The authors acknowledge financial support from the National Science Foundation (award number IGERT-0903715), the University of Utah (Department of Chemical Engineering Seed Grant and the Graduate Research Fellowship Award), and Skolkovo Institute of Science and Technology (Skoltech Fellowship).&#160;

1. Isolation of EVs from a biofluid 
<ol>
	<li>Isolate EVs by one of the established methods, such as the differential ultracentrifugation8, precipitation, or size-exclusion chromatography9.</li>
	<li>Confirm the presence of expected surface and luminal biomarkers and the absence of biomarkers indicating cross-contamination of the preparation. Confirm the lipid bilayer morphology of the isolated particles by electron microscopy. 
	NOTE: When isolating the exosomes, the hydrodynamic size distribution measured by nanoparticle tracking analysis (NTA) or dynamic light scattering should be in the expected range. The details of EV and exosome isolation are beyond the scope of this protocol. The selected method will depend on experimental questions and the goal of the study10. The following steps provide a concrete illustration of the procedure to enrich the exosomes by precipitation from the growth medium of MCF-7 breast cancer cells using a commercially available precipitation kit (Table of Materials).</li>
	<li>Before cell culture expansion, store MCF-7 breast cancer cells in liquid nitrogen. Thaw cells to subculture.</li>
	<li>Following aseptic practices, perform cell plating on 150 mm plates. Use the growth medium composed of the Eagle&#8217;s minimum essential medium, 0.01 mg/mL human recombinant insulin, and 10% exosome-free fetal bovine serum.</li>
	<li>Aerate the culture by 95% air and 5% CO2 and incubate at 37 &#176;C.</li>
	<li>After the cells are settled (approximately 24 h after plating), change the media. Split the plate at 1:10 ratio and culture ten plates, each containing 20 mL of media.</li>
	<li>Harvest and pool media from 9 of these plates (180 mL) at ~70&#8722;80% confluence when cells are still in the growth phase.</li>
	<li>Divide the media into 60 mL and 120 mL, further split into 30 mL/tube, and centrifuge at 3,000 x g for 15 min.</li>
	<li>Transfer the supernatant from each tube to a new sterile 50 mL tube and perform the exosome isolation.</li>
	<li>Isolate exosomes by precipitation according to published protocols (see, for example, reference11) or follow the manufacturer&#8217;s instructions if a commercial isolation kit (Table of Materials) is used. As a first step in the latter case, centrifuge cell medium at 3,000 x g for 15 min. Withdraw supernatant and discard cells and cell debris.</li>
	<li>Add the precipitation solution (1:5 volume ratio) to the supernatant, mix, and refrigerate overnight.</li>
	<li>Centrifuge at 1,500 x g for 30 min at room temperature. Discard the supernatant after centrifugation.</li>
	<li>Spin the remaining exosome pellet for another 5 min at 1,500 x g. Without disturbing the pellet, remove the remaining precipitation solution by aspiration.</li>
	<li>Resuspend the pellet in 100&#8722;500 &#181;L of 1x phosphate-buffered saline (PBS) buffer and divide into multiple aliquots as needed for the downstream analysis.</li>
	<li>Immediately proceed to the surface immobilization of the isolated exosomes for AFM imaging. If necessary, freeze the aliquots at -80 &#176;C for later use while taking precautions to avoid damage to the sample during the freeze-thaw cycle.</li>
</ol>
2. Surface fixation of extracellular vesicles
<ol>
	<li>Use strong double-sided tape, epoxy, or an alternative adhesive to firmly attach a mica disk to an AFM/scanning tunneling microscope (STM) magnetic stainless-steel specimen disk.</li>
	<li>Cleave mica disc by using a sharp razor or utility knife, or by attaching an adhesive tape to the top surface and then pealing it off to remove a layer of material. 
	NOTE: Either method should reveal a virgin surface by removing a thin layer of mica previously exposed to the environment. After the procedure, the attachment of mica to the AFM/STM metal specimen disk must remain firm.</li>
	<li>At room temperature, treat the top surface of mica for 10 s with 100 &#181;L of 10 mM NiCl2 solution, which modifies the surface charge from negative to positive.</li>
	<li>Blot NiCl2 solution with a lint-free wipe or blotting paper. Wash the mica surface 3x with deionized (DI) water and dry it with a stream of dry nitrogen. 
	NOTE: It is a good practice to scan the modified surface with AFM to confirm it is free from contaminants.</li>
	<li>Place the AFM specimen disk with the attached surface-modified mica in a petri dish.</li>
	<li>Dilute the exosome sample from step 1.14 with 1x PBS to obtain a concentration between 4.0 x 109 and 4.0 x 1010 particles per mL of solution. Validate the diluted particle concentration using NTA.</li>
	<li>Form a sessile drop on the surface of mica by emptying 100 &#956;L of the diluted exosome solution from a pipette.</li>
	<li>Place lid on the petri dish and seal it with a paraffin film to reduce sample evaporation. Incubate the sample for 12&#8722;18 h at 4 &#176;C. 
	NOTE: The surface density of the immobilized exosomes will increase with the incubation time and the concentration of EVs in the liquid. Longer incubation time may be necessary if exosomes are present in the sample at lower concentrations.</li>
	<li>After incubation, aspirate 80&#8722;90% of the sample without disturbing the surface. At this point, the exosomes will be electrostatically immobilized on the mica substrate.</li>
	<li>Before imaging hydrated EVs, rinse the surface with 1x PBS. Repeat 3x. Take care to keep the sample hydrated throughout the rinsing process.</li>
	<li>After washing the mica surface with 1x PBS, remove 80%&#8722;90% of liquid, and pipette ~40 &#956;L of fresh 1x PBS to cover the sample.</li>
	<li>When imaging the desiccated EVs, rinse the substrate with DI water. Repeat 3x. 
	NOTE: Rinsing with DI water will prevent the formation of salt crystals and the deposition of solutes on the surface as the substrate dries.</li>
