Atomic Force Microscopy

A conceptually new family of microscopes emerged after the invention of the Scanning Tunneling Microscope (STM) by Binnig et al. in 1982. This family of instruments called Scanning Probe Microscopes (SPM) is based on the strong distance-dependent interaction between a sharp probe or tip and a sample. The Atomic Force Microscope therefore uses the force existing between the probe and the sample to build an image of an object. When thinking about how an AFM works, all notions of conventional microscope design need to be disregarded, since there are no lenses through which the operator looks at the sample.

AFM images are obtained rather by sensing with the probe than by seeing.

The central part of an AFM is therefore the tip that literally feels the sample. A nanometer sharp AFM tip made by micro-fabricating technology is grown on a flexible cantilever that is used as the transductor of the interaction between tip and sample. The reflection of a laser beam focused on the back side of the cantilever is used to amplify and measure the movement of the cantilever. The reflected beam is directed to a photodiode that provides a voltage depending on the position of the laser beam. In our AFM the sample moves with respect to the fixed tip, which is only allowed to move in vertical direction. The fine movements of tip and sample are provided by piezoelectric materials that can move with subnanometer precision. At each position the cantilever deflection is measured, from which a topography map can be constructed. Both tip and scanner are key features in any AFM setup and indeed it was the development of both micro-fabrication and piezoelectric technologies that made the rapid spread and availability of AFMs worldwide possible.

In our group we have two functional multimode AFMs from Nanotec Electronica that we apply to the high resolution characterization of multiple biological molecules both in ambient air and in liquid environment.

AFM-related papers of the group

Barbara Martin-Garcia*, Alejandro Martin-Gonzalez* et al. Nucleic Acids Research 14 May; gky370, (2018).
The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems.

Arroyo et al. Journal of Molecular Biology (2018). Volume 430, Issue 10, Pages 1495-1509. Available online 4 April 2018.
Supramolecular assembly of human pulmonary surfactant protein SP-D.

Fuentes-Pérez ME et al. Scientific Reports Feb 23; 7:43342. doi: 10.1038/srep43342 (2017).
TubZ filament assembly dynamics requires the flexible C-terminal tail.

Ares et al. Nanoscale 8,11818-11826 (2016).
High resolution atomic force microscopy of double-stranded RNA

Torreira et al. Structure 23(1), 183-189 (2015), (Accepted, Nov, 2014).
Amyloid fibers of the bacterial prionoid RepA-WH1 recapitulate the dimer to monomer transitions at initiation of DNA replication

Wegrzyn et al. Nucleic Acids Research 42(12), 7807-7818 (2014).
Sequence-specific interactions of Rep proteins with ssDNA in the AT-rich region of the plasmid replication origin

Carrasco et al. DNA Repair 20, 119-129 (2014) (cover article).
Single molecule approaches to monitor the recognition and resection of double-stranded DNA breaks during homologous recombination

Hernández-Ainsa et al. ACSnano 7 (7), 6024-6031 (2013).
DNA Origami Nanopores for Controlling DNA Translocation

Camunas-Soler et al. ACSnano 7 (6), 5102-5114 (2013).
Electrostatic Binding and Hydrophobic Collapse of Peptide-Nucleic Acid Aggregates Quantified Using Force Spectroscopy

N.A.W. Bell et al. Lab on a Chip 13, 1859-1862 (2013).
Multiplexed ionic current sensing with glass nanopores

M.E. Fuentes-Perez et al. Methods 60, 113-121 (2013).
AFM volumetric methods for the characterization of proteins and nucleic acids

Herrero-Galan et al. The Journal of the American Chemical Society 135(1), 122-131 (2013).
Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level

Moreno-Herrero and J. Gomez-Herrero.
AFM: basic concepts
Chapter in book Atomic Force Microscopy in Liquid. Biological Applications

Arturo M. Baro & Ronald G. Reifenberger, Editors
Wiley-VCH (2012) Print ISBN: 978-3-527-32758-4.

M.E. Fuentes-Perez et al. Biophysical Journal 102, 839-848 (2012).
Using DNA as a fiducial marker to study SMC complex interactions with the Atomic Force Micrsocope

Yeeles JTP et al. Molecular Cell 42, 806-816 (2011).
Recombination hotspots and single-stranded DNA binding proteins couple DNA translocation to DNA unwinding by the AddAB helicase-nuclease

S. Hormeno et al. Biophysical Journal 100, 1996-2006 (2011).
Mechanical Properties of High GoC-content DNA with A-type base-stacking


Univ. Autonoma de Madrid: Julio Gomez Herrero´s Group