To cells and tissues

From single
molecules
To Biomolecularcomplexes

Application Note #131
BioScope Catalyst: Accessing All
Biological Size Scales with HighResolution AFM Imaging
The BioScope TM CatalystTM Atomic Force Microscope(AFM) operates under physiologically relevant conditions
and integrates fully with optical microscopy techniques,
providing life science researchers the ability to study
biological species across a wide-range of size scales.
With its superior engineering and mechanical stability,
the Catalyst is ideally suited for obtaining high-resolution,
three-dimensional images of individual biomolecules andsmall biomolecular complexes. From investigating nucleic
acids and proteins to characterizing protein assemblies andmembranes, high-resolution imaging conducted with theCatalyst offers scientists unique opportunities to researchbiomolecules and biomolecular processes at the singlemolecule level.

Life Sciences Atomic Force Microscopy
Atomic force microscopy allows direct visualization of
the three-dimensional structure of a sample surface withnanoscale resolution. Unlike many other high-resolution
imaging techniques, AFM does not require staining or
coating of the sample, leaving native surfaces unaltered.
Together with the ability to operate in a fluid environment,
this makes AFM an unparalleled technique for studying
biomolecules and the dynamics of biological processes insitu and in real-time.

High-resolution imaging with
the BioScope Catalyst acrossall biological size scales

Biological research encompasses a wide-range of size
scales and structural complexity, from single molecules
to cells to tissues. As such, an instrument or techniquecapable of high-resolution imaging of single biomolecules,
as well as larger biomolecular complexes, can provide
biologists with unique research opportunities. The BioScope
Catalyst AFM was specifically designed with this in mind.
The system can be functionally integrated with various lightmicroscopy techniques (brightfield, phase contrast, DIC, epiand confocal fluorescence, etc.) to allow optically guided
navigation of the AFM probe to regions of a sample for highresolution AFM imaging and the production of correlated
AFM and optical image datasets. With the industry’s largest
closed-loop, X-Y scan range of 150 microns, a Z rangeof ≥20 microns, and capability for environmental control,
the Catalyst repeatedly has demonstrated its unmatchedperformance for combined AFM and optical microscopy
studies of live cells (see figure 1).1-4 However, the Catalyst is
not just for live cell studies. The highest quality engineeringand mechanical stability of the Catalyst AFM facilitates highresolution imaging of smaller biomolecular species as well.
Even when installed on an inverted optical microscope, theCatalyst’s imaging performance is not compromised (seefigure 2).

Figure 1. (A) Registered image overlayof a two-channel confocal laser
scanning fluorescence microscopy
image and AFM topography imageof fibroblast cells labeled with Alexa
Fluo 546 Phalloidin (red) & DAPI
(blue). The BioScope Catalyst MIRO
software enables registration of an
optical field of view to the AFM scanarea. Optical images can then be used
to navigate the AFM probe to a regionof interest to perform high resolution
AFM imaging and/or highly sensitive
force measurements. (B) Region ofinterest obtained from the image
overlay showing correlated AFM andfluorescence data channels. Confocal
fluorescence images were obtainedwith a Leica SP5 confocal system andusing a 40x oil immersion objective.
AFM images were obtained with a
BioScope Catalyst operated in contact
mode in buffer solution using MLCT
AFM probes (k ~0.01N/m).

AFM Deflection

Red FluorescenceBlue Fluorescence

Overlay

Nucleic Acids: DNA
DNA (deoxyribonucleic acid) is the fundamental moleculeof life. As such, much biological research has been focusedon studying its structure and its interactions with otherbiomolecules. Ultimately, understanding how the genetic
code is stored by and expressed from DNA is critical togaining insights into genetically related diseases and thedevelopment of treatment methods or the preventionof these disease states. Much of the information on
DNA structure and function has been resolved using a
combination of molecular biology, x-ray diffraction andelectron microscopy techniques. However, increasingly the
AFM has been an attractive approach to DNA studies with
its ability to study intermolecular interactions and processes
in real-time under near physiological conditions.5-9