	<li>Before imaging desiccated EVs, aspirate as much liquid as possible without touching the surface and dry the rest with a stream of dry nitrogen.</li>
</ol>
3. AFM imaging 
<ol>
	<li>To image the desiccated EVs, select a cantilever designed for scanning in the air in tapping and non-contact imaging modes and mount it onto the probe holder. 
	NOTE: The characteristics of an example cantilever listed in Table of Materials (123 &#956;m length, 40 &#956;m width, 7 nm tip radius, and 37 N/m spring constant) may be used as a guide when selecting a probe compatible with the available AFM instrumentation.
	<ol>
		<li>Place the preparation from step 2.13 on the AFM stage. The magnetic stainless-steel specimen disk will immobilize the sample on the stage. Allow time for the preparation and the stage to equilibrate thermally.</li>
		<li>Use the tapping mode to scan a sufficiently large area of the mica&#8217;s surface. For example, choose an area of 5 x 5 &#181;m, rastered in 512 lines at a scan rate of ~1 Hz. Acquire both the height and phase images as they provide complementary information on the topography and the surface properties of the sample. 
		NOTE: The scan time will increase with the imaged area and the number of lines selected to form the image but decrease with the scan rate defined as the number of lines scanned per second. Fast scan rates may impact the image quality. Therefore, the speed of rastering should judicially balance the tradeoff between the acquisition time and the image quality.</li>
	</ol>
	</li>
	<li>To image hydrated vesicles, select a cantilever appropriate for scanning soft, hydrated samples and mount the cantilever onto a probe holder designed for scanning in liquids. 
	NOTE: When selecting a probe compatible with the available AFM instrumentation, the specifications of the probe listed in Table of Materials (triangular cantilever with 175 &#181;m nominal length, 22 &#181;m width, 20 nm tip radius, 0.07 N/m spring constant, and optimized for imaging with the drive frequency in the range between 4 to 8&#160;kHz) may be used as a guide.
	<ol>
		<li>Wet the tip of the cantilever with 1x PBS to reduce the likelihood of introducing air bubbles into the liquid during scanning.</li>
		<li>Place the preparation from step 2.11 on the AFM stage. The magnetic stainless-steel specimen disk will immobilize the attached mica containing immobilized EVs on its surface.</li>
		<li>Allow time for the preparation and the AFM stage to equilibrate thermally.</li>
		<li>Image the hydrated mica surface in the tapping mode. Acquire both the height and phase images. 
		NOTE: The imaging quality is influenced by the instrumentation, selected probe, and scan parameters. When optimizing the scanning conditions, the following choices may be used as a starting point: 5 x 5 &#181;m area scanned in 512 lines with ~0.8-1.0 Hz scan rate and&#160;drive frequency between 4 to 8 kHz.</li>
	</ol>
	</li>
</ol>
4. Image analysis
NOTE: The following data processing and analysis steps are applied to the acquired height images. A similar procedure may be adapted to analyze the phase data. The description below is specific to Gwyddion12, a free and open source software available under GNU General Public License. Similar capabilities are available in alternative software tools.
<ol>
	<li>Go to Data Process, SPM modes, Tip and choose Model Tip (Figure 2). Select the geometry and the dimensions of the tip used to scan the sample and click OK.</li>
	<li>Correct the tip erosion artifacts by performing the surface reconstruction. Open the image. From the menu, select Data Process, SPM modes, Tip, then choose Surface Reconstruction and click OK (Figure 3).</li>
	<li>Align the imaging plane to match the laboratory XY plane by removing the tilt in the substrate from the scan data. To accomplish this task, select Data Process, Level and choose Plane Level (Figure 4).</li>
	<li>Align rows of the image by selecting Data Process, Correct Data and then choose Align Rows. Several alignment options are available (Figure 5). For example, Median is an algorithm that finds an average height of each scan line and subtracts it from the data.</li>
	<li>Go to Data Process, Correct Data and choose Remove Scars (Figure 6), which removes common scanning errors known as scars.</li>
	<li>Align the mica surface at the zero height, Z = 0, by selecting Flatten Base in Level drop-down menu accessible from Data Process (Figure 7).</li>
	<li>Identify EVs on the scanned surface by using Mark by Threshold in Grains drop-down menu (Figure 8A). This algorithm identifies surface-immobilized exosomes as particles protruding from the zero-surface substrate by the height above the user-selected threshold. Select a threshold in the range between 1 and 3&#160;nm, which will eliminate most of the background interference. Smaller thresholds are used with cleaner background. 
	NOTE: The threshold in Figure 8A is 1.767 nm. The outcome of the MCF-7 exosome identification with this thresholding is shown in Figure 8B. Gwyddion offers several alternatives to thresholding as the algorithm to automatically identify vesicles in the image, including automated thresholding (Otsu&#39;s method), edge detection, and the watershed algorithm. 
	NOTE:&#160;Particle agglomerates, if present in the AFM image, may be masked and excluded from the analysis.</li>
	<li>Perform geometric and dimensional characterization of the identified EVs using the available Distributions algorithms accessible from Grains menu. 
	NOTE: Gwyddion provides tools to assess the distribution of scalar-valued, areal, volumetric, and other properties of immobilized EVs in a hydrated or dessicated state. An example of a scalar-values property is shown in Figure 9, which gives the distribution of maximum heights within the footprint of each identified exosome.</li>
	<li>Export the AFM data from Gwyddion for specialized analysis by other computational tools and custom computer programs.</li>
</ol>

