Graham T. Dempsey

Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes

Recent advances in far-field optical nanoscopy have enabled fluorescence imaging with a spatial resolution of 20 to 50 nanometers. Multicolor super-resolution imaging, however, remains a challenging task. Here, we introduce a family of photo-switchable fluorescent probes and demonstrate multicolor stochastic optical reconstruction microscopy (STORM). Each probe consists of a photo-switchable “reporter” fluorophore that can be cycled between fluorescent and dark states, and an “activator” that facilitates photo-activation of the reporter. Combinatorial pairing of reporters and activators allows the creation of probes with many distinct colors. Iterative, color-specific activation of sparse subsets of these probes allows their localization with nanometer accuracy, enabling the construction of a super-resolution STORM image. Using this approach, we demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nanometer resolution. This technique will facilitate direct visualization of molecular interactions at the nanometer scale.

Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging

One approach to super-resolution fluorescence imaging uses sequential activation and localization of individual fluorophores to achieve high spatial resolution. Essential to this technique is the choice of fluorescent probes; the properties of the probes, including photons per switching event, on-off duty cycle, photostability and number of switching cycles, largely dictate the quality of super-resolution images. Although many probes have been reported, a systematic characterization of the properties of these probes and their impact on super-resolution image quality has been described in only a few cases. Here we quantitatively characterized the switching properties of 26 organic dyes and directly related these properties to the quality of super-resolution images. This analysis provides guidelines for characterization of super-resolution probes and a resource for selecting probes based on performance. Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low–cross-talk, four-color super-resolution imaging.

Photoswitching mechanism of cyanine dyes.

Cyanine dyes have been shown to undergo reversible photoswitching, where the fluorophore can be switched between a fluorescent state and a dark state upon illumination at different wavelengths. The photochemical mechanism by which switching occurs has yet to be elucidated. In this study, we have determined the mechanism of photoswitching by characterizing the kinetics of dark state formation and the spectral and structural properties of the dark state. The rate of switching to the dark state depends on the concentration of the primary thiol in the solution and the solution pH in a manner quantitatively consistent with the formation of an encounter complex between the cyanine dye and ionized thiol prior to their conjugation. Mass spectrometry suggests that the photoconversion product is a thiol−cyanine adduct in which covalent attachment of the thiol to the polymethine bridge disrupts the original conjugated π-electron system of the dye.

Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms

Biofilms Up Close Many bacterial infections involve biofilm formation. Cells within a biofilm are significantly more resistant to immune clearance and antibiotics compared to unattached, planktonic cells. Berk et al. (p. 236) applied superresolution optical methods to image living bacteria with nanometer-scale precision as they form a biofilm. Vibrio cholerae biofilms were observed to have three distinct levels of spatial organization: cells, clusters of cells, and collections of clusters. Each cell cluster was wrapped in a flexible, elastic envelope. Several V. cholerae matrix proteins played complementary architectural roles during biofilm development. RbmA provided cell-cell adhesion, Bap1 allowed the developing biofilm to adhere to surfaces, and heterogeneous mixtures of VPS, RbmC, and Bap1 formed the dynamic, flexible, and ordered envelopes that encase the cell clusters. When imaged in real time, biofilm development can be seen to rely on spatial and temporal intercellular contacts. In their natural environment, microbes organize into communities held together by an extracellular matrix composed of polysaccharides and proteins. We developed an in vivo labeling strategy to allow the extracellular matrix of developing biofilms to be visualized with conventional and superresolution light microscopy. Vibrio cholerae biofilms displayed three distinct levels of spatial organization: cells, clusters of cells, and collections of clusters. Multiresolution imaging of living V. cholerae biofilms revealed the complementary architectural roles of the four essential matrix constituents: RbmA provided cell-cell adhesion; Bap1 allowed the developing biofilm to adhere to surfaces; and heterogeneous mixtures of Vibrio polysaccharide, RbmC, and Bap1 formed dynamic, flexible, and ordered envelopes that encased the cell clusters.

Characterization and development of photoactivatable fluorescent proteins for single-molecule–based superresolution imaging

Significance Photoactivatable fluorescent proteins (PAFPs) are important probes for superresolution fluorescence microscopy, which allows the spatial organization of proteins in living cells to be probed with sub–diffraction-limit resolution. Here, we compare four properties of PAFPs that are critical for superresolution imaging and report two new PAFPs that exhibit excellent performance in all four properties. Photoactivatable fluorescent proteins (PAFPs) have been widely used for superresolution imaging based on the switching and localization of single molecules. Several properties of PAFPs strongly influence the quality of the superresolution images. These properties include (i) the number of photons emitted per switching cycle, which affects the localization precision of individual molecules; (ii) the ratio of the on- and off-switching rate constants, which limits the achievable localization density; (iii) the dimerization tendency, which could cause undesired aggregation of target proteins; and (iv) the signaling efficiency, which determines the fraction of target–PAFP fusion proteins that is detectable in a cell. Here, we evaluated these properties for 12 commonly used PAFPs fused to both bacterial target proteins, H-NS, HU, and Tar, and mammalian target proteins, Zyxin and Vimentin. Notably, none of the existing PAFPs provided optimal performance in all four criteria, particularly in the signaling efficiency and dimerization tendency. The PAFPs with low dimerization tendencies exhibited low signaling efficiencies, whereas mMaple showed the highest signaling efficiency but also a high dimerization tendency. To address this limitation, we engineered two new PAFPs based on mMaple, which we termed mMaple2 and mMaple3. These proteins exhibited substantially reduced or undetectable dimerization tendencies compared with mMaple but maintained the high signaling efficiency of mMaple. In the meantime, these proteins provided photon numbers and on–off switching rate ratios that are comparable to the best achieved values among PAFPs.