2

For AFM imaging, DNA is typically deposited onto a freshly
cleaved mica surface, using either (1) divalent cations (e.g.,
Ni++ or Mg++) to passivate the negatively charged mica
surface,9-13 or (2) chemically modifying the mica surface
itself with a positively charged silane (e.g., APS-mica)14-16,
to facilitate adsorption of the negatively charged DNA
strands. Using either of these immobilization techniques,
the structure of the DNA molecules are easily resolved in
the AFM images, while proteins or enzymes can be directly
introduced into the imaging solution and their interactions
with the DNA observed in real-time (see figure 3).17-21
The Catalyst’s small-volume flow cell provides an enclosed
fluid environment for observing the structure and dynamics
of biomolecules over an extended period of time. Inlet

and outlet ports allow for convenient fluid exchange while
the 60 microliter total volume of the flow cell minimizes
the amount of fluid and sample needed. This is often an
important consideration when using limited or expensive
reagents, such as DNA and proteins/enzymes.

Figure 2. A 1µm Phase Image of a C60H122 alkane. The C60H122 isspincast onto an HOPG substrate with the resulting ultra-thin alkane
layer exhibiting a lamellar structure ~7.5nm in width and ~0.4nm inheight. Images were acquired on a BioScope Catalyst AFM operated
in TappingMode using FESP AFM probes (k ~3N/m).

The recent release of PeakForce Tapping TM and ScanAsystTM
operating modes has further enhanced the ease of highresolution imaging in fluid with Catalyst. ScanAsyst’s
self-optimization imaging capabilities, its ability to maintainvery low imaging forces (<100 piconewtons), as well as
its removal of the need to determine cantilever resonance(cantilever tuning), combine to enable researchers toroutinely achieve high-resolution images of their samples
with consistent results. Figure 3 shows a height image ofLambda DNA obtained using PeakForce Tapping Modeon the BioScope Catalyst. The use of very sharp probes(radius of curvature ~2 nanometers) coupled with theability to maintain optimal surface tracking over extended
periods of time in fluid, not only provides routine imagesof DNA strands with typically ≤6 nanometers diameter but
also opens up opportunities for the observation of timedependent dynamics without loss of resolution.

Proteins
While DNA is the molecule of life, the genetic code thatit makes up allows for the synthesis of numerous protein
molecules necessary to sustain life. Proteins not only
exist as single molecules, they also assemble with otherproteins and molecules to form complexes that play
important roles in the regulation of biological processes.
The direct observation of proteins and their self-assemblyby AFM can offer unique insights into biomolecular
structure-function relationships.
Viruses are infectious agents that spread by infecting
host bacterial or eukaryotic cells. Outside of a cell, a virus
exists as a protein shell, also known as a capsid, which
encapsulates the viral DNA or RNA (ribonucleic acid). This
structure acts to protect the virus until it can find a host.
Once a virus has successfully infected a host cell, this
DNA/RNA is released and the virus uses the cell’s own
DNA/RNA replicating mechanisms to create more virus
particles. These new viruses then infect other host cells
and the infection spreads.

Figure 3. Three-dimensional topography image of pUC plasmid DNA
adsorbed onto a mica substrate. The individual DNA strands areclearly visible against the mica background. Images were acquired
on a BioScope Catalyst AFM operated in PeakForce Tapping in
buffer solution using ScanAsyst Fluid+ AFM probes (k ~0.7N/m).
Image XY-Scale = 2µm.

3Figure 4. (A) Transmission electron micrograph of a Herpes Simplex
Virus capsid. Image courtesy of Wouter Roos, Vrije Universiteit,
Amsterdam, Netherlands (Reprinted with permission. Source: Rooset al., Proc. Natl. Acad. Sci. USA, 2009, Vol. 106, 9673-78) (B) A
250nm AFM Topography image of a single herpes simplex virus
capsid. The arrangement of protein molecules as 3-dimensional
subunits on the surface of the capsid, known as capsomeres, isclearly visible in the AFM image. AFM images were obtained on the
BioScope Catalyst operated in PeakForce Tapping mode in bufferconditions and using ScanAsyst Fluid+ AFM probes (k ~0.7N/m).
Sample courtesy of Wouter Roos and Gijs Wuite, Vrije Universiteit,
Amsterdam, Netherlands.

