Transmission Electron
Microscopy Visualization
Bob Ashley AAS SMFW
Reading List
• Reading List
• Negative Staining 1990 Hayat and Miller
• Baker, T. S., and R. Henderson (2006). Electron
cryomicroscopy. In "International Tables for Crystallography",
Vol. F, ch. 19, pp. 451-463. Baker, T. S., and R. Henderson
• Baker, T. S., N. H. Olson, and S. D. Fuller (2000) Erratum:
Adding the third dimension to virus life cycles: ThreeDimensional reconstruction of icosahedral viruses from cryoelectron micrographs. Microbiol. Molec. Biol. Reviews 64:237.
• Free will vs. Determinism in electron microscopy
• Two methods of viewing in TEM
• Cryo and Negative Stain
Grids and Support Film
• Usually Copper
• How does it react with the specimen?
• Mesh indicates amount of open area
• Higher number less open 50-1000
• We use 400 mesh square
• Very thin films and specimens
• Hexagonal shape openings
• Very delicate
• Even mild bend or buckle can cause distortion of specimen or focus aberration
Grid Types
• Supports used must be strong yet electron transparent
• Plastic (formvar)
• Carbon
• Holey carbon
• Quantifoil
• C-flat
Support Film Concerns
Mass thickness influences
contrast while mechanical
stability increases image clarity
• Films in general must have
• High transparency
• Adequate strength to withstand
E- beam and support specimen
Carbon coated only (6-10 nm)
• Uniformly amorphous
• More elastic scattering events with
e- beam
• Can be stable very thin 1-2nm
• More stable than plastic alone
• Hydrophobic, fragile, time
consuming to make
Plastic only 10-20nm (10-20 nm)
• Formvar
• More clarity with less background
than Carbon alone
• Not as thermally stable and can
cause charging and drift
Carbon Coated with Plastic
• Stability of carbon but will have a
thickness that may impede
All Sides Being Equal?
• Dull Side (coppery)
• More area for film to adhere
• Shiny side (polished)
• Not as much surface area for
films to adhere
• Can cause movement under
e- beam exposure
To Glow or Not
Glow Discharge renders continuous carbon coated grids hydrophilic by applying
a negative charge.
• Aids stain spread more uniformly (increases wettability)
• Helps particles in specimen to adhere to the substrate
• Decreases likelihood of the virus particles being held in aggregates as a result
of the interaction between the virus particles and the surface charge of film
• Two types in electron microscopy
• Amplitude contrast (scattering contrast)
• Subtractive effect where various shades are evident by loss of
• Main source of most electron microscope contrast (except
• Phase Contrast (interference contrast)
• Interference of diffracted waves cause intensity differences
due to loss of energy and the corresponding shorter focal
• Appear as bright ring or halo around the edge of an object
• Fresnel ‘freh-nell’ fringe
The Concept of Negative Stain
• Heavy metal atoms act as barrier to the e- beam
• Allows passage through specimen
• Stain penetration into hydrophilic specimen
• Dries faster than specimen
• Mostly hydrated regions replacing water
• Lipoproteins and proteins
• Stains form around hydrophobic
regions including lipid
• Contrast dependent on stain thickness
• Resolution range 20-40 Å
Negative Contrast
• Dense areas are bright also exclude stain
• Amplitude contrast
• Areas with no stain appear light because there
is nothing for the electron beam to hit and
the transmitted electrons shine through
Simple Microscopy
• Lighter areas have more protein and exclude stain
• Darker areas are where the stain pools
• Indent in support mechanism
Stain Film and Particle
A. Hydrophilic specimen
hydrophilic film
B. Hydrophilic specimen on
hydrophobic film
C. Hydrophobic specimen on
hydrophilic film
D. Hydrophobic specimen on
hydrophobic film
Negative and Positive Staining
A. 4% PTA Negative Stained
B. 4% UA Positive Stained
C. 4% UA Negative Stained
• Three types of staining visible
• Negative staining appearing white
• Negative staining appearing grey
• Positive staining appearing black
• Severe structural distortion
Staining Methods
Factors Controlling Appearance
• pH
Interaction with the support
• Isoelectric Point
• Grid film
• Fixation
• Thickness of stain on film
• Concentration
• Charge and beam interactions
• pH
• Charge
• Buffer and specimen interaction
• Osmolarity
• Can influence structure and
volume of particle
The Effect of the Isoelectric Point of
Protein and Stain
Isoelectric point (pI) or (IEP)
The pH at which a particular molecule or surface carries no net electrical charge
Can be time dependent and is not absolute
Fixation with glutaraldehyde increases net negative charge