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<li>Théry, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Minimal+information+for+studies+of+extracellular+vesicles+2018+%28MISEV2018%29%3A+a+position+statement+of+the+International+Society+for+Extracellular+Vesicles+and+update+of+the+MISEV2014+guidelines%5BTitle%5D)+AND+%22Journal+of+Extracellular+Vesicles%22%5BJournal%5D)">Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines.</a> Journal of Extracellular Vesicles. 8, 1535750(2019).</li>
<li>Weng, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Effective+isolation+of+exosomes+with+polyethylene+glycol+from+cell+culture+supernatant+for+in-depth+proteome+profiling%5BTitle%5D)+AND+%22The+Analyst%22%5BJournal%5D)">Effective isolation of exosomes with polyethylene glycol from cell culture supernatant for in-depth proteome profiling.</a> The Analyst. 141, 4640-4646 (2016).</li>
<li>Nečas, D., Klapetek, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Gwyddion%3A+an+open-source+software+for+SPM+data+analysis%5BTitle%5D)+AND+%22Open+Physics%22%5BJournal%5D)">Gwyddion: an open-source software for SPM data analysis.</a> Open Physics. 10, 181-188 (2012).</li>
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<li>Zhou, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Exosomes+released+by+human+umbilical+cord+mesenchymal+stem+cells+protect+against+cisplatin-induced+renal+oxidative+stress+and+apoptosis+in+vivo+and+in+vitro%5BTitle%5D)+AND+%22Stem+Cell+Research+%26+Therapy%22%5BJournal%5D)">Exosomes released by human umbilical cord mesenchymal stem cells protect against cisplatin-induced renal oxidative stress and apoptosis in vivo and in vitro.</a> Stem Cell Research & Therapy. 4, 34(2013).</li>
<li>Coleman, B. M., Hanssen, E., Lawson, V. A., Hill, A. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Prion-infected+cells+regulate+the+release+of+exosomes+with+distinct+ultrastructural+features%5BTitle%5D)+AND+%22FASEB+Journal%22%5BJournal%5D)">Prion-infected cells regulate the release of exosomes with distinct ultrastructural features.</a> FASEB Journal. 26, 4160-4173 (2012).</li>
<li>Briegel, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Universal+architecture+of+bacterial+chemoreceptor+arrays%5BTitle%5D)+AND+%22Proceedings+of+the+National+Academy+of+Sciences%22%5BJournal%5D)">Universal architecture of bacterial chemoreceptor arrays.</a> Proceedings of the National Academy of Sciences. 106, 17181-17186 (2009).</li>
<li>Akagi, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((On-Chip+Immunoelectrophoresis+of+Extracellular+Vesicles+Released+from+Human+Breast+Cancer+Cells%5BTitle%5D)+AND+%22PLOS+ONE%22%5BJournal%5D)">On-Chip Immunoelectrophoresis of Extracellular Vesicles Released from Human Breast Cancer Cells.</a> PLOS ONE. 10, e0123603(2015).</li>
<li>Sharma, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Structural-mechanical+characterization+of+nanoparticle+exosomes+in+human+saliva%2C+using+correlative+AFM%2C+FESEM%2C+and+force+spectroscopy%5BTitle%5D)+AND+%22ACS+Nano%22%5BJournal%5D)">Structural-mechanical characterization of nanoparticle exosomes in human saliva, using correlative AFM, FESEM, and force spectroscopy.</a> ACS Nano. 4, 1921-1926 (2010).</li>
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</ol>

