imaging speed when used independently. Here, we introduce stimuli-responsive bimodal SERS-dark-field (DF) nanoprobes for rapid and selective imaging of metastatic prostate cancer cells. These nanoprobes utilize legumain enzyme-responsive peptide coatings on plasmonic gold nanocubes and a bio-orthogonal self-condensation mechanism to facilitate enzyme-triggered nanoprobe aggregation. Upon internalization, the nanoprobes selectively aggregate in DU145 cells that overexpress legumain, while remaining uniformly dispersed in LNCaP cells with minimal legumain activity. DF microscopy quickly identifies these aggregates, significantly expediting subsequent SERS imaging. The engineered design of these nanoprobes ensures distinct vibrational signatures specifically correlated to enzyme activity, establishing a direct link between enzymatic presence and SERS signal generation. By combining the rapid localization capabilities of DF imaging with the molecular precision of SERS, our bimodal imaging strategy significantly surpasses conventional single-modal SERS techniques, providing a versatile platform for fast and accurate detection of various diseases through their distinctive enzymatic profiles.

Illuminating life processes by vibrational probes

Vibration of chemical bonds can serve as imaging contrast. Vibrational probes, synergized with major advances in chemical bond imaging instruments, have recently flourished and proven valuable in illuminating life processes. Here, we review how the development of vibrational probes with optimal biocompatibility, enhanced sensitivity, multichromatic colors and diverse functionality has extended chemical bond imaging beyond the prevalent label-free paradigm into various novel applications such as imaging metabolites, metabolic imaging, drug imaging, super-multiplex imaging, vibrational profiling and vibrational sensing. These advancements in vibrational probes have greatly facilitated understanding living systems, a new field of vibrational chemical biology.

Emerging magic bullet: subcellular organelle-targeted cancer therapy

The therapeutic efficacy of anticancer drugs heavily relies on their concentration and retention at the corresponding target site. Hence, merely increasing the cellular concentration of drugs is insufficient to achieve satisfactory therapeutic outcomes, especially for the drugs that target specific intracellular sites. This necessitates the implementation of more precise targeting strategies to overcome the limitations posed by diffusion distribution and nonspecific interactions within cells. Consequently, subcellular organelle-targeted cancer therapy, characterized by its exceptional precision, have emerged as a promising approach to eradicate cancer cells through the specific disruption of subcellular organelles. Owing to several advantages including minimized dosage and side effect, optimized efficacy, and reversal of multidrug resistance, subcellular organelle-targeted therapies have garnered significant research interest in recent years. In this review, we comprehensively summarize the distribution of drug targets, targeted delivery strategies at various levels, and sophisticated strategies for targeting specific subcellular organelles. Additionally, we highlight the significance of subcellular targeting in cancer therapy and present essential considerations for its clinical translation.

Advances in Super-resolution Stimulated Raman Scattering Microscopy

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

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.

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.

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.

Photodynamic O2 Economizer Encapsulated with DNAzyme for Enhancing Mitochondrial Gene-Photodynamic Therapy

Emerging research suggests that mitochondrial DNA is a potential target for cancer treatment. However, achieving precise delivery of deoxyribozymes (DNAzymes) and combining photodynamic therapy (PDT) and DNAzyme-based gene silencing together for enhancing mitochondrial gene-photodynamic synergistic therapy remains challenging. Accordingly, herein, intelligent supramolecular nanomicelles are constructed by encapsulating a DNAzyme into a photodynamic O2 economizer for mitochondrial NO gas-enhanced synergistic gene-photodynamic therapy. The designed nanomicelles demonstrate sensitive acid- and red-light sequence-activated behaviors. After entering the cancer cells and targeting the mitochondria, these micelles will disintegrate and release the DNAzyme and Mn (II) porphyrin in the tumor microenvironment. Mn (II) porphyrin acts as a DNAzyme cofactor to activate the DNAzyme for the cleavage reaction. Subsequently, the NO-carrying donor is decomposed under red light irradiation to generate NO that inhibits cellular respiration, facilitating the conversion of more O2 into singlet oxygen (1 O2 ) in the tumor cells, thereby significantly enhancing the efficacy of PDT. In vitro and in vivo experiments reveal that the proposed system can efficiently target mitochondria and exhibits considerable antitumor effects with negligible systemic toxicity. Thus, this study provides a useful conditional platform for the precise delivery of DNAzymes and a novel strategy for activatable NO gas-enhanced mitochondrial gene-photodynamic therapy.

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.

A Smart Intracellular Self-Assembling Bioorthogonal Raman Active Nanoprobe for Targeted Tumor Imaging

Inspired by the principle of in situ self-assembly, the development of enzyme-activated molecular nanoprobes can have a profound impact on targeted tumor detection. However, despite their intrinsic promise, obtaining an optical readout of enzyme activity with high specificity in native milieu has proven to be challenging. Here, a fundamentally new class of Raman-active self-assembling bioorthogonal enzyme recognition (nanoSABER) probes for targeted tumor imaging is reported. This class of Raman probes presents narrow spectral bands reflecting their vibrational fingerprints and offers an attractive solution for optical imaging at different bio-organization levels. The optical beacon harnesses an enzyme-responsive peptide sequence, unique tumor-penetrating properties, and vibrational tags with stretching frequencies in the cell-silent Raman window. The design of nanoSABER is tailored and engineered to transform into a supramolecular structure exhibiting distinct vibrational signatures in presence of target enzyme, creating a direct causality between enzyme activity and Raman signal. Through the integration of substrate-specific for tumor-associated enzyme legumain, unique capabilities of nanoSABER for imaging enzyme activity at molecular, cellular, and tissue levels in combination with machine learning models are shown. These results demonstrate that the nanoSABER probe may serve as a versatile platform for Raman-based recognition of tumor aggressiveness, drug accumulation, and therapeutic response.

