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

Assessing cholesterol storage in live cells and C. elegans by stimulated Raman scattering imaging of phenyl-Diyne cholesterol

We report a cholesterol imaging method using rationally synthesized phenyl-diyne cholesterol (PhDY-Chol) and stimulated Raman scattering (SRS) microscope. The phenyl-diyne group is biologically inert and provides a Raman scattering cross section that is 88 times larger than the endogenous C = O stretching mode. SRS microscopy offers an imaging speed that is faster than spontaneous Raman microscopy by three orders of magnitude, and a detection sensitivity of 31 μM PhDY-Chol (~1,800 molecules in the excitation volume). Inside living CHO cells, PhDY-Chol mimics the behavior of cholesterol, including membrane incorporation and esterification. In a cellular model of Niemann-Pick type C disease, PhDY-Chol reflects the lysosomal accumulation of cholesterol, and shows relocation to lipid droplets after HPβCD treatment. In live C. elegans, PhDY-Chol mimics cholesterol uptake by intestinal cells and reflects cholesterol storage. Together, our work demonstrates an enabling platform for study of cholesterol storage and trafficking in living cells and vital organisms.

Synthesis of magnetic Fe3O4–Au hybrids for sensitive SERS detection of cancer cells at low abundance

A facile and rapid SERS-based immunoassay for living cancer cells using magnetic Fe₃O₄–Au hybrid nanoparticles is reported.

Towards high-throughput microfluidic Raman-activated cell sorting

Raman-activated cell sorting (RACS) is a promising single-cell analysis technology that is able to identify and isolate individual cells of targeted type, state or environment from an isogenic population or complex consortium of cells, in a label-free and non-invasive manner.

Polymer brushes patterned with micrometer-scale chemical gradients using laminar co-flow

We present a facile microfluidic method for forming narrow chemical gradients in polymer brushes. Co-flow of an alkylating agent solution and a neat solvent in a microfluidic channel forms a diffusion-driven concentration gradient, and thus a gradient in reaction rate at the interface of the two flows, leading to a quaternization gradient in the underlying poly(2-(dimethylamino)ethyl methacrylate) polymer brush. The spatial distribution of the quaternized polymer brush is characterized by confocal Raman microscopy. The quaternization gradient length in the polymer brush can be varied with the injection flow rate and the distance from the co-flow junction. A chemical gradient in the polymer brush as narrow as 5 μm was created by controlling these parameters. The chemical gradient by laminar co-flow is compared with numerical calculations that include only one adjustable parameter: the reaction rate constant of the polymer brush quaternization. The calculated chemical gradient agrees with the experimental data, which validates the numerical procedures established in this study. Flow of multiple laminar streams of reactive agent solutions enables single-run fabrication of brush gradients with more than one chemical property. As one example, four laminar streams-neat solvent/benzyl bromide solution/propargyl bromide solution/neat solvent-generate multistep gradients of aromatic and alkyne groups. Because the alkyne functional group is a click-reaction available site, the alkyne gradient could allow small gradient formation with a wide variety of chemical properties in a polymer brush.

High specific detection and near-infrared photothermal therapy of lung cancer cells with high SERS active aptamer-silver-gold shell-core nanostructures

Lung cancer is the leading cause of cancer death worldwide. Its early detection is of paramount importance for diagnosis, classification, treatment, and improvement of survivorship. However, current methods are not sensitive enough to detect lung cancer in its nascent stage. We reported an aptamer-Ag-Au shell-core nanostructure-based surface-enhanced Raman scattering (SERS) assay for sensitive and specific detection, and near-infrared (NIR) photothermal therapy of lung adenocarcinoma cells (A549 cells). The nanostructures target the cells with high affinity and specificity via the specific interaction between the aptamer (a 45-base oligonucleotide) and the cell, and distinguish A549 cells from other types of cancer cells (HeLa and MCF-7 cells) and subtypes of lung cancer cells (NCI-H157, NCI-H520, NCI-H1299, and NCI-H446 cells). The nanostructures have a high capability to absorb NIR irradiation and are able to perform photothermal therapy of the cells at a very low irradiation power density (0.20 W cm(-2)) without destroying the healthy cells and the surrounding normal tissues. In addition, the nanostructures exhibit a high SERS activity. Based on the SERS signal of the labeled Raman reporter (Rh6G molecules), we can specifically detect A549 cells at a very low abundance (~10 cells per mL) and monitor the therapy process of the cancer cells. Therefore, this nanostructure-based SERS assay has great potential in specific recognition, sensitive detection, and effective photothermal therapy of lung cancer.

