binding of molecules to the substrate.
A typical example is the binding of
DNA molecules onto a mica surface
treated with APTES(Aminopropytriethoxysilane), which
renders the surface positively charged 31.

Figure 2. Schematic representation of thesilanization process.

Plasma treatment
Plasma processing can change
the hydration properties of the tip.
Glow discharge in a hexafluoro–
propene–atmosphere, resulting in a
Teflon-like coating of the tip, renders
silicon nitride cantilevers hydrophobic
due to the hydration properties of
Teflon27. One minute glow discharge
in air renders silicon nitride probeshydrophilic23,28 by “cleaning” theorganically contaminated surface.
Silanization
Silanization (Figure 2) is anotherpossibility for changing the wetting
properties and the surface charge of atip. Organochloro- or organoalkoxysilanes are chemically bound to theprobe surface. Non-reactive groups
such as alkyls provide hydrophobicity.
For example, trimethoxysilylpropyldiethylene- triamine (DETA) renders asilicon oxide surface (oxide-sharpened
cantilevers) positively charged andhydrophobic29. Lubricant coating –N-3(3- triethoxysilylpropyl)perfluoro(polyisopropoxy 2-methylacethyl)amide for example – can also be
used to render silicon nitride tipshydrophobic and, thus, reduce
adhesion forces that might damage
the sample30.
Note that Silanization is also useful for
modifying the surface chemistry of thesubstrates used for sample support inbiology, for example to promote the2

Tip Functionalization
Functionalization of tips by coatingthem with molecules has opened a
new research area for studying
specific interactions on a molecularlevel, e.g. ligand-receptor pairs orcell-cell-interactions (Figure 3).
• Chemical coating of probes ismainly done by silanization or byfunctionalized thiols and is often
a first step before biological
functionalization.
• Biological coating has been mostly
used for mapping the distribution ofbinding partners on samples32-34, as
well as for force measurements13,35,36.
It becomes therefore possible toinvestigate molecular forces, like:– forces between a receptor anda ligand13,37, including
antigen-antibody-pairs38.
– forces between moleculesand cells.
– forces between cells36,39.

and this thiol group can bind to agold coated silicon nitride tip. An
amine group at the other end of the
PEG molecule attaches proteins(antibodies for example) via a
covalent bond41.
• To coat the tip with biotin, it ispossible to first coat the tip withbovine serum albumin (BSA), whichallows the attachment of biotin.
• Oligonucleotides can be covalently
attached to the tip and to probe
sequence specific interactions.
• Cells can be grown onto tiplesscantilevers or onto cantilevers withsmall beads at the end. They canalso be chemically attached via
polyethyleneimine (PEI) interactions
for example42.

Important probe Parameters
Two fundamental parameters of an
AFM probe are tip shape andmechanical parameters (the cantilever
spring constant, resonance frequency
and quality factor “Q”).

Intramolecular forces have also beenmeasured with great success40.
Many protocols can be performed toattach proteins to a tip. Sometimes
non-specific binding is enough, butmore complicated protocols may berequired. Most of them use a spacer
to covalently bind the proteins. The
advantage is that it is possible to orient
the protein in order to expose specificsite(s) of the proteins (enzymatic site forexample). Here are a few examples:• Polyethyleneglycol (PEG) is acommon spacer. A terminal thiolgroup can be first attached to PEG

Figure 3. Functionalized cantilever for force
measurements on ligand-receptor pairs14.

synthetic calibration standard likecolloidal gold particles48, latex
beads49 and calibration arrays, or byscanning well known biomolecules
like DNA50. Note that the Tip
Evaluation Option available on the
Digital Instruments NanoScope®
software contains a calibration
standard to estimate tip shape.

Figure 4. Dissecting a cell membrane
locally by applying too high forces.

Tip shape
The radius of curvature of the tip, or
tip sharpness, determines the lateral
resolution. An AFM image is always a‘combination’ between the tip shapeand the sample topography. Therefore
the duller the tip is, the wider the
topography appears (“tip broadening”
effect). Most of the time, optimal
resolution on biomolecules requires
the minimum possible tip radius43.
Nevertheless, it is sometimes
preferable to use dull tips rather than
sharp tips, when imaging cells forexample, because the pressure exerted
on the sample is less44. A sharp tip canpoke through the membrane anddamage the cell45,46 (Figure.4).