The authors have nothing to disclose.&#160;

The immobilization of EVs from a biological fluid, surface scanning, and image analysis are the essential steps of the developed protocol for the AFM characterization of EVs in liquid. The number of vesicles amenable to AFM imaging scales with the imaged surface area and the surface concentration of the vesicles immobilized on the substrate. Given a negative zeta potential of EVs and exosomes18, we advocate electrostatic fixation of EVs from liquid samples to the AFM substrate. The immobilization is effective when the surface is positively charged. Prior to EV immobilization, the positive surface charge may need to be imparted to the substrate, as in the case of mica &#8213; a layered silicate mineral with general formula KAl2(AlSi3O10)(OH)2. Freshly cleaved mica&#8217;s surface is close to perfectly flat, which is ideal for imaging nanoparticles by the AFM, but its surface charge is negative and, thus, must be modified. The protocol describes the procedure to impart a positive surface change to the AFM substrate. The representative results show marked improvement in EV fixation from a biofluid to the modified mica substrate. 
&#160; 
When imaging hydrated vesicles, it is important to minimize sample evaporation which causes the surface deposition artifacts and convective flows and increases the liquid concentration of the vesicles with time, leading to higher surface concentration of immobilized EVs than expected, especially during prolonged incubations. Probe holders explicitly designed for liquid samples eliminate or slow evaporation and should be used to image hydrated EVs. Nonspecific bindings to the scanning probe are reduced in the presence of ionic species. Therefore, when imaging hydrated EVs, it is preferable to cover the substrate with a buffered medium, such as PBS, instead of DI water.
Importance of surface immobilization&#160; 
The consistent and predictable immobilization of EVs on the modified substrate removes the primary source of variability in the AFM results. All downstream steps, from scanning to data analysis, are more easily controlled by the selection of instrumentation, probes, scanning parameters, and the data analysis sequence and algorithms. The user should be aware of upstream variability in biological samples and EV isolation protocols, which are important issues beyond the scope of this work.
We recommend performing surface immobilization of EV on the modified mica&#8217;s surface from liquid samples even when the goal is to characterize desiccated vesicles in the air &#8212; the need is less evident since vesicles will unavoidably deposit on any substrate as the liquid evaporates. In fact, the AFM results for desiccated EV obtained without modifying mica&#8217;s surface charges, which is a prerequisite step for electrostatic immobilization of EVs from a liquid, have been reported in the past19,20,21. When EVs are not fixed to the surface from the liquid sample, however, their passive deposition by evaporation will produce artifacts collectively known as a coffee ring effect22. Two such artifacts, occurring as a drying liquid recedes, are illustrated in the SEM image (Figure 13A) of serum exosomes deposited by evaporation on a negatively charged glass surface. Significant variations in the surface concentration of precipitated vesicles are immediately apparent. The second artifact, quantified in Figure 13B, is the considerable variability in vesicle sizes in different areas within the perimeter of the dried sample. Given these artifacts, the AFM characterization of passively deposited vesicles from a drying liquid may produce biased or inconsistent results unless the entire surface area initially occupied by a now-dried liquid sample is scanned.&#160;
Two additional issues should be considered when imaging the desiccated samples obtained without firm immobilization of vesicles on the substrate. Recall that our protocol instructs users to thoroughly wash the surface with DI water after the vesicles are immobilized from a liquid sample. This step intends to prevent ionic and other non-vesicular solutes from forming surface deposits during the evaporation of complex biofluids with considerable osmolarity. If EVs are not fixed, thorough washing will detach a large number of vesicles from the surface, potentially biasing the results and leaving too few particles for analysis. Another common difficulty, reduced by immobilizing EVs on the modified mica surface before the AFM imaging, is the adhesion of particles to the probe23 and the misleading artifacts caused by this phenomenon. 
&#160; 
Control of surface density of immobilized EVs 
The two easily controllable factors identified in the protocol allow the user to customize the surface concentration of the immobilized EVs on the modified mica substrate: the concentration of the vesicles in the liquid sample and the time the sample is incubated on the substrate. A high density of immobilized vesicles, achieved with longer incubation times and higher concentration of EVs in the liquid, increases the number of vesicles analyzed during the scanning and the statistical power of conclusions arrived by the analysis of the AFM data. At the same time, an excessively dense surface concentration, as in the case shown in Figure 10C where particles tightly cover the entire surface with no intervening areas of the substrate, complicates the image analysis and the interpretation of results and may lead to scanning artifacts caused by the interaction between closely spaced particles.
Influence of electrostatic screening and hydrodynamic mobility of EVs 
The transparent control over the surface concentration of immobilized EVs as a function of factors influencing it allows a user to customize experimental conditions to meet the specific needs of a study. When performing customization, it is important to recognize that the electrostatic surface immobilization is a transport-limited process influenced by the ionic strength of the biofluid.&#160;
The concentration of ionic and positively charged species inversely impacts the Debye length over which the surface and vesicle charges are screened. Beyond this length, the electrostatic forces are negligible. The boundary layer of the substrate&#8217;s electrostatic attraction will be much smaller in ionically-rich PBS than in DI water. This difference implies that, after a short incubation corresponding to the time needed to deplete the layer of liquid where the electrostatic attractions are felt, a surface density of EVs immobilized from the suspension in DI water will be higher than from PBS suspension, assuming the concentration of EVs is the same in both liquids. Put differently, more vesicles must be immobilized to deplete a thicker attraction layer in DI water than in PBS under otherwise identical conditions.&#160;
After the vesicles are depleted from the boundary layer, the immobilization becomes an entirely transport-limited process. In this regime, the rate of the deposition will not depend on the suspending medium (e.g., DI water or PBS) as long as the viscosity is the same and the transport is entirely diffusive. However, the transport of vesicles into the attraction boundary layer may not be entirely diffusive. For instance, if the sample in a sessile drop on the AFM substrate partially evaporates during the incubation, the fluid inside the drop will be subjected to the evaporation-driven flow, and the transport of the vesicles towards the substrate will have, both, diffusive and convective contributions. When the evaporation is not adequately controlled, the contribution of a convective transport will be considerable, and the rate of immobilization will be higher than expected. The impact of the convective transport will change with the thickness of the attraction layer, which itself depends on the ionic content of the liquid. Furthermore, the evaporation will enhance the vesicle immobilization on the substrate by concentrating EVs in the solution. At higher EV concentrations, the concentration gradient between the attraction layer and the adjacent liquid will increase, creating a larger thermodynamic driving force to the migration of vesicles towards the substrate.
Immobilized vesicles may represent a liquid sample with a bias. For the case when the rate of immobilization is limited by diffusion, vesicles with smaller hydrodynamic sizes, determined by the combination of the vesicle size and the thickness of the coronal layer surrounding it (Figure 1), are more likely to enter the attraction layer because of their higher mobility. Consequently, after the initial depletion period, the hydrodynamically small EVs will be overrepresented on the substrate compared to their contribution to the EV population in the liquid sample. Note that a smaller hydrodynamic size does not automatically point at EVs with smaller vesicle sizes because of the heterogeneity in the thickness of the coronal layer3. The biased representation is avoided with long incubations that deplete the entire population of EVs in the liquid by its immobilization on the substrate. When a user aims at immobilizing all EVs from the biofluid, to avoid excessively dense coverage of the surface with the immobilized vesicles, it may be necessary to reduce the EV concentration in the liquid below the range suggested in the protocol.&#160;
Deformation of EVs on the substrate 
Extracellular vesicles in their native hydrated state and after desiccation can be characterized by the AFM, as described in the protocol. The electrostatic forces24 that immobilize EVs on the mica surface also distort their shape from globular geometry in which they exist in the solution. The impact of the desiccation on the size and morphology of immobilized EVs may be analyzed by rescanning the same surface area before and after the sample is allowed to dry.&#160;
It is instructive to examine the impact of the sample preparation on the shape of the desiccated EVs. The electrostatically immobilized EVs maintain the highly oblate geometry after drying but are further flattened by the desiccation. The height above the surface of the desiccated vesicles becomes smaller than in Figure 12A, while their footprint area increases (data not shown). On the other hand, when vesicles are deposited passively during the liquid evaporation and without prior immobilization on the surface, they tend to attain a cup-shape geometry upon desiccation, as has long been observed in the SEM images and, more recently, in AFM scans. This cupped shape is now recognized as a sample preparation artifact25 caused by non-uniformity in capillary forces during surface desiccation, as mechanistically explained in Figure 141. 
&#160; 
Image analysis and interpretation of AFM data 
The responses to electrostatic and capillary forces acting to distort the shape of EVs provide valuable information on structural and compositional properties of EVs. For example, a multidimensional set of biophysical characteristics, such as the deformed size and shape extracted from the AFM data, were recently used to demonstrate the feasibility to differentiate between exosomes secreted by different host cells5. The distortions can also be taken into account and compensated. For example, we showed how to use the AFM data to characterize the globular size of vesicles in the solution by estimating the diameters of spheres that encapsulate the same volume as immobilized exososmes3.&#160;

