http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

We report the specific transduction, via surface stress changes, of DNA hybridization and receptor-ligand binding into a direct nanomechanical response of microfabricated cantilevers. Cantilevers in an array were functionalized with a selection of biomolecules. The differential deflection of the cantilevers was found to provide a true molecular recognition signal despite large nonspecific responses of individual cantilevers. Hybridization of complementary oligonucleotides shows that a single base mismatch between two 12-mer oligonucleotides is clearly detectable. Similar experiments on protein A-immunoglobulin interactions demonstrate the wide-ranging applicability of nanomechanical transduction to detect biomolecular recognition.

https://science.sciencemag.org/content/sci/288/5464/316.full.pdf

Translating biomolecular recognition into nanomechanics.

Regarding the activation of chemical reactions, today’s chemist is used to thinking in terms of thermochemistry, electrochemistry, and photochemistry, which is reflected in the organization and content of the standard physical chemistry textbooks. The fourth way of chemical activation, mechanochemistry, is usually less well-known. The purpose of the present review is to give a survey of the classical works in mechanochemistry and put the key mechanochemical phenomena into perspective with recent results from atomic force microscopy and quantum molecular dynamics simulations. A detailed historical account on the development of mechanochemistry, with an emphasis on the mechanochemistry of solids, was recently given by Boldyrev and Tkáčová.1 The first written document of a mechanochemical reaction is found in a book by Theophrastus of Ephesus (371-286 B.C.), a student of Aristotle, “De Lapidibus” or “On stones”. If native cinnabar is rubbed in a brass mortar with a brass pestle in the presence of vinegar, metallic mercury is obtained. The mechanochemical reduction probably follows the reaction:1-3 * To whom correspondence should be addressed. Telephone: ++49-89-289-13417. Fax: ++49-89-289-13416. E-mail: martin.beyer@ch.tum.de (M.K.B.); Telephone: ++49-89-12651417. Fax: ++49-89-1265-1480. E-mail: clausen-schaumann@ fhm.edu (H.C.-S.). † Technische Universität München. ‡ Institut für Strahlenschutz. § Current address: Munich University of Applied Sciences. HgS + Cu f Hg + CuS (1) Volume 105, Number 8

http://depa.fquim.unam.mx/amyd/archivero/MECANOQUIMICA_3426.pdf

Mechanochemistry: the mechanical activation of covalent bonds.

The atomic force microscope (AFM) is a powerful tool for imaging individual biological molecules attached to a substrate and placed in aqueous solution. At present, however, it is limited by the speed at which it can successively record highly resolved images. We sought to increase markedly the scan speed of the AFM, so that in the future it can be used to study the dynamic behavior of biomolecules. For this purpose, we have developed a high-speed scanner, free of resonant vibrations up to 60 kHz, small cantilevers with high resonance frequencies (450–650 kHz) and small spring constants (150–280 pN/nm), an objective-lens type of deflection detection device, and several electronic devices of wide bandwidth. Integration of these various devices has produced an AFM that can capture a 100 × 100 pixel2 image within 80 ms and therefore can generate a movie consisting of many successive images (80-ms intervals) of a sample in aqueous solution. This is demonstrated by imaging myosin V molecules moving on mica (see http://www.s.kanazawa-u.ac.jp/phys/biophys/bmv_movie.htm).

/pdf/a-high-speed-atomic-force-microscope-for-studying-biological-4smr4a4q35.pdf

A high-speed atomic force microscope for studying biological macromolecules.

Because of its piconewton force sensitivity and nanometer positional accuracy, the atomic force microscope (AFM) has emerged as a powerful tool for exploring the forces and the dynamics of the interaction between individual ligands and receptors, either on isolated molecules or on cellular surfaces. These studies require attaching specific biomolecules or cells on AFM tips and on solid supports and measuring the unbinding forces between the modified surfaces using AFM force spectroscopy. In this review, we describe the current methodology for molecular recognition studies using the AFM, with an emphasis on strategies available for preparing AFM tips and samples, and on procedures for detecting and localizing single molecular recognition events.

https://www.rug.nl/research/biomaterials/publications/presentations/hjb4/hinterdorfer-nature_methods_2006.pdf

Detection and localization of single molecular recognition events using atomic force microscopy

We have used a simple process to fabricate small rectangular cantilevers out of silicon nitride. They have lengths of 9–50 μm, widths of 3–5 μm, and thicknesses of 86 and 102 nm. We have added metallic reflector pads to some of the cantilever ends to maximize reflectivity while minimizing sensitivity to temperature changes. We have characterized small cantilevers through their thermal spectra and show that they can measure smaller forces than larger cantilevers with the same spring constant because they have lower coefficients of viscous damping. Finally, we show that small cantilevers can be used for experiments requiring large measurement bandwidths, and have used them to unfold single titin molecules over an order of magnitude faster than previously reported with conventional cantilevers.

Small cantilevers for force spectroscopy of single molecules

We have used a prototype small cantilever atomic force microscope to observe, in real time, the interactions between individual protein molecules. In particular, we have observed individual molecules of the chaperonin protein GroES binding to and then dissociating from individual GroEL proteins, which were immobilized on a mica support. This work suggests that the small cantilever atomic force microscope is a useful tool for studying protein dynamics at the single molecule level.

/pdf/probing-protein-protein-interactions-in-real-time-50ybzc0lx4.pdf

Probing protein-protein interactions in real time.

This paper presents the first known image reconstruction of complex probe tip shapes and the removal of those shapes from reentrant topologies that are encountered in critical dimension (CD) measurements. Algorithm improvements are described that enable reentrant image reconstruction. In addition, a solution is presented which eliminates image artifacts that result from noise when using Legendre transform or “slope-matching” reconstruction techniques. The new methods are compared to existing technology and demonstrated on reentrant features. Although demonstrated with two-dimensional profiles, the methods are readily extendable to three-dimensional morphologies. Tip wear effects on CD measurement are investigated and compared with the previous state-of-the-art method (“tip width subtraction”) and fully reconstructed images, clearly showing superior measurement stability for the image reconstruction method. Finally, CD measurements derived from reconstructed images are compared directly with Hitachi S4000 ...

Tip characterization and surface reconstruction of complex structures with critical dimension atomic force microscopy

A method and apparatus for manipulating the surface of a sample including a cantilever, a first tip mounted on the cantilever, and a second tip mounted on the cantilever, the first and the second tip being configured to combine to form an imaging probe and to separate to form a manipulation probe. The first and second tips are configured to form a first position characterized in that the tips combine to form an imaging tip and the first and the second tip are configured to form a second position characterized in that the tips separate to manipulate particles on a surface of a sample. The tips can be configured to form the first position when a voltage is applied across the tips, and preferable extend downwardly from the cantilever substantially perpendicular thereto.

Method and apparatus for manipulating a sample

This invention provides a sensor to measure physical and/or chemical properties of viscous fluids. The sensor is based on microfabricated piezoresistive cantilevers. Deflection of these cantilevers is read out using, e.g., a wheatstone bridge to amplify and convert the deflection into a voltage output. The cantilevers and/or tips attached thereto, can be chemically or physically modified using reagents specific to interact with analytes to be detected in the fluid. The cantilevers can be integrated in a microfluidic system for easy fluid handling and the ability to manage small quantities of fluids.

Piezoresistive cantilever based nanoflow and viscosity sensor for microchannels

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