Identification of single fluorescent labels using spectroscopic microscopy

A Wide-Field Imaging Approach for Simultaneous Super-Resolution Surface-Enhanced Raman Scattering Bioimaging and Spectroscopy

High spatial resolution imaging and chemical-specific detection in living organisms is important in a wide range of fields from medicine to catalysis. In this work, we characterize a wide-field surface-enhanced Raman scattering (SERS) imaging approach capable of simultaneously capturing images and SERS spectra from nanoparticle SERS tags in cancer cells. By passing the image through a transmission diffraction grating before it reaches an array detector, we record the image and wavelength dispersed signal simultaneously on the camera sensor. Optimization of the experiment provides an approach with better spectral resolution and more rapid acquisition than liquid crystal tunable filters commonly used for wide-field SERS imaging. Intensity fluctuations inherent to SERS enabled localization algorithms to be applied to both the spatial and spectral domain, providing super-resolution SERS images that are correlated with improved peak positions identified in the spectrum of the SERS tag. The detected Raman signal is shown to be sensitive to the focal plane, providing three-dimensional (3D) sectioning abilities for the detected nanoparticles. Our work demonstrates spectrally resolved super-resolution SERS imaging that has the potential to be applied to complex physical and biological imaging applications.

Super-Resolution SERS Spectral Bioimaging

Advances in nanotechnology enable the detection of trace molecules from the enhanced Raman signal generated at the surface of plasmonic nanoparticles. We have developed technology to enable super-resolution imaging of plasmonic nanoparticles, where the fluctuations in the surface enhanced Raman scattering (SERS) signal can be analyzed with localization microscopy techniques to provide nanometer spatial resolution of the emitting molecule's location. Additional work now enables the super-resolved SERS image and the corresponding spectrum to be acquired simultaneously. Here we will discuss how this approach can be applied to provide new insights into biological cells.

Fluorescence sensors for imaging membrane lipid domains and cholesterol

Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.

Deterministic Assembly of Single Sub-20 nm Functional Nanoparticles Using a Thermally Modified Template with a Scanning Nanoprobe

A deterministic assembly technique for single sub-20 nm functional nanoparticles is developed based on nanostructured templates fabricated by hot scanning nanoprobes. With this technique, single nanoparticles including quantum dots, polystyrene fluorescent nanobeads, and gold nanoparticles are successfully assembled into 2D arrays with high yields. Experimental and theoretical analyses show that the key for the high yields is the hot-probe-based template fabrication technique, which creates geometrical nanotraps and modifies their surface energy simultaneously. In addition to single nanoparticle patterning, further experiments demonstrate that this technique is also capable of building complex nanostructures, such as nanoparticle clusters with well-defined shapes and heterogeneously integrated nanostructures consisting of quantum dots and silver nanowires. It opens the door to many important applications.

Enhancing Textile Fiber Identification with Detergent Fluorescence

Discovering common origins of trace evidential textile fibers can be a challenging task when fiber structure or dye composition does not provide exclusive identifying information. Introduction of new chemical species after mass production and distribution of a textile may be exploited to trace its history and identify the origin of its fibers. In this article, fluorescence microscopy is used to examine the alteration in the fluorescence spectral fingerprint of single fibers resulting from exposure to commonly used detergents that contain fluorescent whitening agents. Dyed acrylic, cotton, and nylon fibers were laundered and the spectral contribution of the detergent on single fibers was quantified and shown to reach a maximum after five sequential washes; some detergents showed statistically meaningful differences to fiber spectra after only a single wash. Principal component cluster analysis was used to determine that the spectra of laundered fibers are distinct from the spectra of dyed, unwashed cotton or nylon, but not acrylic, fibers.

Uptake and bio-reactivity of polystyrene nanoparticles is affected by surface modifications, ageing and LPS adsorption: in vitro studies on neural tissue cells

Because of their capacity of crossing an intact blood-brain barrier and reaching the brain through an injured barrier or via the nasal epithelium, nanoparticles have been considered as vehicles to deliver drugs and as contrast materials for brain imaging. The potential neurotoxicity of nanoparticles, however, is not fully explored. Using particles with a biologically inert polystyrene core material, we investigated the role of the chemical composition of particle surfaces in the in vitro interaction with different neural cell types. PS NPs within a size-range of 45-70 nm influenced the metabolic activity of cells depending on the cell-type, but caused toxicity only at extremely high particle concentrations. Neurons did not internalize particles, while microglial cells ingested a large amount of carboxylated but almost no PEGylated NPs. PEGylation reduced the protein adsorption, toxicity and cellular uptake of NPs. After storage (shelf-life >6 months), the toxicity and cellular uptake of NPs increased. The altered biological activity of "aged" NPs was due to particle aggregation and due to the adsorption of bioactive compounds on NP surfaces. Aggregation by increasing the size and sedimentation velocity of NPs results in increased cell-targeted NP doses. The ready endotoxin adsorption which cannot be prevented by PEG coating, can render the particles toxic. The age-dependent changes in otherwise harmless NPs could be the important sources for variability in the effects of NPs, and could explain the contradictory data obtained with "identical" NPs.