• The sample topography can also be
calculated by estimating the tip shapewith mathematical morphology
operations without using a known
standard topography (“blind”
mathematical restoration)51-55. These
non-linear mathematical operations(dilation and erosion) consist in an
over- and under-estimation of the tip
broadening effect (Figure 5).
Due to variations in etching during
production, double tips can sometimes
be generated, yielding images in which
the topography appears repeated(Figure 6). This is a very common
artifact, and any user should be able
to recognize it.
Spring constant
The spring constant k is defined as theratio between the applied force F andthe cantilever deflection ∆d:

For force measurements it is crucial toknow the value of the spring constant.
The accuracy of the force measurement
is determined by the error of the force
constant and by any errors in thedetection system.
Different methods have been proposed
to determine the spring constant:• Acquiring the thermal vibration
spectrum of a cantilever anddeducing the spring constantof the cantilever from theequipartition theorem56,57.
• Measuring the change of theresonance frequency while loading
the cantilever with small weights58.
• Measuring the resonance frequency
and calculating the spring constantfrom the geometrical dimensions of
the cantilever59 or from its quality
factor, Q60.
• Measuring the deflection of thecantilever when loading with small
weights61 or while exerting a force
with another cantilever of known
force constant62.

(Hooke’s Law)

To help quantify the tip broadening
it may be useful to do a quality
assessment of the probe. Knowing thetip shape is then essential to restore thesample surface. The following methods
help for studying the tip shape andrestoring the true sample surface:• Imaging and measuring the tips withelectron microscopy47, or with field
ion emission microscopy.
• It is also possible to estimate the tip
shape by scanning a sample ofknown topography such as aa.

b.

Figure 5. Morphological filter applied to an AFM image (a) to reconstruct the DNA shape (b).

3

Resonance frequency andquality factor
The resonance frequency is
the first natural mode of vibrationof a cantilever and is determinedby the material, geometry and theenvironment (air or liquid).
TappingMode is performed with acantilever oscillating preferentiallyclose to its first natural mode ofvibration. In air, typical values ofresonance frequencies are 900Hz to
88kHz for silicon nitride cantilevers
and 60kHz to 400kHz for siliconcantilevers, depending upon the
cantilever geometry. In liquid, withsilicon nitrides probes (100µm long,narrow legs, spring constant =0.06N/m), we recommend choosing
a frequency between 8 and 10kHz.
Note that it is important to tune thefrequency very close to the surface
because there can be a frequency shift
as the tip approaches the surface.

the surface or from the sample itself,
like proteins. This can result in double
tip images (Figure 6) and/or reductionof the lateral resolution. Imaging
tips with electron microscopy after
imaging with an AFM can show thecontamination of the tip47. A change
in the image during a scan should
always alert the user about analteration of tip quality.

where:
m = cantilever mass
= resonance frequency∆F = width of the resonance peakb = damping factor

Plasma ashing/etching, also derived
from the electronics industry, is known
to remove organic contaminants. Here,hydrogen, oxygen and argon plasma
react with carbon compounds or

The quality factor Q of the cantilever isanother parameter of interest affecting
the scan speed and the sensitivity. Q isdefined as

Q is a measure of the dissipation
mechanisms that damp the oscillationof the cantilever. A high Q is desirable
for TappingMode to optimize thesensitivity63. Typical values of Q for
cantilevers in air are 100 to 300,
and around 1 in water due tohydrodynamic damping64,65.

Cleaning tips
Cleaning a tip is a good way todecrease contamination from thefabrication process or storage. This
precaution can increase the image
resolution. The most popular cleaning
method is UV-light treatment that
produces ozone and removes organic
debris66. Another possibility is to
incubate the cantilevers in a piranhasolution (mixture of sulfuric acid andhydrogen peroxide) for 30 minutes.
This procedure is used to clean siliconand silicon nitride surfaces in theelectronics industry and also removes
the silicone oil contamination often
introduced from the cantileverpacking material67.

Problems of Tip Contamination
Tips can easily become contaminatedduring the scanning process. This isespecially the case for biologicalsamples that can easily detach from

4

Figure 6. “Double tip” image of two
DNA molecules.

oxides on the surface68. For example,
exposing cantilevers to argon plasma(80W) for 30 seconds seems tosufficiently clean probes for tip
functionalization28. CO2 snow also
removes organic debris from thesurface because of a transient
formation of liquid CO269.
Note that a “cleaned” probe is
generally hydrophilic because of theremoval of the organic contaminants
that are generally present inambient air.