The presence of a fixed negative or positive charge influences the deposition of any given
• In general proteins
• Combine (positive stain) with cations (UA+) on the alkaline side of the pI
• Combine with anions (PTA-) on the acidic side of the pI
Protein pI
• Stain pH greater than pI applies negative charge
• Stain pH lower than pI applies positive charge
• Ex. Protein with a pI of 5.0 is negatively charged at pH 7.0 with PTA- which is
higher than the pI of the protein therefore the stain repels and is excluded by the
Other Effects of pH
• Optimal pH for stains is not known but each has a
satisfactory range
• At high pH the stain penetration is usually enhanced with
long stain time
• At low pH the surface detail is usually highlighted due to
acidic environment
• May change with stain storage and with stain drying
• Use fresh stain preferable and check before staining specimen
Ex. stained with PTA at 5.0 pH, influenza virus surface spikes well preserved
same sample stained with 7.5 pH PTA stain penetrates virus envelope
Ex. PTA with pH of 4.5 recommended for resolving antibody particles bound to
Negative Stains
• Negative stain should:
• Have minimal interaction with specimen (pos. stain)
• High solubility in solution (precipitates and crystalizes in e- beam)
• High density (must be at least twice the density of the specimen to
be visualized)
• High melting point to avoid beam damage
• Small grain size
• Chemical pH stability
Types of Stains
Uranyl Acetate+ (cation)
Uranyl Oxalate+(cation)
• Can be used in pH from 5.0-7.0
(ideal at 6.5-6.8)
• Most widely used
• Density of 2.87 g/cm^3
• Desirable for pH sensitive specimens
• Ion diameter .4-.8 nm
• Provides the contrast and
penetration of UA without the
• pH of 4.0-5.5 (usually used at 4.5
unstable at 6.0)
• Concentrations .5-5% ideal as 1%
• Desirable for virus proteins below
the pI or low molecular weight
• Can act as fixative
• Higher contrast than PTA
• Stabilizes lipids therefore may
minimize drying effect of virus
Uranyl Formate+(cation)
• Smallest grain size for better
penetration of interstices of sample
• Useful for high-res
• pH of 4.0-5.5 (usually used around
• Density of 3.68 g/cm^3
• Ideal as .75%
Types of Stains Continued
Along with UA most widely used
Density 4 g/cm^3
Grain size of 1.2 nm (not useful for high res work)
At neutral pH very little interaction with the specimen (avoids most positive staining)
Very stable in e- beam
Will not fix a specimen
Not stable over time with storage <1 month
May dissociate quaternary proteins into small units
Ammonium Molybdate
• Used for osmotically sensitive specimens
• pH from 5.0-8.0 useful at 7.0-7.4
• Higher contrast than PTA
Methylamine Tungstate (NanoW)
• pH 6.4-7.0
• Tolerates concentrated buffers
Drawbacks of Negative Stain
Tends to concentrate sample
Cellular debris and other junk
Positive staining
Beam irradiation
• Lower kV=more damage potential
• Leads to distortion of particle
• Will usually happen perpendicular to support mechanism
• Makes sample typically larger in diameter to known size
Cryo EM
• Negative Stain
Light areas indicate density
• Cryo Fixation Advantages
• Keeps sample in near native state
Higher resolution – 8-15 Å
• No artifacts from stain
• Cryo
Contrast reversal of negative stain,
dark areas indicate density- Phase
Types of Ice
• Amorphous or glassy ice
• Target state of cryoEM samples
• Liquid nitrogen -195° C
• Heat capacity too low- Liedenfrost Effect
• Liquid ethane
• Liquid propane
• Cubic ice
• Water in crystalline lattice obscures beam
• Usually around -140° C
• Vanilla Ice
• Too hot to handle yet too cold to hold
The Grid in Cryo
The Mechanism
• Plunge Freezing
• Manual Blotting
Advanced Grid Freezing- Gatan
Visualizing Ice on the Grid
Search for suitable area on grid
Low Dose
• Ice is beam sensitive
• E- cause irradiated sample
• High res data can be lost in a matter of seconds
• Focus on area that is not photographed and correct
for astigmatism
• Keep levels to around 5-20 E/A^2
• Can be a software automated process
Visibility of Particles
Irradiation Damage
Defocus Tradeoff
• Focus adjacent region of interest to true focus
• No inherent contrast from sample in ice
• No tone ring visible in FFT
• Reset to range desirable -2 to -5 ųm
Drawbacks of Cryo EM
Low contrast
Low signal to noise ratio
Size limitation
Time intensive
Labor intensive
Beam irradiation
• Lower kV=more damage
• Must be > 400kD for proper
Smallest published to date is 260kD
Cryo negative stain as possible solution
Phase plates
The End Result
Try the best
you can to
achieve your
EM dreams!
Thank You

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