Multicolor live-cell chemical imaging by isotopically edited alkyne vibrational palette

Vibrational imaging such as Raman microscopy is a powerful technique for visualizing a variety of molecules in live cells and tissues with chemical contrast. Going beyond the conventional label-free modality, recent advance of coupling alkyne vibrational tags with stimulated Raman scattering microscopy paves the way for imaging a wide spectrum of alkyne-labeled small biomolecules with superb sensitivity, specificity, resolution, biocompatibility, and minimal perturbation. Unfortunately, the currently available alkyne tag only processes a single vibrational "color", which prohibits multiplex chemical imaging of small molecules in a way that is being routinely practiced in fluorescence microscopy. Herein we develop a three-color vibrational palette of alkyne tags using a (13)C-based isotopic editing strategy. We first synthesized (13)C isotopologues of EdU, a DNA metabolic reporter, by using the newly developed alkyne cross-metathesis reaction. Consistent with theoretical predictions, the mono-(13)C ((13)C≡(12)C) and bis-(13)C ((13)C≡(13)C) labeled alkyne isotopologues display Raman peaks that are red-shifted and spectrally resolved from the originally unlabeled ((12)C≡(12)C) alkynyl probe. We further demonstrated three-color chemical imaging of nascent DNA, RNA, and newly uptaken fatty-acid in live mammalian cells with a simultaneous treatment of three different isotopically edited alkynyl metabolic reporters. The alkyne vibrational palette presented here thus opens up multicolor imaging of small biomolecules, enlightening a new dimension of chemical imaging.

Live-cell stimulated Raman scattering imaging of alkyne-tagged biomolecules

Alkynes can be metabolically incorporated into biomolecules including nucleic acids, proteins, lipids, and glycans. In addition to the clickable chemical reactivity, alkynes possess a unique Raman scattering within the Raman-silent region of a cell. Coupling this spectroscopic signature with Raman microscopy yields a new imaging modality beyond fluorescence and label-free microscopies. The bioorthogonal Raman imaging of various biomolecules tagged with an alkyne by a state-of-the-art Raman imaging technique, stimulated Raman scattering (SRS) microscopy, is reported. This imaging method affords non-invasiveness, high sensitivity, and molecular specificity and therefore should find broad applications in live-cell imaging.

Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering

Sensitive and specific visualization of small biomolecules in living systems is highly challenging. We report stimulated Raman-scattering imaging of alkyne tags as a general strategy for studying a broad spectrum of small biomolecules in live cells and animals. We demonstrate this technique by tracking alkyne-bearing drugs in mouse tissues and visualizing de novo synthesis of DNA, RNA, proteins, phospholipids and triglycerides through metabolic incorporation of alkyne-tagged small precursors.

Direct meso-alkynylation of metalloporphyrins through gold catalysis for hemoprotein engineering

A method was developed for the direct functionalization of metalloporphyrins at the methine protons (meso positions) to yield asymmetric alkynylated derivatives by using gold catalysis and hypervalent iodine reagents. This single-step procedure was applied to b-type heme and the product was incorporated into a gas-sensor heme protein. The terminal alkyne allows fluorophore labeling through copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Hemoproteins with this type of engineered cofactor have several potential applications in labeling and imaging technologies. Additionally, the alkyne provides a handle for modulating porphyrin electron density, which affects cofactor redox potential and ligand affinity. This method will be helpful for investigating the chemistry of natural heme proteins and for designing artificial variants with altered properties and reactivities.