Extracellular vesicles (EVs) are present in all body fluids, including blood, urine, saliva, milk, and the amniotic fluid. Exosomes form a district class of EVs differentiated from other EVs by endosomal biogenesis, the markers of the endosomal pathway, and the smallest size among all EVs. The size of exosomes is often reported with substantial variability between studies. The sizing results were found to be method dependent, reflecting the difference in physical principles employed by different analytical techniques to estimate EV sizes1,2. For example, the nanoparticle tracking analysis (NTA) &#8213; the most widely used size characterization technique &#8213; estimates the size of EVs as their hydrodynamic diameters, which characterize the resistance to the Brownian mobility of EVs in the solution. A larger hydrodynamic diameter of a vesicle implies its lower mobility in liquid. The coronal layer around vesicles, consisting of surface proteins and other molecules anchored or adsorbed to the membrane surface, substantially impedes the mobility and increases the hydrodynamic size of EVs. In relative terms, this increase is particularly large for the exosomes3, as illustrated in Figure 1.&#160;
The cryogenic transmission electron microscopy (cryo-TEM) imaging is a definitive technique in characterizing vesicle sizes and morphology in their hydrated states. However, the high cost of the instrumentation and the specialized expertise needed to use it correctly motivate the exploration of alternative techniques that can image hydrated EVs. A relatively small number of EVs observed or characterized in the acquired cryo-TEM images is another notable disadvantage of this technique.
Atomic force microscopy (AFM) visualizes the three-dimensional topography of hydrated or desiccated EVs4,5,6 by scanning a probe across the substrate to raster the image of the particles on the surface. The essential steps of the protocol to characterize EVs by AFM are outlined in this study. Before imaging the vesicles in liquid, they must be immobilized on a substrate by either tethering to a functionalized surface, trapping in a filter, or by electrostatic attraction7. The electrostatic fixation on a positively charged substrate is a particularly convenient option for immobilization of exosomes known to have a negative zeta potential. However, the same electrostatic forces that immobilize the extracellular vesicles on the surface also distort their shape, which makes post-imaging data analysis essential. We elaborate this point by describing the algorithm that estimates the size of the globular vesicles in the solution based on the AFM data on the distorted shape of the exosomes immobilized on the surface.
In the developed protocol, the procedure for the robust electrostatic immobilization of vesicles is presented and followed by the steps needed to perform atomic force imaging in the hydrated or desiccated states. The factors that influence the surface concentration of the immobilized vesicles are identified. The guidance is given on how to perform the electrostatic immobilization for samples with different concentrations of EVs in the solution. The selection of experimental conditions permitting the estimation of empirical probability distributions of different biophysical properties based on a sufficiently large number of immobilized vesicles is discussed. Examples of post-imaging analysis of the AFM data are given. Specifically, an algorithm is described for determining the size of vesicles in the solution based on the AFM characterization of immobilized EVs. The representative results show the consistency of the vesicle sizing by AFM with the results of cryo-TEM imaging.&#160;

<table><tbody><tr><td>AFM/STM Controller&amp;nbsp;</td><td>Bruker</td><td>Multimode Nanoscope V</td><td>This AFM controller supports imaging of biological samples in liquid and air.&amp;nbsp;</td></tr><tr><td>AFM/STM metal specimen discs (10 mm)</td><td>TedPella</td><td>16207</td><td>Metal specimen disc on which a mica disk is attached by a double-sided tape or other means.</td></tr><tr><td>AFM/STM Mica discs (10 mm)</td><td>TedPella</td><td>50</td><td>Highest quality grade V1 mica, 0.21mm (0.0085&amp;rdquo;) thick. Interleaved, in packages of 10. Can be mounted on AFM/STM discs. Available in four diameters</td></tr><tr><td>AFM probe for imaging in the air</td><td>Bruker</td><td>TESP-V2</td><td>High quality etched silicon probes for tapping mode and non-contact mode for scanning in the air.</td></tr><tr><td>AFM probe for soft sample imaging in liquid</td><td>Bruker</td><td>MLCT</td><td>Soft silicon nitride cantilevers with silicon nitride tips, which are well-suited for liquid operation.&amp;nbsp; The range in force constants enables users to image extremely soft samples in contact mode as well as high load vs distance spectroscopy.</td></tr><tr><td>Double sided tape</td><td>Spectrum</td><td>360-77705</td><td>Used to fix the mica disk on the metal specimen disc.</td></tr><tr><td>ExoQuick-TC</td><td>System Biosciences</td><td>EXOTC50A-1</td><td>ExoQuick-TC is a proprietary polymer-based kit designed for exosome isolation from tissue culture media.&amp;nbsp;</td></tr><tr><td>Glass probe AFM holder for imaging in liquid</td><td>Bruker</td><td>&amp;nbsp;MTFML-V2</td><td>This glass probe holder is designed for scanning in fluid with the MultiMode AFM.&amp;nbsp; The holder can be used in peak force tapping mode, contact mode, tapping mode, and force modulation.&amp;nbsp; The probe is acoustically driven by a separate piezo oscillator for larger amplitude modulation.&amp;nbsp; The holder is supplied with two ports, required fittings, and accessories kit for adding and removing fluids.</td></tr><tr><td>Gwyddion</td><td>Czech Metrology Institute.</td><td>Version 2.52</td><td>Open Source software for visualization and analysis of data fields obtained by scanning probe microscopy techniques.</td></tr><tr><td>Lint-free blotting paper</td><td>GE Healthcare Whatman&amp;nbsp;</td><td>Grade GB003 Blotting Paper</td><td>Use this blotting paper to remove NiCl&lt;sub&gt;2&lt;/sub&gt; after the modification of the mica&#039;s substrate.&amp;nbsp;&amp;nbsp;</td></tr><tr><td>Lint-free cleanroom wipes</td><td>Texwipe</td><td>AlphaWipe TX1004</td><td>Use these polyester wipes for surface cleaning.&amp;nbsp;</td></tr><tr><td>Nickel(II) chloride (NiCl&lt;sub&gt;2&lt;/sub&gt;)</td><td>Sigma-Aldrich</td><td>339350</td><td>Powder used to make 10 mM NiCl&lt;sub&gt;2&lt;/sub&gt; in DI water</td></tr><tr><td>Phosphate Buffered Saline (1x)</td><td>Gibco</td><td>10010023</td><td>PBS, pH 7.4</td></tr></tbody></table>

