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AFM for Research of Biomolecules, Membranes, and Biomolecular Assemblies

Atomic force microscopy image shows the sub-structure of actin filaments

Atomic force microscopy is a powerful tool capable of resolving the structure of molecules under near-physiological conditions. Samples can be imaged in their native state: fully hydrated and at biologically relevant temperatures. No additional sample processing, such as fixation, coating, and dehydration, is required. A key strength of the AFM is its ability to monitor dynamic events. Due to its minimal sample preparation, the interaction between molecules and the response of molecules to external factors can be observed. Another capability is the AFM’s ability to measure the mechanical properties of molecules. Piconewton forces can be detected and intra- and inter-molecular forces can be measured. This allows researchers to increase their understanding of protein dynamics, such as how proteins are assembled and the forces needed to unravel them.

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  • High resolution imaging of biomolecules and biomembranes (sub-nanometer lateral, sub-Angstrom vertical resolution)
  • Operate in biologically relevant solutions
  • Fluid exchange (e.g. change buffer composition, add other biomolecules, drugs, etc. in solution)
  • Single molecule force spectroscopy
  • DNA structure and DNA-protein interactions
  • DNA origami
  • Structure of membrane proteins
  • Protein aggregation / fibril formation (e.g. amyloid, actin, insulin)
  • Pulling modular proteins
  • Lipid bilayers / supported lipid bilayers

J. N. Abraham, D. Kedracki, E. Prado, C. Gourmel, P. Maroni, and C. Nardin, "Effect of the Interaction of the Amyloid β (1-42) Peptide with Short Single-Stranded Synthetic Nucleotide Sequences: Morphological Characterization of the Inhibition of Fibrils Formation and Fibrils Disassembly," Biomacromolecules 15, 3253-3258 (2014). doi:10.1021/bm501004q

R. B. Best, S. B. Fowler, J. L. T. Herrera, A. Steward, E. Paci, and J. Clarke, "Mechanical Unfolding of a Titin Ig Domain: Structure of Transition State Revealed by Combining Atomic Force Microscopy, Protein Engineering and Molecular Dynamics Simulations," J. Mol. Biol. 330, 867-877 (2003). doi:10.1016/s0022-2836(03)00618-1

R. B. Best, B. Li, A. Steward, V. Daggett, and J. Clarke, "Can Non-Mechanical Proteins Withstand Force? Stretching Barnase by Atomic Force Microscopy and Molecular Dynamics Simulation," Biophys. J. 81, 2344-2356 (2001). doi:10.1016/s0006-3495(01)75881-x

S. A. Contera, K. Voïtchovsky, and J. F. Ryan, "Controlled ionic condensation at the surface of a native extremophilemembrane," Nanoscale 2, 222-229 (2010). doi:10.1039/b9nr00248k

Y. Ebenstein, N. Gassman, S. Kim, and S. Weiss, "Combining atomic force and fluorescence microscopy for analysis of quantum-dot labeled protein-DNA complexes," J. Mol. Recognit. 22, 397-402 (2009). doi:10.1002/jmr.956

C. A. Grant, D. J. Brockwell, S. E. Radford, and N. H. Thomson, "Effects of hydration on the mechanical response of individual collagen fibrils," Appl. Phys. Lett. 92, 233902 (2008). doi:10.1063/1.2937001

S. Guo, and B. B. Akhremitchev, "Packing Density and Structural Heterogeneity of Insulin Amyloid Fibrils Measured by AFM Nanoindentation," Biomacromolecules 7, 1630-1636 (2006). doi:10.1021/bm0600724

C. wen Hsieh, and S. Hsieh, "Nanoparticle chain formation on functional surfaces using insulin fibrils as a structure directing agent," J. Mater. Chem. 21, 16900 (2011). doi:10.1039/c1jm10136f

M. S. Z. Kellermayer, A. Karsai, M. Benke, K. Soos, and B. Penke, "Stepwise dynamics of epitaxially growing single amyloid fibrils," PNAS 105, 141-144 (2007). doi:10.1073/pnas.0704305105

A. S. Mostaert, R. Crockett, G. Kearn, I. Cherny, E. Gazit, L. C. Serpell, and S. P. Jarvis, "Mechanically functional amyloid fibrils in the adhesive of a marine invertebrate as revealed by Raman spectroscopy and atomic force microscopy," Arch. Histol. Cytol. 72, 199-207 (2009). doi:10.1679/aohc.72.199

A. S. Mostaert, M. J. Higgins, T. Fukuma, F. Rindi, and S. P. Jarvis, "Nanoscale Mechanical Characterisation of Amyloid Fibrils Discovered in a Natural Adhesive," J. Biol. Phys. 32, 393-401 (2006). doi:10.1007/s10867-006-9023-y

E. Oroudjev, J. Soares, S. Arcidiacono, J. B. Thompson, S. A. Fossey, and H. G. Hansma, "Segmented nanofibers of spider dragline silk: Atomic force microscopy and single-molecule force spectroscopy," PNAS 99, 6460-6465 (2002). doi:10.1073/pnas.082526499

M. Schlierf, and M. Rief, "Temperature Softening of a Protein in Single-molecule Experiments," J. Mol. Biol. 354, 497-503 (2005). doi:10.1016/j.jmb.2005.09.070

K. H. Sheikh, C. Giordani, J. I. Kilpatrick, and S. P. Jarvis, "Direct Submolecular Scale Imaging of Mesoscale Molecular Order in Supported Dipalmitoylphosphatidylcholine Bilayers," Langmuir 27, 3749-3753 (2011). doi:10.1021/la104640v

A. G. Végh, K. Nagy, Z. Bálint, Á. Kerényi, Gá. Rákhely, G. Váró, and Z. Szegletes, "Effect of Antimicrobial Peptide-Amide: Indolicidin on Biological Membranes," J. Biomed. Biotechnol. 2011, 1-6 (2011). doi:10.1155/2011/670589

K. Voïtchovsky, S. A. Contera, M. Kamihira, A. Watts, and J. Ryan, "Differential Stiffness and Lipid Mobility in the Leaflets of Purple Membranes," Biophys. J. 90, 2075-2085 (2006). doi:10.1529/biophysj.105.072405

N. Y. Wong, C. Zhang, L. H. Tan, and Y. Lu, "Site-Specific Attachment of Proteins onto a 3D DNA Tetrahedron through Backbone-Modified Phosphorothioate DNA," Small 7, 1427-1430 (2011). doi:10.1002/smll.201100140

R. Zhang, X. Hu, H. Khant, S. J. Ludtke, W. Chiu, M. F. Schmid, C. Frieden, and J.-M. Lee, "Interprotofilament interactions between Alzheimer's Aβ1-42 peptides in amyloid fibrils revealed by cryoEM," PNAS 106, 4653-4658 (2009). doi:10.1073/pnas.0901085106