Interaction of differently functionalized fluorescent silica nanoparticles with neural stem- and tissue-type cells

Engineered amorphous silica nanoparticles (SiO2 NPs), due to simple and low cost production, are increasingly used in commercial products and produced on an industrial scale. Despite the potential benefits, there is a concern that exposure to certain types of SiO2 NPs may lead to adverse health effects. As some NPs can cross the blood--brain barrier and may, in addition, reach the central nervous system through the nasal epithelium, this study addresses the responses of different neural tissue-type cells including neural stem cells, neurons, astrocytes and microglia cells to increasing doses of 50 nm fluorescent core/shell SiO2 NPs with different [-NH2, -SH and polyvinylpyrrolidone (PVP)] surface chemistry. The SiO2 NPs are characterized using a variety of physicochemical methods. Assays of cytotoxicity and cellular metabolism indicates that SiO2 NPs cause cell death only at high particle doses, except PVP-coated SiO2 NPs which do not harm cells even at very high concentrations. All SiO2 NPs, except those coated with PVP, form large agglomerates in physiological solutions and adsorb a variety of proteins. Except PVP-NPs, all SiO2 NPs adhere strongly to cell surfaces, but internalization differs depending on neural cell type. Neural stem cells and astrocytes internalize plain SiO2, SiO2-NH2 and SiO2-SH NPs, while neurons do not take up any NPs. The data indicates that the PVP coat, by lowering the particle-biomolecular component interactions, reduces the biological effects of SiO2 NPs on the investigated neural cells.

Spectroscopic microscopy analysis of the interior pH of individual phospholipid vesicles

The use of phospholipid vesicles as reaction containers, as vehicles for pharmaceutical drug delivery, and as model systems for cells has prompted the development of new methods for analyzing the structure of vesicles and their contents. The pH of the interior of vesicles is of particular interest when analytes are encapsulated and concentrated with the use of a pH gradient. While the interior pH is generally measured for large populations of vesicles, we report the measurement of the interior pH of individual vesicles as their buffer contents are titrated by transfer of N-methylbutylamine (NMBA) into the vesicle by a pH gradient. The initially acidic buffer within the vesicles is titrated along with a small concentration of an encapsulated pH sensitive dye, 5,6-carboxy SNARF-1-dextran. Images of the indicator fluorescence from each vesicle and its dispersed fluorescence spectrum are recorded using epi-illumination spectral fluorescence microscopy. From a fit of the spectra to the respective acid and base forms of the fluorescent indicator, the interior pH of individual vesicles as a function of the concentration of the NMBA titrant in the external solution could be determined.

Quantitative fluorescence microscopy to determine molecular occupancy of phospholipid vesicles

Encapsulation of molecules in phospholipid vesicles provides unique opportunities to study chemical reactions in small volumes as well as the behavior of individual proteins, enzymes, and ribozymes in a confined region without requiring a tether to immobilize the molecule to a surface. These experiments generally depend on generating a predictable loading of vesicles with small numbers of target molecules and thus raise a significant measurement challenge, namely, to quantify molecular occupancy of vesicles at the single-molecule level. In this work, we describe an imaging experiment to measure the time-dependent fluorescence from individual dye molecules encapsulated in ~130 nm vesicles that are adhered to a glass surface. For determining a fit of the molecular occupancy data to a Poisson model, it is critical to count empty vesicles in the population since these dominate the sample when the mean occupancy is small, λ ≤ ~1. Counting empty vesicles was accomplished by subsequently labeling all the vesicles with a lipophilic dye and reimaging the sample. By counting both the empty vesicles and those containing fluors, and quantifying the number of fluors present, we demonstrate a self-consistent Poisson distribution of molecular occupancy for well-solvated molecules, as well as anomalies due to aggregation of dye, which can arise even at very low solution concentrations. By observation of many vesicles in parallel in an image, this approach provides quantitative information about the distribution of molecular occupancy in a population of vesicles.

Multimodal spectral imaging of cells using a transmission diffraction grating on a light microscope

A multimodal methodology for spectral imaging of cells is presented. The spectral imaging setup uses a transmission diffraction grating on a light microscope to concurrently record spectral images of cells and cellular organelles by fluorescence, darkfield, brightfield, and differential interference contrast (DIC) spectral microscopy. Initially, the setup was applied for fluorescence spectral imaging of yeast and mammalian cells labeled with multiple fluorophores. Fluorescence signals originating from fluorescently labeled biomolecules in cells were collected through triple or single filter cubes, separated by the grating, and imaged using a charge-coupled device (CCD) camera. Cellular components such as nuclei, cytoskeleton, and mitochondria were spatially separated by the fluorescence spectra of the fluorophores present in them, providing detailed multi-colored spectral images of cells. Additionally, the grating-based spectral microscope enabled measurement of scattering and absorption spectra of unlabeled cells and stained tissue sections using darkfield and brightfield or DIC spectral microscopy, respectively. The presented spectral imaging methodology provides a readily affordable approach for multimodal spectral characterization of biological cells and other specimens.

Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point

We demonstrate the use of a microfluidic stagnation point flow to trap and extend single molecules of double-stranded (ds) genomic DNA for detection of target sequences along the DNA backbone. Mutant EcoRI-based fluorescent markers are bound sequence-specifically to fluorescently labeled ds lambda-DNA. The marker-DNA complexes are introduced into a microfluidic cross slot consisting of flow channels that intersect at ninety degrees. Buffered solution containing the marker-DNA complexes flows in one channel of the cross slot, pure buffer flows in the opposing channel at the same flow rate, and fluid exits the two channels at ninety degrees from the inlet channels. This creates a stagnation point at the center of a planar extensional flow, where marker-DNA complexes may be trapped and elongated along the outflow axis. The degree of elongation can be controlled using the flow strength (i.e., a non-dimensional flow rate) in the device. Both the DNA backbone and the markers bound along the stretched DNA are observed directly using fluorescence microscopy, and the location of the markers along the DNA backbone is measured. We find that our method permits detection of each of the five expected target site positions to within 1.5 kb with standard deviations of <1.5 kb. We compare the method's precision and accuracy at molecular extensions of 68% and 88% of the contour length to binding distributions from similar data obtained via molecular combing. We also provide evidence that increased mixing of the sample during binding of the marker to the DNA improves binding to internal target sequences of dsDNA, presumably by extending the DNA and making the internal binding sites more accessible.