A

Viruses can cause any number of diseases. The key totreating and preventing these diseases is in understanding
the different processes of how viruses infect host cells.
An important aspect of this is the identification andclassification of viruses based on similar structure orfunction. For example, viruses are classified into families
based on their capsid structure, which is determinedby the arrangement of the protein molecules that form
the capsid architecture. Researchers have visualized thestructure of viral capsids using a variety of techniques,
including x-ray crystallography, nuclear magnetic resonance(NMR) imaging, and transmission and scanning electron
microscopy (see figure 4A). While these techniques provide
valuable structural information, they often require complex
sample preparation with coating, staining or crystallization of
the virus particles. AFM imaging, however, requires minimal
sample preparation and the imaging is performed on theunaltered, native capsid surface.22-24 Figure 4B shows the
structure of a single Herpes Simplex Virus particle obtainedwith the BioScope Catalyst. The arrangement of protein
molecules as three-dimensional subunits on the surface ofthe capsid, also known as capsomeres, is clearly visible in
the AFM image.

B

200nm

C

200nm

200nm

Figure 5. PeakForce QNM images of amyloid fibers adsorbed onto a freshly cleaved mica surface. (A) Topography images reveal some of thefibers to have a twisted structure (blue arrows) while others do not (red arrows). (B) The Modulus data and the (C) Deformation data channels
are obtained simultaneously to the topography image. These images indicate the amyloid to have a lower modulus (darker color scale) andcorrespondingly, a higher degree of deformation (lighter color scale) than the underlying mica substrate. It is also observed that the twisted
amyloid fibers have a slightly lower modulus value as compared to those fibers that are not twisted (i.e. twisted fibers appear slight darker
than the straight fibers in the modulus image). Images were obtained on a BioScope Catalyst operated in PeakForce Tapping mode using
ScanAsyst AFM probes (k ~0.4N/m). Sample courtesy of Xingfei Zhou, Ningbo University, China.

4Figure 6. Setup of the BioScope Catalyst Perfusion Stage Incubator (PSI). (1) The PSI supports standard glass bottom
petri dishes for compatibility with high NA objectives. (2) The flow diffuser directs liquid flow in laminar fashion acrossthe sample area, ensuring even fluid exchange and isolating noise from the liquid inlet and outlet. (3) The perfusion clamp
stabilizes the petri dish and contained stainless steel inlet and outlet tubes that are in thermal contact with the heatingstage to preheat the incoming liquid and gas. (4) A silicone baffle seals between the petri dish and probe holder, reducing
evaporation and allowing control of the gas space above the liquid. (5) The specialized PSI probe holder contains atemperature sensor for local monitoring of temperature. The right-side image shows the PSI fully assembled together withthe sample heating stage on the BioScope Catalyst AFM.

While self-assembly and association with other molecules
is most often the desired behavior of proteins required
for the progression of biological signals and processes,
there are often instances where this is not the case.
Abnormal protein assembly and aggregation of proteinsin the brain is associated with the development of various
neurodegenerative diseases, such as Alzheimer’s,
Parkinson’s, and prion diseases. In Alzheimer’s disease, thisnon-native self-assembly of the typically soluble amyloidbeta (A-β) protein results in the formation of plaques, calledamyloid. As these amyloid plaques accumulate in the brain
they become toxic, eventually leading to cell degenerationand the symptomatic progression of Alzheimer’s disease.
The goal of Alzheimer’s research is not only to understandthe pathogenesis of the disease, but also to provide
insights into treating and preventing Alzheimer’s and otherrelated neurodegenerative diseases. While the formationand structure of A-β fibers has been extensively studied
using a variety of analytical techniques, findings must

often be interpreted carefully based on the type of sample
preparation required for the technique used (coating,dehydration, etc.), which may influence the results. AFM
not only allows researchers to conduct studies in fluid
under near-physiological conditions, it also allows themto investigate and determine, in situ, the conditions underwhich soluble, monomeric A-β proteins may be prone tofiber formation.25-27 Figure 5 shows AFM images obtainedusing PeakForce QNM™ (Quantitative Nano-Mechanical)
imaging on the BioScope Catalyst of A-β fibers deposited
onto a mica surface. Interestingly, AFM imaging revealed
some of the fibers to have a twisted structure while others
did not. PeakForce QNM imaging of the fibers not only
provides details as to the structure of the fibers (topography,
see figure 5A), it can also reveal important information on
their nanomechanical properties. PeakForce QNM images
include individual data channels, such as modulus, adhesion,
deformation, and dissipation, that correlate directly to thesimultaneously obtained topography data channel. Using5