Choosing Probes
Table 1 is a guide to choosing probes
for various and typical biologicalsamples as deduced from a wealthof user experience. As previously
mentioned, the main choice of probes
is between two families — siliconand silicon nitride probes, differing
primarily by their spring constant.
The table indicates the probe as afunction of sample type, as well as
the preferred imaging mode
(TappingMode vs. Contact Mode).
Unless otherwise noted, when
discussing TappingMode in liquid, weare referring to the indirect drive fluid
cell. Magnetic actuated TappingModeis discussed separately. For moredetail about these and other probes,
please visit www.veecoprobes.com.

SiliconNitrideSiliconSiliconNitrideBiomaterials

SiliconBiomaterials
Force Measurements
Force Measurements

CONTACT

SiliconNitrideTissues

TAPPING

Biomolecules (Nucleic
Acids, Proteins, Lipids,
Carbohydrates, etc.)

Tissues

AIR

Silicon

Cells

x
x
x
—
—
—

x
x
x
x
x
x

—
—
—

NP-STT
OTR4

—
—
—
x
x
x

(D)NP

x

—

x

x

TESP
(D)NP
(D)NP-S

—
x
x
—

x
x
x
x

—
—

FESP

x
—
—
x

x
x

—

x

—

PROBE
FAMILY/MODEL

Biomolecules (Nucleic
Acids, Proteins, Lipids,
Carbohydrates, etc.)

AFM MODELIQUIDSAMPLE TYPE

EXPERIMENTOTESPARTESPTESP(D)NP-S

x
x
x

—
—

OTESPATESP——

SiliconNitride(D)NP-Sxxx—

SiliconNitride

(D)NP

x

—

—

x

MSCT

x

—

—

—

—

Table 1. Recommended probe types for specific biological samples and imaging modes.

Key to Probe Model Names
Silicon Probes:
OTESPA: TappingMode Etched Silicon
Probe. General purpose, air,TappingMode probe with backside
coating for increased laser reflectivity.
RTESP: TappingMode Etched Silicon
Probe. General purpose, air,TappingMode probe with the tip
rotated to optimize sidewall angle
symmetry in the fast scan direction.
While advantageous on some samples
with tall, sharp step features, thisfeature is not generally important on
most biological samples.
TESP: TappingMode Etched Silicon
Probe. General purpose, air,TappingMode probe, interchangeablewith RTESP in most applications.
FESP: Force Modulation Etched Silicon
Probe. Originally intended for force
modulation experiments, this probe
also works well for general purpose
TappingMode in air in case where its
lower spring constant is advantageous(i.e. soft samples).

Silicon Nitride Probes:(D)NP-S: Oxide-Sharpened Silicon
Nitride Probe. General purpose
probe for both contact mode andTappingMode in fluid. Four different
cantilevers on each substrate allow anappropriate choice of spring constantfor different experiments. Optional“D” prefix indicates low stresscantilevers recommended for Digital
Instruments Dimension-series scanners.
(D)NP: Silicon Nitride Probe. Sameas (D)NP-S probes, except that the tip
is not oxide-sharpened, resulting in aless sharp tip. This is advantageous
on some samples, especially cells,
where a sharp tip may damage
the sample. Optional “D” prefix
indicates low stress cantilevers
recommended for Digital Instruments
Dimension-series scanners.

sharper tip. However, a second,
shorter tip is also formed near themain tip as result of the process.
The second tip is not intended for
imaging and can result in “doubletip” artifacts if it contacts the sample.
For this reason the NP-STT probes
are restricted to samples with small
vertical features (typically lessthan 100 nm).
OTR4: Oxide-Sharpened Silicon
Nitride Probes. General purpose
probe for both contact mode andTappingMode in fluid. Two different
cantilever spring constants. Generallyinterchangeable with NP-S probes.
MSCT: Sharpened Contact
MicroLevers with Backside Gold
Coating, oxide sharpened tip.
General purpose probe for bothcontact mode and TappingModein fluid. Six different cantilevers offer
a wide range of spring constants.
These are particularly popular forpiconewton-scale for measurements
as some of the spring constants arevery low. Also unique in that oneof the levers is rectangular, rather
than triangular like most silicon
nitride levers.

Conclusion
Choosing the correct probe is a
crucial part of working on biologicalsamples. The chemical and physicalparameters of the probe greatly
affect AFM measurements and can
reduce resolution. A large numberof commercially available probes
already enable many different
applications and skilled users are
increasingly modifying these probes
to achieve their specific goals.

NP-STT: Oxide-Sharpened Silicon
Nitride Probe Twin Tip. These probes
are very similar to the NP-S probes
except their tips are formed by aprocess that produces a considerably5References
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7