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Method Article
We present a protocol for the application of interferometric PhotoActivated Localization Microscopy (iPALM), a 3-dimensional single-molecule localization super resolution microscopy method, to the imaging of the actin cytoskeleton in adherent mammalian cells. This approach allows light-based visualization of nanoscale structural features that would otherwise remain unresolved by conventional diffraction-limited optical microscopy.
Fluorescence microscopy enables direct visualization of specific biomolecules within cells. However, for conventional fluorescence microscopy, the spatial resolution is restricted by diffraction to ~ 200 nm within the image plane and > 500 nm along the optical axis. As a result, fluorescence microscopy has long been severely limited in the observation of ultrastructural features within cells. The recent development of super resolution microscopy methods has overcome this limitation. In particular, the advent of photoswitchable fluorophores enables localization-based super resolution microscopy, which provides resolving power approaching the molecular-length scale. Here, we describe the application of a three-dimensional super resolution microscopy method based on single-molecule localization microscopy and multiphase interferometry, called interferometric PhotoActivated Localization Microscopy (iPALM). This method provides nearly isotropic resolution on the order of 20 nm in all three dimensions. Protocols for visualizing the filamentous actin cytoskeleton, including specimen preparation and operation of the iPALM instrument, are described here. These protocols are also readily adaptable and instructive for the study of other ultrastructural features in cells.
The visualization of complex cellular structures has long been integral to biological insights and discovery. Although fluorescence microscopy can image cells with high molecular specificity, its resolving power is limited by diffraction to ~ 200 nm in the image plane (x,y, or lateral dimension) and > 500 nm along the optical axis (z, or axial dimension)1,2. Hence, the observation of ultrastructural features has historically been limited to electron microscopy (EM). Fortunately, the recent development of super resolution microscopy has circumvented this limit, enabling spatial resolution in the 10 - 100 nm range1-6. In particular, super resolution approaches based on single molecule localization, known by acronyms such as PALM (PhotoActivated Localization Microscopy)4, FPALM (Fluorescence PhotoActivated Localization Microscopy)5 (d)STORM (direct Stochastic Optical Reconstruction Microscopy)6,7, PAINT (Point Accumulation for Imaging Nanoscale Topography)8, GSDIM (Ground State Depletion Microscopy followed by individual molecular return)9, or SMACM (Single-Molecule Active-Control Microscopy)10, as well as their 3-dimensional (3D) implementations, such as interferometric PALM (iPALM)11 or 3D-STORM12, have been valuable in revealing novel insights into the nanoscale organization of numerous biological structures, including neuronal axons and synapses13, focal adhesions14,15, cell-cell junctions16, nuclear pores17, and centrosomes18-20, to name a few.
Another ultrastructural feature in cells for which super resolution microscopy is potentially useful is the actin cytoskeleton. The complex meshwork of filamentous (f)-actin in the cell cortex plays an essential role in the control of cellular shape and mechanical properties21. The organization of f-actin is actively and dynamically regulated though numerous regulatory proteins that strongly influence polymerization, crosslinking, turnover, stability, and network topology22. However, although the characterization of the f-actin meshwork architecture is important for mechanistic insights into a diverse range of cellular processes, the small size (~ 8 nm) of the f-actin filaments hampers their observation by conventional diffraction-limited light microscopy; thus, the visualization of actin fine structure has hitherto been exclusively performed by EM. Here, we describe protocols for visualizing the f-actin cytoskeleton in adherent mammalian cells, using the iPALM super resolution microscopy technique to take advantage of its very high precision capability in 3D11,23. Although the iPALM instrument is highly specialized, instruction on setting up such an instrument has been described recently23, while access to the iPALM microscope hosted by the Howard Hughes Medical Institute has also been made available to the research community with minimal cost. Additionally, the specimen preparation methods described herein are directly applicable to alternative 3D super resolution approaches, such as those based on astigmatic defocusing of the point spread function (PSF)12 or bi-plane detection24, which are more broadly available.
We note that a necessary ingredient for single-molecule localization-based super resolution microscopy in general is the photoswitchable fluorophore25, which allows the three critical requirements for single-molecule localization-based super resolution microscopy to be fulfilled: i) high single-molecule brightness and contrast relative to background signals; ii) sparse distribution of single molecules in a given image frame; and iii) high spatial density of labeling sufficient to capture the profile of the underlying structure (also known as Nyquist-Shannon sampling criterion)26. Thus, for satisfactory results, emphasis should be placed equally on both the proper preparation of specimens to optimize fluorophore photoswitching and to preserve the underlying ultrastructure, as well as on the instrumentation and acquisition aspects of the experiments.
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1. Imaging Specimen Preparation
2. Sample Placement and iPALM Alignment
3. Calibration of the iPALM Setup
NOTE: Since fluorescence emission is incoherent, for interference to be observed in iPALM, the path lengths through the top and bottom objectives must be close to each other, within a few microns. This can be achieved as follows:
4. Data Acquisition
5. Data Processing and Analysis
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Critical requirements for iPALM are the alignment, registration, and calibration of the optical systems. These are necessary to ensure proper interference within the 3-way beam splitter requisite for z-coordinate extraction. To enable continuous monitoring, constant point sources of fluorescence are necessary. This can be achieved using fluorescent Au or bi-metallic nanoparticles23 whose photoluminescence arise from localized surface plasmon resonance (LSPR). They act as a stab...