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.

Multi-stimuli-responsive molecular fluorescent probes for bioapplications

Stimuli-responsive fluorescent probes have been widely utilized in detecting the physiological and pathological states of living systems. Numerous stimuli-responsive fluorescent probes have been developed due to their advantages of good sensitivity, high resolution, and high contrast fluorescent signals. In this feature article, the progress of multi-stimuli-responsive probes, including organic molecules and metal complexes, for the detection of various biomarkers for bio-applications is summarized. The feature article focuses on the applications of organic-molecule- and metal-complex-based molecular probes in biological systems for detecting different biomarkers of cancer or other diseases. The current challenges and potential future directions of these probes for applications in biological systems are also discussed.

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.

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.

Multicolor emission based on a N, N'-Disubstituted dihydrodibenzo [a, c] phenazine crown ether macrocycle

Dynamic fluorophore 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine (DPAC) affords a new platform to produce diverse emission outputs. In this paper, a novel DPAC-containing crown ether macrocycle D-6 is synthesized and characterized. Host-guest interactions of D-6 with different ammonium guests produced a variety of fluorescence with hypsochromic shifts up to 130 nm, which are found to be affected by choice of solvent or guest and host/guest stoichiometry. Formation of supramolecular complexes were confirmed by UV-vis titration, ¹H NMR and HRMS spectroscopy.

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.

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.

Real-time precision opto-control of chemical processes in live cells

Precision control of molecular activities and chemical reactions in live cells is a long-sought capability by life scientists. No existing technology can probe molecular targets in cells and simultaneously control the activities of only these targets at high spatial precision. We develop a real-time precision opto-control (RPOC) technology that detects a chemical-specific optical response from molecular targets during laser scanning and uses the optical signal to couple a separate laser to only interact with these molecules without affecting other sample locations. We demonstrate precision control of molecular states of a photochromic molecule in different regions of the cells. We also synthesize a photoswitchable compound and use it with RPOC to achieve site-specific inhibition of microtubule polymerization and control of organelle dynamics in live cells. RPOC can automatically detect and control biomolecular activities and chemical processes in dynamic living samples with submicron spatial accuracy, fast response time, and high chemical specificity.

There is a need to control molecular activities at high spatial precision. Here the authors report a real-time precision opto-control technology that detects a chemical-specific optical response from molecular targets, and precisely control photoswitchable microtubule polymerization inhibitors in cells.

Bringing Vibrational Imaging to Chemical Biology with Molecular Probes

As an emerging optical imaging modality, stimulated Raman scattering (SRS) microscopy provides invaluable opportunities for chemical biology studies using its rich chemical information. Through rapid progress over the past decade, the development of Raman probes harnessing the chemical biology toolbox has proven to play a key role in advancing SRS microscopy and expanding biological applications. In this perspective, we first discuss the development of biorthogonal SRS imaging using small tagging of triple bonds or isotopes and highlight their unique advantages for metabolic pathway analysis and microbiology investigations. Potential opportunities for chemical biology studies integrating small tagging with SRS imaging are also proposed. We next summarize the current designs of highly sensitive and super-multiplexed SRS probes, as well as provide future directions and considerations for next-generation functional probe design. These rationally designed SRS probes are envisioned to bridge the gap between SRS microscopy and chemical biology research and should benefit their mutual development.

Chemical biology tools for imaging-based analysis of organelle membranes and lipids

Membrane biology studies have revealed that in addition to providing structural support for compartment formation and membrane protein function, subcellular biomembranes are also critically involved in many biological events. To facilitate our understanding of the functions, biophysical properties and structural dynamics of organelle membranes, various exciting chemical biology tools have recently emerged. This short review aims to describe the latest molecular probes for organelle membrane studies. In particular, we will feature chemical strategies to visualize and quantitatively analyze the dynamic propeties of organelle membranes and lipids and discuss current limitations and potential future directions of this challenging research area.

A novel dual-capability naphthalimide-based fluorescent probe for Fe3+ ion detection and lysosomal tracking in living cells

We design and synthesize a novel 1,8-naphthalimide-based fluorescent probe MNP that features the dual capabilities of tracking lysosomes in living HeLa cells and sensitively detecting Fe³⁺ ions in aqueous solution. The MNP is obtained by modifying the morpholine group with a lysosomal targeting function and the piperazine group with an Fe³⁺ ion recognition function on the 1,8-naphthalimide matrix. In the presence of Fe³⁺ ions, the MNP acts as a recognition ligand to coordinate with the central Fe³⁺ ion, and the protonated [MNPH]⁺ is eventually generated, in which significant fluorescence enhancements are observed due to the intramolecular photo-induced electron transfer (PET) process being blocked. The limit of detection of Fe³⁺ ions is as low as 65.2 nM. A cell imaging experiment shows that the MNP has low cytotoxicity and excellent lysosomal targeting ability. Therefore, the MNP offers a promising tool for lysosomal tracking and relevant life process research.

A newly prepared 1,8-naphthalimide-based fluorescent probe, MNP, allows the detection of Fe³⁺ ions in aqueous medium and lysosomal tracking in living cells. MNP was used in situ for the imaging of lysosomes in HeLa cells, a new strategy for lysosome-related medical diagnosis.

[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.