Multicolor Super‐Resolution Fluorescence Imaging via Multi‐Parameter Fluorophore Detection

Understanding the complexity of the cellular environment will benefit from the ability to unambiguously resolve multiple cellular components, simultaneously and with nanometer-scale spatial resolution. Multicolor super-resolution fluorescence microscopy techniques have been developed to achieve this goal, yet challenges remain in terms of the number of targets that can be simultaneously imaged and the crosstalk between color channels. Herein, we demonstrate multicolor stochastic optical reconstruction microscopy (STORM) based on a multi-parameter detection strategy, which uses both the fluorescence activation wavelength and the emission color to discriminate between photo-activatable fluorescent probes. First, we obtained two-color super-resolution images using the near-infrared cyanine dye Alexa 750 in conjunction with a red cyanine dye Alexa 647, and quantified color crosstalk levels and image registration accuracy. Combinatorial pairing of these two switchable dyes with fluorophores which enhance photo-activation enabled multi-parameter detection of six different probes. Using this approach, we obtained six-color super-resolution fluorescence images of a model sample. The combination of multiple fluorescence detection parameters for improved fluorophore discrimination promises to substantially enhance our ability to visualize multiple cellular targets with sub-diffraction-limit resolution.

Phosphine-Quenching of Cyanine Dyes as a Versatile Tool for Fluorescence Microscopy

We report that the cyanine dye Cy5 and several of its structural relatives are reversibly quenched by the phosphine tris(2-carboxyethyl)phosphine (TCEP). Using Cy5 as a model, we show that the quenching reaction occurs by 1,4-addition of the phosphine to the polymethine bridge of Cy5 to form a covalent adduct. Illumination with UV light dissociates the adduct and returns the dye to the fluorescent state. We demonstrate that TCEP quenching can be used for super-resolution imaging as well as for other applications, such as differentiating between molecules inside and outside the cell.

A User’s Guide to Localization-Based Super-Resolution Fluorescence Imaging

Advances in far-field fluorescence microscopy over the past decade have led to the development of super-resolution imaging techniques that provide more than an order of magnitude improvement in spatial resolution compared to conventional light microscopy. One such approach, called Stochastic Optical Reconstruction Microscopy (STORM) uses the sequential, nanometer-scale localization of individual fluorophores to reconstruct a high-resolution image of a structure of interest. This is an attractive method for biological investigation at the nanoscale due to its relative simplicity, both conceptually and practically in the laboratory. Like most research tools, however, the devil is in the details. The aim of this chapter is to serve as a guide for applying STORM to the study of biological samples. This chapter will discuss considerations for choosing a photoswitchable fluorescent probe, preparing a sample, selecting hardware for data acquisition, and collecting and analyzing data for image reconstruction.

Fluorescence Imaging at Sub-Diffraction-Limit Resolution with Stochastic Optical Reconstruction Microscopy

Fluorescence microscopy is an essential tool in biological research. One major drawback of conventional light microscopy, however, is its relatively low resolution, which is limited by the diffraction of light to several hundreds of nanometers. In recent years, a number of fluorescence imaging techniques with sub-diffraction-limit resolution have been developed, achieving a spatial resolution of tens of nanometers in both the lateral and axial dimensions. This chapter focuses on one of these methods, stochastic optical reconstruction microscopy (STORM), which utilizes photoswitchable flourescent probes to separate spatially overlapping images of individual fluorophores in time and construct superresolution images from the precise positions of these fluorophores determined from the single-molecule images. Application of this technique has been extended to imaging fluorophores of different colors simultaneously, in three dimensions, and in living cells. This chapter describes the implementation of multicolor and three-dimensional STORM to imaging cellular structures. It begins by discussing the choice of photoswitchable fluorescent probe and the scheme with which to label a cellular target of interest. The instrumentation and methods for performing a STORM experiment are then described, followed by an outline of the analysis routines used for creating a STORM image. Applications of the technique along with general protocols and troubleshooting are given at the conclusion of the chapter.

Sub-Diffraction-Limit Imaging with Stochastic Optical Reconstruction Microscopy

Light microscopy is a widely used imaging method in biomedical research. However, the resolution of conventional optical microcopy is limited by the diffraction of light, making structures smaller than 200 nm difficult to resolve. To overcome this limit, we have developed a new form of fluorescence microscopy - Stochastic Optical Reconstruction Microscopy (STORM). STORM makes use of single-molecule imaging methods and photo-switchable fluorescent probes to temporally separate the otherwise spatially overlapping images of individual molecules. An STORM image is acquired over a number of imaging cycles, and in each cycle only a subset of the fluorescent labels is switched on such that each of the active fluorophores is optically resolvable from the rest. This allows the position of these fluorophores to be determined with nanometer accuracy. Over the course of many such cycles, the positions of numerous fluorophores are determined and used to construct a super-resolution image. Using this method, we have demonstrated multi-color, three-dimensional (3D) imaging of biomolecules and cells with ∼ 20 nm lateral and ∼ 50 nm axial resolutions. In principle, the resolution of this technique can reach the molecular scale.