a calibrated AFM probe, researchers can easily obtain
quantitative measurements of these mechanical properties
as a function of spatial location across the surface of theirsample. Not only are these data channels quantitative, they
are acquired at the typical pixel density resolution requiredfor high-resolution imaging. Figure 5B reveals the fibers tohave a lower modulus as compared to the underlying mica
surface. When comparing the two different fiber structures,the twisted fibers also appear to have a slightly lower
modulus than the straight fibers. Figure 5C also shows theamyloid fibers to undergo larger deformation relative tothe mica surface, which is reflected in the softer modulus
measurements of the fibers.
Researchers are often interested in observing the interactionand effects of these amyloid proteins on live cells.28-29
The BioScope Catalyst Perfusion Stage Incubator (PSI)
provides the necessary environmental control to enable
long duration live cell experiments required for this type ofstudy. The PSI, integrated with the Catalyst heating stage,
maintains ideal cell culture conditions, including temperatureand media/fluid and gas perfusion (see figure 6). The PSI
is fully integrated with the Catalyst system, allowing for
uncompromised optical imaging using all the system’s
imaging modes (brightfield, phase contrast, DIC,
epifluorescence, CLSM, etc). Using the combination of theCatalyst AFM, the PSI accessory, and MIRO (Microscopy
Image Registration and Overlay) software, which allows
optical images to be registered to and overlaid with AFM
images and to use these optical images to navigate theAFM probe, researchers can perform true correlated opticaland AFM imaging or AFM force measurements to examine
any changes in cell structure or mechanical properties in
response to amyloid fiber formation.

Membranes and Membrane Proteins
Cell membranes surround cells, physically separating theintracellular components from the extracellular environment.
Cell membranes are involved in many important functions,
including anchoring the cytoskeleton and providing shape
to the cell, as well as facilitating the transport of nutrientsand materials needed for survival in- and outside of the cell.
The movement of substances across the cell membrane isfacilitated by various protein molecules embedded withinor associated with the membrane. This movement may
be triggered as a result of a response to some chemical orion gradient, or in response to the binding of a molecule tothe extracellular portion of a membrane protein, causing
a conformational change in the protein structure and theopening of a channel in the membrane to the inside of
the cell.

A

B

500nm

200nm

Figure 7. (A) AFM phase image of bacterial S-layers from E. coli. The bacterial membranes were excised from the cells and the membranepatches immobilized onto a freshly cleaved mica surface. The lattice pattern formed by the S-layer proteins is clearly evident in the phase
image and is observed to have a periodicity of ~18nm. (B) High-resolution image of the S-layer lattice periodicity observed on a single
membrane patch. Images were obtained on a BioScope Catalyst operated in TappingMode in buffer conditions using SNL AFM probes(k ~0.32N/m). Sample courtesy of Hans Oberleithner, Institute for Physiology II, University of Muenster, Germany.

6

Studying the structure of membrane proteins has presented
researchers with quite a challenge. The majority oftechniques available have been developed and applied
to soluble proteins. However, unlike soluble proteins,membrane proteins contain hydrophobic domains thatspan the membrane. As a result, the solubilization of theprotein from the cell membrane required for most analyticaltechniques, often leads to changes in the protein’s native
structure in an attempt to shield the hydrophobic domain(s)from the surrounding aqueous environment. It is thisinstability outside the membrane that has limited thestructural and functional studies of membrane proteins.
AFM imaging, however, not only allows for examinationof membrane proteins within their native membrane
environment, studies can also be conducted in fluid, undernear-physiological conditions, providing researchers theunique opportunity to observe membrane protein dynamics.
While AFM is capable of imaging live cells, high-resolution
imaging of the structure of cell membranes and theorganization of membrane-associating proteins is typicallyconducted on either excised cell membrane patches
deposited onto an atomically flat substrate (e.g., mica)
or supported planar lipid bilayers in which the proteins ofinterest have been reconstituted.36,37
Figure 7a is an image of bacterial membrane patches
adsorbed onto a mica surface. High-resolution imaging
of individual membrane patches (figure 7b) reveals theorganization of membrane-associated proteins as a twodimensional crystalline lattice structure, known as an
S-layer. S-layer proteins are associated with the surface ofthe cell membrane. While the S-layer plays a role in various
functions of the cell, as the outermost layer of bacteria
and archaea, its essential function is the mechanical andchemical protection of the cell.38 In the AFM image, thelateral spacing of the individual protein molecules in the
S-layer is ~18 nanometers. The small lattice periodicities
of S-layers have been shown to be attractive forbiomimetic or nanotechnology applications, such as theimmobilization matrices for the templating of biomoleculararrays or nanoparticles required for nanoelectronics andnonlinear optics.39,40