Sensitive SERS glucose sensing in biological media using alkyne functionalized boronic acid on planar substrates

In this work, we propose a novel glucose binding mechanism on a highly sensitive SERS substrate, in order to overcome challenges in specific glucose detection in bio-fluids. We make use of phenylboronic acid as a receptor for saccharide capture onto the substrate and the ability of the captured glucose molecule to undergo secondary binding with an alkyne-functionalized boronic acid to form a glucose-alkyne-boronic acid complex. The formation of this complex shows high selectivity for glucose, over other saccharides. In addition, the alkyne group of the alkyne-functionalized boronic acid exhibits a distinct Raman peak at 1996 cm(-1) in a biological silent region (1800-2800 cm(-1)) where most endogenous molecules, including glucose, show no Raman scattering, thus offering a high sensitivity over other SERS glucose sensing. The substrate offers long-term stability, as well as high SERS enhancement to the glucose-alkyne boronic acid complex on substrate. In addition, the reversibility of SERS signals at various incubation stages also shows reusability capabilities, whereas positive results in clinical urine samples demonstrate clinical feasibility. All these strongly suggest that this newly developed SERS-based assay offers great potential in glucose sensing.

Insights into the mechanism of polymer coating self-healing using Raman spectroscopy

Self-healing polymer coatings are an emerging class of smart materials. Upon mechanical damage the material properties may be restored by self-healing, which can be triggered externally, e.g., by an increased temperature. An alternative approach relies on embedding capsules with repair agents into the polymers, the rupture of which is induced by the mechanical damage, and the release of the repair agents triggers the self-repair reaction. The work at hand presents in situ Raman spectroscopic investigations on the reaction dynamics in such self-healing polymer coatings. Analysis of the Raman spectra allows one to assign specific Raman bands characteristic for the progress of the self-healing reaction.

Chemical reporters for biological discovery

Functional tools are needed to understand complex biological systems. Here we review how chemical reporters in conjunction with bioorthogonal labeling methods can be used to image and retrieve nucleic acids, proteins, glycans, lipids and other metabolites in vitro, in cells as well as in whole organisms. By tagging these biomolecules, researchers can now monitor their dynamics in living systems and discover specific substrates of cellular pathways. These advances in chemical biology are thus providing important tools to characterize biological pathways and are poised to facilitate our understanding of human diseases.

Exterior design: strategies for redecorating the bacterial surface with small molecules

Recombinant techniques for expressing heterologous proteins and sugars on the surface of bacteria have been known since the 1980s, and have proven useful in a variety of settings from biocatalysis to vaccinology. The past decade has also seen the emergence of novel methods that allow modification of bacterial surfaces with small non-biological compounds. Such technologies enable researchers to harness the unique properties of synthetic materials on a live bacterial platform, opening the door to an exciting new set of applications. Here we review strategies for bacterial surface display and describe how they have been applied thus far. We believe that chemical surface display holds great potential for advancing research in basic bacteriology and applied fields of biotechnology and biomedicine.

Modern Raman imaging: vibrational spectroscopy on the micrometer and nanometer scales

Raman microscopes are currently used in various fields of research because they allow for label-free sample investigation. Moreover, the inherently low scattering cross section of Raman spectroscopy, as well as its diffraction-limited lateral resolution, has been overcome by new Raman microscopy techniques. Nonlinear methods such as coherent anti-Stokes Raman spectroscopy and stimulated Raman spectroscopy reduce measurement times and improve z resolution, allowing for three-dimensional spectroscopic imaging of biological samples. Moreover, tip-enhanced Raman spectroscopy, a near-field optical technique that combines scanning-probe microscopy with the enhancement offered by surface-enhanced Raman scattering, enables Raman spectroscopic imaging far below the optical diffraction limit. We cover the theoretical and technical aspects of Raman microscopy and related new imaging techniques and review some very recent applications in graphene research and cell biology.