imaging of extracellular vesicles by atomic force microscopy

Exosomes and other extracellular vesicles (EVs) are molecular complexes consisting of a lipid membrane vesicle, its surface decoration by membrane proteins and other molecules, and diverse luminal content inherited from a parent cell, which includes RNAs, proteins, and DNAs. The characterization of the hydrodynamic sizes of EVs, which depends on the size of the vesicle and its coronal layer formed by surface decorations, has become routine. For exosomes, the smallest of EVs, the relative difference between the hydrodynamic and vesicles sizes is significant. The characterization of vesicles sizes by the cryogenic transmission electron microscopy (cryo-TEM) imaging, a gold standard technique, remains a challenge due to the cost of the instrument, the expertise required to perform the sample preparation, imaging and data analysis, and a small number of particles often observed in images. A widely available and accessible alternative is the atomic force microscopy (AFM), which can produce versatile data on three-dimensional geometry, size, and other biophysical properties of extracellular vesicles. The developed protocol guides the users in utilizing this analytical tool and outlines the workflow for the analysis of EVs by the AFM, which includes the sample preparation for imaging EVs in hydrated or desiccated form, the electrostatic immobilization of vesicles on a substrate, data acquisition, its analysis, and interpretation. The representative results demonstrate that the fixation of EVs on the modified mica surface is predictable, customizable, and allows the user to obtain sizing results for a large number of vesicles. The vesicle sizing based on the AFM data was found to be consistent with the cryo-TEM imaging.&#160;

Watch this Scientific Journal Video about Imaging of Extracellular Vesicles by Atomic Force Microscopy at JoVE.com

Imaging of Extracellular Vesicles by Atomic Force Microscopy

A step-by-step procedure is described for label-free immobilization of exosomes and extracellular vesicles from liquid samples and their imaging by atomic force microscopy (AFM). The AFM images are used to estimate the size of the vesicles in the solution and characterize other biophysical properties.&#160;

Exosomes and other extracellular vesicles (EVs) are molecular complexes consisting of a lipid membrane vesicle, its surface decoration by membrane ...

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Biochemistry

13.2K Views.  University of Utah. A step-by-step procedure is described for label-free immobilization of exosomes and extracellular vesicles from liquid samples and their imaging by atomic force microscopy (AFM). The AFM images are used to estimate the size of the vesicles in the solution and characterize other biophysical properties. 

Video: Imaging of Extracellular Vesicles by Atomic Force Microscopy

Rapid Fluorescence-based Characterization of Single Extracellular Vesicles in Human Blood with Nanoparticle-tracking Analysis

Extracellular vesicles (EVs), including exosomes, are specialized membranous nano-sized vesicles found in bodily fluids that are constitutively released from many cell types and play a pivotal role in regulating cell-cell communication and a diverse range of biological processes. Many different methods for the characterization of EVs have been described. However, most of these methods have the disadvantage that the preparation and characterization of the samples are very time-consuming, or it is extremely difficult to analyze specific markers of interest due to their small size and due to the lack of discrete populations. While methods for analysis of EVs have been considerably improved over the last decade, there is still no standardized method for characterization of single EVs. Here, we demonstrate a semi-automated method for characterization of single EVs by fluorescence-based nanoparticle-tracking analysis. The protocol that is presented addresses the common problem of many researchers in this field and provides the complete workflow for rapid isolation of EVs and characterization with PKH67, a general cell membrane linker, as well as with specific surface markers such as CD63, CD9, vimentin, and lysosomal-associated membrane protein 1 (LAMP-1). The presented results show a high level of reproducibility, as confirmed by other methods, such as Western blotting. In the conducted experiments, we exclusively used EVs isolated from human serum samples, but this method is also suitable for plasma or other body fluids and can be adjusted for characterization of EVs from cell culture supernatants. Irrespective of the future progress of research on EV biology, the protocol that is presented here provides a rapid and reliable method for rapid characterization of single EVs with specific markers.

In this protocol, we describe the complete workflow for rapid isolation of extracellular vesicles from human whole blood and characterization of specific markers by fluorescence-based nanoparticle-tracking analysis. The presented results show a high level of reproducibility and can be adjusted to cell culture supernatants.

Extracellular vesicles (EVs), including exosomes, are specialized membranous nano-sized vesicles found in bodily fluids that are constitutively released ...

Atomic Force Microscopy Imaging and Force Spectroscopy of Supported Lipid Bilayers

Atomic force microscopy (AFM) is a versatile, high-resolution imaging technique that allows visualization of biological membranes. It has sufficient magnification to examine membrane substructures and even individual molecules. AFM can act as a force probe to measure interactions and mechanical properties of membranes. Supported lipid bilayers are conventionally used as membrane models in AFM studies. In this protocol, we demonstrate how to prepare supported bilayers and characterize their structure and mechanical properties using AFM. These include bilayer thickness and breakthrough force. 
The information provided by AFM imaging and force spectroscopy help define mechanical and chemical properties of membranes. These properties play an important role in cellular processes such as maintaining cell hemostasis from environmental stress, bringing membrane proteins together, and stabilizing protein complexes.