Conclusions
AFM provides many advantages for high-resolution
studies of single biomolecules. With a high signal-to-noise
ratio, the elimination of the need for coating, staining, or
crystallization of a sample, and the ability to operate in fluid,

today’s high-performance life science AFM facilitates thestudy of biomolecules under near-physiological conditions
in real-time and in situ. From single molecules to live cells,
the BioScope Catalyst provides high-resolution imaging of
biological samples across all biomolecular size scales. The
mechanical stability of the Catalyst when integrated withan inverted optical microscope allows researchers to takeadvantage of many of the features of this AFM, including
PeakForce Tapping, ScanAsyst, and PeakForce QNM
imaging modes, the small volume flow cell, MIRO software
capabilities, as well as the environmental control affordedby the sample stage heater and Perfusion Stage Incubator(PSI), which together open the door to a wide-range of
unique high-resolution imaging experiments.

References
1. A. Berquand, A. Holloschi, and P. Kioschis, “Characterizing the Effectof Anticytoskeletal Drugs on Living Cells Using MIRO Software and the
BioScope Catalyst AFM,” Bruker Application Note AN125 (2010).
2. F. Lafont and A. Berquand, “Atomic Force Microscopy with BioScope II:
Detecting Specific Ligand-Receptor Interactions on Live Cancer Cells in situ,”
Bruker Application Note AN111 (2008).
3. A. Berquand, A. Holloschi, S. Ritz, M. Hafner, and P. Kioschis, “AFM and
Neurodegenerative Diseases (Part I): Correlating Atomic Force Microscopy(AFM) and Fluorescence Microscopy to Detect Changes in Cell Morphology
Caused by Protein Aggregates of Mutant Huntingtin,” Bruker Application Note
AN117 (2008).
4. A. Berquand, S. Ritz, A. Holloschi, M. Hafner, and P. Kioschis, “AFM and
Neurodegenerative Diseases (Part II): Correlating Atomic Force Microscopy(AFM) and Fluorescence Microscopy to Study the Interaction between
Dopamine and the D1-Receptor in SH-SY5Y Cells,” Bruker Application Note
AN118 (2008).
5. A.L. Weisenhorn, H.E. Gaub, and H.G. Hansma, “Imaging Single-Stranded
DNA, Antigen-Antibody Reaction and Polymerizes Langmuir-Blodgett Films
with an Atomic Force Microscope,” Scanning Microscopy 4: 511 -16 (1990).
6. H.G. Hansma, J. Vesenka, C. Siegerist, G. Kelderman, H. Morett, R.L.
Sinsheimer, V. Elings, C. Bustamante, and P.K. Hansma, “Reproducible
Imaging and Dissection of Plasmid DNA Under Liquid with the Atomic ForceMicroscope,” Science 256: 1180 -84 (1992).
7. Y. Lyubchenko, L. Shlyakhtenko, R. Harrington, P. Oden, and S. Lindsay,“Atomic Force Microscopy of Long DNA: Imaging in Air and Under Water,”Proc. Natl. Acad. Sci. USA 90: 2137 -40 (1993).
8. H.G. Hansma, D.E. Laney, M. Bezanilla, and R.L. Sinsheimer, “Applications
for Atomic Force Microscopy of DNA,” Biophys. J. 68: 1672 -77 (1995).
9. D. Pastre, O. Pietrement, S. Fusil, F. Landousy, J. Jeusset, M-O. David, L.
Hamon, E. Le Cam, and A. Zozime, “Adsoprtion of DNA to Mica Mediated by
Divalent Counterions: A Theoretical and Experimental Study,” Biophys. J. 85:
2507 -18 (2003).
10. J. Vesenka, M. Guthold, C. L. Tang, D. Keller, E. Delain, and C.
Bustamante, “Substrate Preparation for Reliable Imaging of DNA Moleculeswith the Scanning Force Microscope,” Ultramicroscopy 42 -44: 1243 -49(1992).

7

27. C.M. Yip and J. McLaurin, “Amyloid-b Peptide Assembly: A Critical Step in
Fibrillogenesis and Membrane Disruption,” Biophys. J. 80: 1359 -71 (2001).