Alkyne-tag Raman imaging for visualization of mobile small molecules in live cells

Alkyne has a unique Raman band that does not overlap with Raman scattering from any endogenous molecule in live cells. Here, we show that alkyne-tag Raman imaging (ATRI) is a promising approach for visualizing nonimmobilized small molecules in live cells. An examination of structure-Raman shift/intensity relationships revealed that alkynes conjugated to an aromatic ring and/or to a second alkyne (conjugated diynes) have strong Raman signals in the cellular silent region and can be excellent tags. Using these design guidelines, we synthesized and imaged a series of alkyne-tagged coenzyme Q (CoQ) analogues in live cells. Cellular concentrations of diyne-tagged CoQ analogues could be semiquantitatively estimated. Finally, simultaneous imaging of two small molecules, 5-ethynyl-2'-deoxyuridine (EdU) and a CoQ analogue, with distinct Raman tags was demonstrated.

Raman detection of cell proliferation probes with antiresonance-guiding hollow fibers

Antiresonance-guiding hollow-core fibers are shown to enable highly sensitive detection of cell proliferation probes using Raman scattering within the region where the cellular Raman activity is minimal. We demonstrate that such fibers can substantially reduce the level of the background compared to standard index-guiding optical fibers, thus radically improving the sensitivity of Raman detection of DNA synthesis in cells and offering a powerful tool for fiber-based live-cell imaging.

Aptamer-guided silver-gold bimetallic nanostructures with highly active surface-enhanced Raman scattering for specific detection and near-infrared photothermal therapy of human breast cancer cells

The aptamer (S2.2)-guided Ag-Au nanostructures (aptamer-Ag-Au) have been synthesized by photoreduction and validated by ultraviolet-visible light (UV-vis) spectra and transmission electron microscopy (TEM) images. Differential interference contrast (DIC), fluorescence, and TEM images, and surface-enhanced Raman scattering (SERS) spectra indicated that the aptamer-Ag-Au nanostructures can target the surface of human breast cancer cells (MCF-7) with high affinity and specificity. This targeting is completed via the specific interaction between S2.2 aptamer (a 25-base oligonucleotide) and MUC1 mucin (a large transmembrane glycoprotein, whose expression increased at least 10-fold at MCF-7 cells in primary and metastatic breast cancers). However, the nanostructures cannot target HepG2 (human liver cancer cells) or MCF-10A cells (human normal breast epithelial cells), because these cells are MUC1-negative expressed. Moreover, the synthesized nanostructures exhibited a high SERS activity. Based on these results, a new assay for specifically detecting MCF-7 cells has been proposed. This assay can also discriminate MCF-7 cells from MCF-10A cells and different cancer cell lines, such as HepG2 cells. In addition, the aptamer-Ag-Au nanostructures have a high capability of adsorpting near-infrared (NIR) irradiation and are able to perform photothermal therapy of MCF-7 cells at a very low irradiation power density (0.25 W/cm(2)) without destroying the healthy cells and the surrounding normal tissue. Therefore, the proposed assay is significant for the diagnosis of tumors in their nascent stage. The synthesized nanostructures could offer a protocol to specifically recognize and sensitively detect the cancer cells, and would have great potential for application in the photothermal therapy of the cancers.

Chemical reporters for monitoring RNA synthesis and poly(A) tail dynamics

A versatile "clickable" nucleoside: Metabolic labeling of cells is useful in studying the dynamics of biological molecules. N(6) pA can be utilized by all three mammalian RNA polymerases, as well as poly(A) polymerase. Because of its alkyne modification, RNA labeled with N(6) pA can be visualized and purified by using click chemistry.

Label-free Raman observation of cytochrome c dynamics during apoptosis

We performed label-free observation of molecular dynamics in apoptotic cells by Raman microscopy. Dynamic changes in cytochrome c distribution at the Raman band of 750 cm(-1) were observed after adding an apoptosis inducer to the cells. The comparison of mitochondria fluorescence images and Raman images of cytochrome c confirmed that changes in cytochrome c distribution can be distinguished as release of cytochrome c from mitochondria. Our observation also revealed that the redox state of cytochrome c was maintained during the release from the mitochondria. Monitoring mitochondrial membrane potential with JC-1 dye confirmed that the observed cytochrome c release was associated with apoptosis.