We describe a protocol for preparation of supported lipid bilayers and its characterization using atomic force microscopy and force spectroscopy.

Atomic force microscopy (AFM) is a versatile, high-resolution imaging technique that allows visualization of biological membranes. It has sufficient ...

Bioengineering

Freeze-Fracture Electron Microscopy for Extracellular Vesicle Analysis

Extracellular vesicles (EVs) are membrane-limited structures released from the cells into the extracellular space and are implicated in intercellular communication. EVs consist of three populations of vesicles, namely microvesicles (MVs), exosomes, and apoptotic bodies. The limiting membrane of EVs is crucially involved in the interactions with the recipient cells, which could lead to the transfer of biologically active molecules to the recipient cells and, consequently, affect their behavior. The freeze-fracture electron microscopy technique is used to study the internal organization of biological membranes. Here, we present a protocol for MV isolation from cultured cancerous urothelial cells and the freeze-fracture of MVs in the steps of rapid freezing, fracturing, making and cleaning the replicas, and analyzing them with transmission electron microscopy. The results show that the protocol for isolation yields a homogenous population of EVs, which correspond to the shape and size of MVs. Intramembrane particles are found mainly in the protoplasmic face of the limiting membrane. Hence, freeze-fracture is the technique of choice to characterize the MVs' diameter, shape, and distribution of membrane proteins. The presented protocol is applicable to other populations of EVs.

We present a protocol for the isolation and freeze-fracturing of extracellular vesicles (EVs) originating from cancerous urothelial cells. The freeze-fracture technique revealed the EVs' diameter and shape and-as a unique feature-the internal organization of the EV membranes. These are of immense importance in understanding how EVs interact with the recipient membranes.

Extracellular vesicles (EVs) are membrane-limited structures released from the cells into the extracellular space and are implicated in intercellular ...

Cancer Research

Sample Preparation and Imaging of Exosomes by Transmission Electron Microscopy

Exosomes are nano-sized extracellular vesicles secreted by body fluids and are known to represent the characteristics of cells that secrete them. The contents and morphology of the secreted vesicles reflect cell behavior or physiological status, for example cell growth, migration, cleavage, and death. The exosomes&#39; role may depend highly on size, and the size of exosomes varies from 30 to 300 nm. The most widely used method for exosome imaging is negative staining, while other results are based on Cryo-Transmission Electron Microscopy, Scanning Electron Microscopy, and Atomic Force Microscopy. The typical exosome&#39;s morphology assessed through negative staining is a cup-shape, but further details are not yet clear. An exosome well-characterized through structural study is necessary particular in medical and pharmaceutical fields. Therefore, function-dependent morphology should be verified by electron microscopy techniques such as labeling a specific protein in the detailed structure of exosome. To observe detailed structure, ultrathin sectioned images and negative stained images of exosomes were compared. In this protocol, we suggest transmission electron microscopy for the imaging of exosomes including negative staining, whole mount immuno-staining, block preparation, thin section, and immuno-gold labelling.

This protocol describes the various techniques necessary for transmission electron microscopy including negative staining, ultrathin sectioning for detailed structure, and immuno-gold labelling to determine the positions of specific proteins in exosomes.

Exosomes are nano-sized extracellular vesicles secreted by body fluids and are known to represent the characteristics of cells that secrete them. The ...

Biology

Extracellular Vesicle Uptake Assay via Confocal Microscope Imaging Analysis

There is a need for practical assays to visualize and quantify the cells' extracellular vesicle (EV) uptake. EV uptake plays a role in intercellular communication in various research fields; cancer biology, neuroscience, and drug delivery. Many EV uptake assays have been reported in the literature; however, there is a lack of practical, detailed experimental methodology. EV uptake can be assessed by fluorescently labeling EVs to detect their location within cells. Distinguishing between internalized EVs in cells and the superficial EVs on cells is difficult, yet critical, to accurately determine the EV uptake. Therefore, an assay that efficiently quantifies EV uptake through three-dimensional (3D) fluorescence confocal microscopy is proposed in this work. Fluorescently labeled EVs were prepared using a nano-filtration-based microfluidic device, visualized by 3D confocal microscopy, and then analyzed through advanced image-processing software. The protocol provides a robust methodology for analyzing EVs on a cellular level and a practical approach for efficient analysis.

Extracellular Vesicle Uptake Assay via Confocal Microscope Imaging Analysis

Extracellular vesicles (EVs) contribute to cellular biology and intercellular communications. There is a need for practical assays to visualize and quantify EVs uptake by the cells. The current protocol proposes the EV uptake assay by utilizing three-dimensional fluorescence imaging via confocal microscopy, following EV isolation by a nano-filtration-based microfluidic device.

There is a need for practical assays to visualize and quantify the cells' extracellular vesicle (EV) uptake. EV uptake plays a role in intercellular ...

Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often require indirect methods due to their small diameter (40-250 nm), which is beneath the diffraction limit of typical light microscopy. We have developed a super-resolution microscopy-based visualization of EVs to bypass the diffraction limit in both two and three dimensions. Using this approach, we can resolve the three-dimensional shape of EVs to within +/- 20 nm resolution on the XY-axis and +/- 50 nm resolution along the Z-axis. In conclusion, we propose that super-resolution microscopy be considered as a characterization method of EVs, including exosomes, as well as enveloped viruses.

Direct stochastic optical reconstruction microscopy (dSTORM) is used to bypass the typical diffraction limit of light microscopy and to view exosomes at the nanometer scale. It can be employed in both two and three dimensions to characterize exosomes.