12. N.H. Thomson, S. Kasas, B.L. Smith, H.G. Hansma, and P.K. Hansma,“Reversible Binding of DNA to Mica for AFM Imaging,” Langmuir 12: 5905
-08 (1996).

28. I. Peters, U. Igbavboa, T. Schutt, S. Haidari, U. Hartig, S. Bottner, E.
Copanaki, T. Deller, D. Kogel, W.G. Wood, W.E. Muller, and G.P. Eckert, “Theinteraction of beta-amyloid protein with cellular membranes stimulates its own
production,” Biochim. Biophys. Acta. 1788: 964 -72 (2009).

13. Y. Jiao, D.I, Cherny, G. Heim, T.M. Jovin, and T.E. Schaffer, “Dynamic
Interactions of p53 with DNA in Solution by Time-Lapse Atomic ForceMicroscopy,” J. Mol. Biol. 314: 233 -43 (2001).

29. D.A. Bateman and A. Chakrabartty, “Cell Surface Binding andInternalization of A Modulated by Degree of Aggregation”, Int. J. Alzheimers
Dis., In Press (2011).

14. Y.L. Lyubchenko, A.A. Gall, L.S. Shlyakhtenko, R.E. Harringtion, P.I. Oden,
B.L. Jacobs, and S.M. Lindsay, “Atomic Force Microscopy Imaging of Double
Stranded DNA and RNA,” J. Biomolec. Struc, Dyn. 9: 589 -606 (1992).

30. C. Moller, M. Allen, V. Elings, A. Engel, and D. J. Mueller, “Tapping-Mode
Atomic Force Microscopy Produces Faithful High-Resolution Images ofProtein Surfaces,” Biophys. J. 77: 1150 -58 (1999).

15. Y.L. Lyubchenko, B.L. Jacobs, and S. M. Lindsay, “Atomic ForceMicroscopy of Reovirus dsRNA: A Routine Technique for Length
Measurements,” Nucl. Acids Res. 20: 3983 -86 (1992).

31. S. Scheuring, F. Reiss-Husson, A. Engel, J-L. Rigaud, and J-L. Ranck,“High-Resolution AFM Topographs of Rubrivivax gelatinosus Light-Harvesting
Complex LH2,” EMBO J. 20: 3029 -35 (2001).

16. Y.L. Lyubchenko and S.M. Lindsay, “DNA, RNA, and Nucleoprotein
Complexes Immobilized on AP-Mica and Imaged with AFM,” Procedures in
Scanning Probe Microscopy, Ed. R.J. Colton., J. Wiley & Sons, Ltd: 493 -96(1998).

32. A. Slade, J. Luh, S. Ho, and C.M. Yip, “Single Molecule Imaging ofSupported Planar Lipid Bilayer-Reconstituted Human Insulin Receptors by In
Situ Scanning Probe Microscopy,” J. Struc. Biol. 137: 283 -91 (2002).
33. A. Philippsen, W. Im, A. Engel, T. Schirmer, B. Roux, D.J. Mueller,“Imaging the Electrostatic Potential of Transmembrane Channels: Atomic
Probe Microscopy of OmpF Porin,” Biophys. J. 82: 1667 -76 (2002).
34. D.J. Mueller and A. Engel, “Atomic Force Microscopy and Spectroscopy of
Native Membrane Proteins,” Nature Protocols 2: 2191 -97 (2007).

18. M. Guthold, X. Zhu, C. Rivettis, G.Yang, N.H. Thomson, S. Kasas, H.G.
Hansma, B. Smith, P.K. Hansma, and C. Bustamante, “Direct Observationof One-Dimensional Diffusion and Transciption by Escherichia coli RNAPolymerase,” Biophys. J. 77: 2284 -94 (1999).

35. B. Seantier, M. Dezi, F. Gubellini, A. Berquand, C. Godefroy, P. Dosset,
D. Levy, and P-E. Milhiet, “Transfer on Hydrophobic Substrates and AFM
Imaging of Membrane Proteins Reconstituted in Planar Lipid Bilayers,” J. Mol.
Recog. In Press (2011).

19. F. Landousy and E. Le Cam, “Probing DNA-Protein Interactions with
Atomic Force Microscopy,” Bruker Application Note AN89 (2006).

