Molecular Recognition and Adhesion of Individual DNA Strands Studied by Dynamic Force Microscopy

Grange, Wilfried; Strunz, Torsten; Schumakovitch, Irina; Güntherodt, H.‐J.; Hegner, Martin

doi:10.1002/1438-5171(200107)2:2<75::aid-simo75>3.0.co;2-8

Cited by 27 publications

(6 citation statements)

References 23 publications

(22 reference statements)

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“…This dependence is physically reasonable; for example, the maximal length of a duplex that will spontaneously dissociate (rupture at f = 0) in a time scale of milliseconds is clearly much less than the maximal length that will spontaneously dissociate in a time scale of years. It is also consistent with the fact that, when stress is increased over time, rather than held constant, the duplex rupture force increases with the rate at which the force is applied. − ,− Nevertheless, regardless of how long the observation time, for infinite length chains, the critical force will still plateau at f c (∞) = Δ G bp /δ; this limiting behavior is simply reached more slowly with N for larger τ obs .…”

supporting

confidence: 69%

“…Conversely, stress-induced rupture has also been proposed as a method to detect sequence complementarity . The importance of the response of DNA to stress and recent progress in single-molecule force spectroscopy techniques , have led to many detailed investigations of stress-induced duplex disruption. − Simultaneously, theoretical models have been developed to predict and explain the experimental results. ,,,− ,− …”

mentioning

confidence: 99%

“…Shearing of a duplex involves applying antiparallel forces to either the opposite 3′–3′ or 5′–5′ ends of the bound duplex, as shown in Figure a. Such a setup has been explored experimentally ,− ,− and theoretically. ,,,,,,,, In early experiments, − ,− loads were increased dynamically; more recently, Hatch et al were able to use a constant force . Clearly, for any nonzero constant force, the stable state involves widely separated strands: the energetic benefit of an arbitrarily large separation necessarily overwhelms any attractive interactions.…”

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confidence: 99%

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Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

et al. 2015

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The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.

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supporting

confidence: 69%

mentioning

confidence: 99%

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confidence: 99%

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Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

et al. 2015

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“…These studies reveal that the average dissociation force increases logarithmically with the pulling speed as has been found in the study of intermolecular protein-protein interactions (see section 5.2.1). Similar experiments have been carried out to investigate the kinetics of short DNA hairpins using SMF [161,162] or AFM [163][164][165][166][167], finding slower kinetics of unfolding/refolding depending on the length of the sequence as predicted by some theoretical models [133,168]. Mechanical unfolding of single RNA molecules through nanopores has also been proposed as a method to determine the secondary structure [169].…”

Section: Systemsmentioning

confidence: 90%

Single-molecule experiments in biological physics: methods and applications

Ritort

2006

J. Phys.: Condens. Matter

389

463

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Abstract. I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques.

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“…AFM can be used to measure the force in a wide range from 10 to 10 6 pN [19], which is suitable for measuring the small adhesion forces between biomolecules, including DNA entanglement [20], antigen-antibody complexes [21] and cellintegrin binding [9]. However, the AFM tip is made of silicon or silicon nitride.…”

Section: Introductionmentioning

confidence: 99%

Interactions between chitosan and cells measured by AFM

Hsiao¹,

Thiện²,

Ho³

et al. 2010

Biomed. Mater.

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Chitosan, a biocompatible material that has been widely used in bone tissue engineering, is believed to have a high affinity to osteoblastic cells. This research is the first to prove this hypothesis. By using atomic force microscopy (AFM) with a chitosan-modified cantilever, quantitative evaluation of the interforce between chitosan and cells was carried out. A chitosan tip functionalized with Arg-Gly-Asp (RGD) was also used to measure the interforce between RGD-chitosan and osteoblastic cells. This research concluded by examining cell adhesion and spreading of chitosan substrates as further characterization of the interactions between cells and chitosan. The force measured by AFM showed that the interforce between chitosan and osteoblasts was the highest (209 nN). The smallest adhesion force (61.8 nN) appeared between chitosan and muscle fibroblasts, which did not demonstrate any osteoblastic properties. This result proved that there was a significant interaction between chitosan and bone cells, and correlated with the observations of cell attachment and spreading. The technique developed in this research directly quantified the adhesion between chitosan and cells. This is the first study to demonstrate that specific interaction exists between chitosan and osteoblasts.

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Molecular Recognition and Adhesion of Individual DNA Strands Studied by Dynamic Force Microscopy

Cited by 27 publications

References 23 publications

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

Single-molecule experiments in biological physics: methods and applications

Interactions between chitosan and cells measured by AFM

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