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often ...

Single-Particle Interferometric Reflectance Imaging Characterization of Individual Extracellular Vesicles and Population Dynamics

Extracellular vesicles (EVs) are nanometer-sized vesicles with a lipid bilayer that are secreted by most cells. EVs carry a multitude of different biological molecules, including protein, lipid, DNA, and RNA, and are postulated to facilitate cell-to-cell communication in diverse tissues and organs. Recently, EVs have attracted significant attention as biomarkers for diagnostics and therapeutic agents for various diseases. Many methods have been developed for EV characterization. However, current methods for EV analysis all have different limitations. Thus, developing efficient and effective methods for EV isolation and characterization remains one of the crucial steps for this cutting-edge research field as it matures. Here, we provide a detailed protocol outlining a single-particle interferometric reflectance imaging sensor (SP-IRIS), as a method that is capable of detecting and characterizing EVs from unpurified biological sources and purified EVs by other methodologies. This advanced technique can be used for multi-level and comprehensive measurements for the analysis of EV size, EV count, EV phenotype, and biomarker colocalization.

This protocol presents single-particle interferometric reflectance imaging that is designed for the multi-level and comprehensive measurements of extracellular vesicles (EV) size, EV count, EV phenotype, and EV biomarker colocalization.

Extracellular vesicles (EVs) are nanometer-sized vesicles with a lipid bilayer that are secreted by most cells. EVs carry a multitude of different ...

Single Extracellular Vesicle Transmembrane Protein Characterization by Nano-Flow Cytometry

Single particle characterization has become increasingly relevant for research into extracellular vesicles, progressing from bulk analysis techniques and first-generation particle analysis to comprehensive multi-parameter measurements such as nano-flow cytometry (nFCM). nFCM is a form of flow cytometry that utilizes instrumentation specifically designed for nano-particle analysis, allowing for thousands of EVs to be characterized per minute both with and without the use of staining techniques. High resolution side scatter (SS) detection allows for size and concentration to be determined for all biological particles larger than 45 nm, while simultaneous fluorescence (FL) detection identifies the presence of labeled markers and targets of interest. Labeled subpopulations can then be described in quantitative units of particles/mL or as a percentage of the total particles identified by side scatter.
Here, EVs derived from conditioned cell culture media (CCM) are labeled with both a lipid dye, to identify particles with a membrane, and antibodies specific for CD9, CD63, and CD81 as common EV markers. Measurements of comparison material, a concentration standard and a size standard of silica nanospheres, as well as labeled sample material are analyzed in a 1-minute analysis. The software is then used to measure the concentration and size distribution profile of all particles, independent of labeling, before determining the particles that are positive for each of the labels.
Simultaneous SS and FL detection can be utilized flexibly with many different EV sources and labeling targets, both external and internal, describing EV samples in a comprehensive and quantitative manner.

The latest generation of EV characterization tools are capable of single EV analysis across multiple parameters simultaneously. Nano-flow cytometry measures all biological particles larger than 45 nm without labeling and identifies specific characteristics of subpopulations by a variety of fluorescent labeling techniques.

Single particle characterization has become increasingly relevant for research into extracellular vesicles, progressing from bulk analysis techniques and ...

Multimodal Analytical Platform on a Multiplexed Surface Plasmon Resonance Imaging Chip for the Analysis of Extracellular Vesicle Subsets

Extracellular vesicles (EVs) are membrane-derived, tiny vesicles produced by all cells that range from 50 to several hundreds of nanometers in diameter and are used as a means of intercellular communication. They are emerging as promising diagnostic and therapeutic tools for a variety of diseases. There are two main biogenesis processes used by cells to produce EVs with differences in size, composition, and content. Due to their high complexity in size, composition, and cell origin, their characterization requires a combination of analytical techniques. This project involves the development of a new generation of multiparametric analytical platforms with increased throughput for the characterization of subpopulations of EVs. To achieve this goal, the work starts from the nanobioanalytical platform (NBA) established by the group, which allows an original investigation of EVs based on a combination of multiplexed biosensing methods with metrological and morphomechanical analyses by atomic force microscopy (AFM) of vesicular targets trapped on a microarray biochip. The objective was to complete this EV investigation with a phenotypic and molecular analysis by Raman spectroscopy. These developments enable the proposal of a multimodal and easy-to-use analytical solution for the discrimination of EV subsets in biological fluids with clinical potential

This paper proposes a new generation of multiparametric analytical platforms with increased throughput for the characterization of extracellular vesicle subsets. The method is based on a combination of multiplexed biosensing methods with metrological and morphomechanical analyses by atomic force microscopy, coupled with Raman spectroscopy, to qualify vesicular targets trapped on a microarray biochip.

Extracellular vesicles (EVs) are membrane-derived, tiny vesicles produced by all cells that range from 50 to several hundreds of nanometers in diameter ...

Immunocapture and Flow Cytometry of Extracellular Vesicles for Antigenic Characterization

Source: Arakelyan, A. et al., <a href="https://app-jove-com.remotexs.ntu.edu.sg/v/55020">Flow Virometry to Analyze Antigenic Spectra of Virions and Extracellular Vesicles.</a>&#160;J. Vis. Exp. (2017)
This video demonstrates the immunocapture of extracellular vesicles using fluorescent-labeled capture antibody-magnetic nanoparticle conjugates. The process involves complex formation, staining with fluorescently labeled detection antibodies, magnetic separation, and flow cytometric analysis for antigenic characterization.

1. Coupling of Magnetic Nanoparticles (MNPs)

	Use commercial coupling procedure and reagents to couple MNPs with antibodies (Abs) (typically 1 mg). Iron ...

Imaging of Extracellular Vesicles by Atomic Force Microscopy

Summary

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Immunocapture and Flow Cytometry of Extracellular Vesicles for Antigenic Characterization