36. D.J. Mueller, J.B. Heymann, F. Oesterhelt, C. Moller, H. Gaub, G. Buldt,
and A. Engel, “Atomic Force Microscopy of Native Purple Membrane,”Biochim. Biophys. Acta 1460: 27 -38 (2000).

20. Y.L. Lyubchenko and, L.S. Shlyakhtenko, “AFM for Analysis of Structure
and Dynamics of DNA and Protein-DNA Complexes,” Methods 47: 206 -13(2009).
21. D. Pastre, L. Hamon, I. Sorel, E. Le Cam, P.A. Curmi, and O. Pietrement,“Specific DNA-Protein Interactions on Mica Investigated by Atomic ForceMicroscopy,” Langmuir 26: 2618 -23 (2010).
22. Y.G. Kuznetsov, A.J. Malkin, R.W. Lucas, M. Plomp, and A. McPherson,“Imaging of Viruses by Atomic Force Microscopy,” J. Gen. Virol. 82: 2025 -34(2001).
23. A.J. Malkin, A. McPherson, and P.D. Gershon, “Structure of Intracellular
Vaccinia Virus Visualized by In Situ Atomic Force Microscopy,” J. Virol. 77:
6332 -40 (2003).
24. W.H. Roos, K. Radtke, E. Kniesmeijer, H. Geertsema, B. Sodeik, and
G.J.L. Wuite, “Scaffold Expulsion and Genome Packaging Trigger Stabilizationof Herpes Simplex Virus Capsids,” Proc. Natl. Acad. Sci. USA 106: 9673 -78(2009).
25. T. Kowalewski and D. Holtzman, “In Situ Atomic Force Microscopy Studyof Alzheimer’s b-Amyloid Peptide on Different Substrates: New Insights into
Mechanism of b-Sheet Formation,” Proc. Natl. Acad. Sci. USA 96: 3688 -93(1999).

37. D. Fotiadis and A. Engel, “High-Resolution Imaging of Bacteriorhodopsin
by Atomic Force Microscopy,” Methods Mol. Biol. 242: 291 -303 (2004).
38. G. Seltmann and O. Holst, “Chapter 6: Components Outside the Cell
Wall,” The Bacterial Cell Wall, Springer-Verlag (2002).
39. U.B. Sleytr and T.J. Beveridge, “Bacterial S-layers,” Trends Microbiol. 7:
253 -60 (1999).
40. U.B. Sleytr, C. Huber, N. Ilk, D. Pum, B. Schuster, and E.M. Egelseer,“S-Layers as a Tool Kit for Nanobiotechnological Applications,” FEMS
Microbiol. Lett. 267: 131 -44 (2007).

Authors
Andrea L. Slade, Bruker Nano Surfaces Division,(andrea.slade@bruker-nano.com)
Alexandre Berquand, Bruker Nano Surfaces Division(alexandre.berquand@bruker-nano.com)
Peter DeWolf, Bruker Nano Surfaces Division(peter.dewolf@bruker-nano.com)

26. H.K.L. Blackley, G.H.W. Sanders, M.C. Davies, C.J. Roberts, S.J.B.
Tendler, and M.J. Wilkinson, “In-situ Atomic Force Microscopy Study ofb-Amyloid Fibrillization,” J. Mol Biol. 298: 833 -40 (2000).

Bruker Nano Surfaces Division
Santa Barbara, CA · USA+1.805.967.1400/800.873.9750
productinfo@bruker-nano.com
8

www.bruker.com

and ScanAsyst are trademarks of Bruker Corporation. AN131, Rev. A0

17. S.J.T. van Noort, K.O. van der Werf, A.P.M. Eker, C. Wyman, B.G. de
Grooth, N.F. Van Hulst, and J. Greve, “Direct Visualization of Dynamic ProteinDNA Interactions with a Dedicated Atomic Force Microscope,” Biophys. J. 74:
2840 -49 (1998).

©2011 Bruker Corporation. All rights reserved. BioScope, Catalyst, PeakForce Tapping, PeakForce QNM, MIRO,

11. M. Bezanilla, B. Drake, E. Nudler, M. Kashlev, P.K. Hansma, and H.G.
Hansma, “Motion and Enzymatic Degradation of DNA in the Atomic ForceMicroscope,” Biophys. J. 67: 2454 -59 (1994).