Visualizing water molecule distribution by atomic force microscopy

Kimura, Kenjiro; Ido, Shinichiro; Oyabu, Noriaki; Kobayashi, Kei; Hirata, Yoshiki; Imai, Takashi; Yamada, Hirofumi

doi:10.1063/1.3408289

Cited by 160 publications

(199 citation statements)

References 20 publications

(22 reference statements)

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“…Both SFA and atomic force microscopy (AFM) have been used to probe the structure of hydration water (Jarvis et al 2000;Kimura et al 2010;Li et al 2007). We focus here on AFM because, in principle, through the use of narrow tips (e.g., carbon nanotubes), this method could be used to sample narrow surface regions commensurate to point defects and surface heterogeneities (Avanesyan et al 2005).…”

Section: Atomic Force Microscopymentioning

confidence: 99%

From Interfacial Water to Macroscopic Observables: A Review

Striolo

2011

Adsorption Science & Technology

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ABSTRACT:The scientific community has always been fascinated by the properties of water and, consequently, a number of investigations continue to address this ubiquitous fluid responsible for life on this planet. Interfacial water plays an important role in a number of physical phenomena that include proteinfolding, structure/function relationships in enzymes, the design of nano-fluidic devices, and even macroscopic effects including drag reduction. Interfacial water is attracting renewed interest because of applications such as electrical double layer capacitors, and also for the microbial conversion of cellulose to biofuels. Current scientific explorations regarding interfacial water take advantage of innovations in experimental capabilities, theoretical models and computational tools. Particular attention has been devoted recently to uncovering the relationships between macroscopic properties, often summarized under the hydrophobic/hydrophilic characterization of solid surfaces, to the atomic-level behaviour of water near interfaces. The goal of the present review is to compile recent results obtained along these research objectives, for the most part obtained by simulation studies, to discuss some experimental techniques that appear most adequate to validate the simulation results (specular X-ray reflectivity, ultrafast IR spectroscopy, atomic force microscopy, and others), and to propose possible research topics to further develop this field. Because of our recent interests, the surfaces considered herein are mainly oxides.

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Section: Atomic Force Microscopymentioning

confidence: 99%

From Interfacial Water to Macroscopic Observables: A Review

Striolo

2011

Adsorption Science & Technology

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“…On the other hand, the importance of water distribution [7] and hydration in structural studies of biological macromolecules was directly shown by comparison of the AFM images of DNA obtained in air and in aqueous solutions [8]. The heights of DNA double helices and superhelices measured in air were more than twice lower than in water.…”

Section: Introductionmentioning

confidence: 99%

Global architecture of human poly(A)-specific ribonuclease by atomic force microscopy in liquid and dynamic light scattering

Niedzwiecka

Lekka

Nilsson

et al. 2011

Biophysical Chemistry

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Deadenylation is the initial and often rate-limiting step in the main pathways of eukaryotic mRNA decay. Poly(A)-specific ribonuclease (PARN) is a eukaryotic enzyme that efficiently degrades mRNA poly(A) tails. Structural and functional studies have shown that human PARN is composed of at least three functional domains, i.e. the catalytic nuclease domain and two RNA binding domains, the R3H and the RNA recognition motif (RRM), respectively. However, the complete structure of the full length protein is still unknown. We have investigated the global architecture of human PARN by atomic force microscopy (AFM) imaging in buffered milieu and report for the first time the dimensions of the full length protein at subnanometre resolution. The AFM images of single PARN molecules reveal compact ellipsoidal dimers (10.9 × 7.6 × 4.6 nm). The dimeric form of PARN was confirmed by dynamic light scattering (DLS) measurements that rendered a molecular weight of 161 kDa, in accordance with previous crystal structures of PARN fragments showing a dimeric composition. We discuss a putative internal arrangement of three functional domains within the full length PARN dimer.

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“…In contrast, several methods have recently been proposed for imaging 3D distribution of forces acting on a tip (F t ) near the sample surface. [16][17][18][19][20][21] In these methods, a tip is scanned in Z direction (i.e. perpendicular to the surface) as well as in XY directions to image the whole 3D interfacial space.…”

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confidence: 99%

Spatial Distribution of Lipid Headgroups and Water Molecules at Membrane/Water Interfaces Visualized by Three-Dimensional Scanning Force Microscopy

et al. 2012

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At biological interfaces, flexible surface structures and mobile water interact with each other to present non-uniform three-dimensional (3D) distributions. In spite of their impact on the biological functions, molecular-scale understanding of such phenomena has remained elusive. Here we show direct visualization of such interfacial structures with subnanometer-scale resolution by 3D scanning force microscopy (3D-SFM). We measured a 3D force distribution at an interface between a model biological membrane and buffer solution by scanning a sharp tip within the 3D interfacial space. We found that vertical cross sections of the 3D image taken along a specific lateral direction shows characteristic molecular-scale contrasts tilted at 30 • † Membrane/Water Interfaces Visualized by 3D-SFM

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Visualizing water molecule distribution by atomic force microscopy

Cited by 160 publications

References 20 publications

From Interfacial Water to Macroscopic Observables: A Review

From Interfacial Water to Macroscopic Observables: A Review

Global architecture of human poly(A)-specific ribonuclease by atomic force microscopy in liquid and dynamic light scattering

Spatial Distribution of Lipid Headgroups and Water Molecules at Membrane/Water Interfaces Visualized by Three-Dimensional Scanning Force Microscopy

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