Catch and release of alkyne-tagged molecules in water by a polymer-supported cobalt complex

A cobalt-phosphine complex supported on PS-PEG beads was found to react with a propargyl carbamate tag, and the tagged molecules immobilized on the beads could be released by acidic treatment through the Nicholas reaction pathway. These reactions work in aqueous media at 4 °C, so that this catch and release procedure is compatible with conditions generally used in biochemical experiments.

Bioorthogonal chemical reporters for analyzing protein lipidation and lipid trafficking

Protein lipidation and lipid trafficking control many key biological functions in all kingdoms of life. The discovery of diverse lipid species and their covalent attachment to many proteins has revealed a complex and regulated network of membranes and lipidated proteins that are central to fundamental aspects of physiology and human disease. Given the complexity of lipid trafficking and the protein targeting mechanisms involved with membrane lipids, precise and sensitive methods are needed to monitor and identify these hydrophobic molecules in bacteria, yeast, and higher eukaryotes. Although many analytical methods have been developed for characterizing membrane lipids and covalently modified proteins, traditional reagents and approaches have limited sensitivity, do not faithfully report on the lipids of interest, or are not readily accessible. The invention of bioorthogonal ligation reactions, such as the Staudinger ligation and azide-alkyne cycloadditions, has provided new tools to address these limitations, and their use has begun to yield fresh insight into the biology of protein lipidation and lipid trafficking. In this Account, we discuss how these new bioorthogonal ligation reactions and lipid chemical reporters afford new opportunities for exploring the biology of lipid-modified proteins and lipid trafficking. Lipid chemical reporters from our laboratory and several other research groups have enabled improved detection and large-scale proteomic analysis of fatty-acylated and prenylated proteins. For example, fatty acid and isoprenoid chemical reporters in conjunction with bioorthogonal ligation methods have circumvented the limited sensitivity and hazards of radioactive analogues, allowing rapid and robust fluorescent detection of lipidated proteins in all organisms tested. These chemical tools have revealed alterations in protein lipidation in different cellular states and are beginning to provide unique insights in mechanisms of regulation. Notably, the purification of proteins labeled with lipid chemical reporters has allowed both the large-scale analysis of lipidated proteins as well as the discovery of new lipidated proteins involved in metabolism, gene expression, and innate immunity. Specific lipid reporters have also been developed to monitor the trafficking of soluble lipids; these species are enabling bioorthogonal imaging of membranes in cells and tissues. Future advances in bioorthogonal chemistry, specific lipid reporters, and spectroscopy should provide important new insight into the functional roles of lipidated proteins and membranes in biology.

Thymidine analogues for tracking DNA synthesis

Replicating cells undergo DNA synthesis in the highly regulated, S-phase of the cell cycle. Analogues of the pyrimidine deoxynucleoside thymidine may be inserted into replicating DNA, effectively tagging dividing cells allowing their characterisation. Tritiated thymidine, targeted using autoradiography was technically demanding and superseded by 5-bromo-2-deoxyuridine (BrdU) and related halogenated analogues, detected using antibodies. Their detection required the denaturation of DNA, often constraining the outcome of investigations. Despite these limitations BrdU alone has been used to target newly synthesised DNA in over 20,000 reviewed biomedical studies. A recent breakthrough in “tagging DNA synthesis” is the thymidine analogue 5-ethynyl-2′-deoxyuridine (EdU). The alkyne group in EdU is readily detected using a fluorescent azide probe and copper catalysis using ‘Huisgen’s reaction’ (1,3-dipolar cycloaddition or ‘click chemistry’). This rapid, two-step biolabelling approach allows the tagging and imaging of DNA within cells whilst preserving the structural and molecular integrity of the cells. The bio-orthogonal detection of EdU allows its application in more experimental assays than previously possible with other “unnatural bases”. These include physiological, anatomical and molecular biological experimentation in multiple fields including, stem cell research, cancer biology, and parasitology. The full potential of EdU and related molecules in biomedical research remains to be explored.

Bringing chemistry to life

Bioorthogonal chemistry allows a wide variety of biomolecules to be specifically labeled and probed in living cells and whole organisms. Here we discuss the history of bioorthogonal reactions and some of the most interesting and important advances in the field.