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The optical system of iPALM is based on a 4-π dual-opposed objective design, as shown in Figure 1A. The setup is constructed using both custom-machined and commercial opto-mechanical parts, as described earlier23 and listed in Table 1. In addition to our setup, the Howard Hughes Medical Institute (HHMI) hosts a system that is accessible to the scientific community at the Advanced Imaging Center at the Janelia Research Campus. For the full mechanical drawi...
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The authors have nothing to disclose.
YW and PK gratefully acknowledge funding support from the Singapore National Research Foundation, awarded to PK (NRF-NRFF-2011-04 and NRF2012NRF-CRP001-084). We also thank the MBI open lab and microscopy core facilities for infrastructure support.
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Name | Company | Catalog Number | Comments |
optical table | Newport, CA | RS4000 | iPALM, installed on 4 Newport Stabilizer vibration isolators |
vibration isolator for optical table | Newport, CA | S-2000 | |
laser-642 | Newport, CA | 1185055 | output power=100 mw |
laser-561 | Newport, CA | 1168931 | output power=200 mw |
laser-488 | Newport, CA | 1137970 | output power=200 mw |
laser-405 | Newport, CA | 1142279 | output power=100 mw |
broadband dielectric mirrors | Thorlabs, NJ | BB1-E02 | laser combiner |
dichroic beamsplitter | Semrock, NY | LM01-427-25 | |
acousto-optic tunable filter | AA Opto-Electronic, France | AOTFnC-VIS-TN | |
Linear polarizer | Newport, CA | 05LP-VIS-B | |
baseplate | local workshop | customized | |
turning mirror (22.5°) | Reynard Corpporation, CA | customized | 22.5° mirror |
motorized optic mounts | New Focus, CA | 8816 | |
motorized XYZ translation stage | Thorlabs, NJ | MT3/M-Z6 | sample holder |
T-Cube DC servo motor controller | Thorlabs, NJ | TDC001 | |
Piezo Phase Shifter | Physik Instrumente, Germany | S-303.CD | |
objective lens | Nikon, Japan | MRD01691 | objective. Apo TIRF 60X/1.49 oil |
translation stage | New Focus, CA | 9062-COM-M | |
Pico Motor Actuator | New Focus, CA | 8301 | |
rotary Solenoid/Shutter | DACO Instruments, CT | 5423-458 | |
3-way beam splitter | Rocky Mountain Instruments, CO | customized | beamsplitter |
Piezo Z/Tip/Tilt scanner | Physik Instrumente, Germany | S-316.10 | |
motorized five-axis tilt aligner | New Focus, CA | 8081 | |
Picmotor ethernet controller | New Focus, CA | 8752 | |
Piezo controllers/amplifier/digital operation module | Physik Instrumente, Germany | E-509/E-503/E-517 | |
band-pass filter | Semrock, NY | FF01-523/20 | filters |
band-pass filter | Semrock, NY | FF01-588/21 | |
band-pass filter | Semrock, NY | FF01-607/30 | |
band-pass filter | Semrock, NY | FF01-676/37 | |
notch filter | Semrock, NY | NF01-405/488/561/635 | |
motorized filter wheel with controllter | Thorlabs, NJ | FW103H | |
EMCCD | Andor, UK | DU-897U-CSO-#BV | 3 sets |
Desktop computers for controlling cameras and synchronization | Dell | Precision T3500 | PC, 4 sets |
coverslips with fiducial | Hestzig, VA | 600-100AuF | sample preparation. fiducial marks with various density and spectra available |
fibronectin | Millipore, MT | FC010 | |
paraformaldehyde | Electron Microscopy Sciences, PA | 15710 | fixation. 16% |
glutaraldehyde | Electron Microscopy Sciences, PA | 16220 | 25% |
triton X-100 | Sigma aldrich, MO | T8787 | |
HUVEC cells | Life Technologies, CA | C-015-10C | |
Medium 200 | Life Technologies, CA | M-200-500 | |
Large Vessel Endothelial Factors | Life Technologies, CA | A14608-01 | |
Dulbecco's Phosphate Buffered Saline | 14190367 | ||
Pennicillin/Streptomycin | 15140122 | ||
Trypsin/EDTA | Life Technologies, CA | 25200056 | |
PIPES | Sigma aldrich, MO | P1851 | PHEM |
HEPES | 1st base, Malaysia | BIO-1825 | |
EGTA | Sigma aldrich, MO | E3889 | |
MgCl2 | Millipore, MT | 5985 | |
Alexa Fluor 647 Phalloidin | Invitrogen, CA | A22287 | staining |
sodium borohydride (NaBH4) | Sigma aldrich, MO | 480886 | quenching |
glucose | 1st base, Malaysia | BIO-1101 | imaging buffer |
glucose oxidase | Sigma aldrich, MO | G2133 | |
catalase | Sigma aldrich, MO | C9322 | |
cysteamine | Sigma aldrich, MO | 30070 | |
Epoxy | Thorlabs, NJ | G14250 | |
vaseline | Sigma aldrich, MO | 16415 | sample sealing |
lanolin | Sigma aldrich, MO | L7387 | |
parafin wax | Sigma aldrich, MO | 327204 | |
Immersion oil | Electron Microscopy Sciences, PA | 16915-04 | imaging. Cargille Type HF |
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