Biological physics by high-speed atomic force microscopy

Casuso, Ignacio; Redondo-Morata, Lorena; Rico, Félix

doi:10.1098/rsta.2019.0604

Cited by 23 publications

(16 citation statements)

References 131 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…By extensive improvements of AFM instruments, such as in the cantilevers, detectors, and scanners, HS-AFM has now materialized, resulting in capturing images of biological molecules within 100 ms or less [ 190 , 191 , 192 ]. HS-AFM imaging has captured a wide range of dynamic events in biomolecular processes [ 190 , 191 , 192 , 193 , 194 ]. Combining the DNA-origami frame (see Section 2.7 ) and HS-AFM, the dynamic behavior of biomolecular processes, such as enzymatic reactions [ 88 , 89 , 101 , 195 ] and DNA structural changes [ 103 , 104 , 196 ], has been directly observed at a nanolevel.…”

Section: Single-molecule Imaging For Biological Processesmentioning

confidence: 99%

DNA Manipulation and Single-Molecule Imaging

2021

View full text Add to dashboard Cite

DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

show abstract

Section: Single-molecule Imaging For Biological Processesmentioning

confidence: 99%

DNA Manipulation and Single-Molecule Imaging

2021

View full text Add to dashboard Cite

show abstract

“…This meant information on events could be gathered in the few tens of milliseconds range, allowing the possibility of investigating faster dynamics in biological events. High speed AFM has been used to study the process of DNA-protein interaction [ 85 ], DNA-translocation and looping by restriction enzyme EcoP15I [ 86 ], and DNA translational freedom [ 87 ], among other biological materials [ 88 , 89 ].…”

Section: Insights Into Helix Morphology: Microscopic Approachesmentioning

confidence: 99%

“…Graphene as ultrathin support for imaging [75][76][77] Cryogenic Electron Microscopy for imaging [78][79][80] Atomic Force Microscopy Imaging, force spectroscopies, and mechanical studies [81][82][83][84][85][86][87][88][89][90][91][92][93][94] Spectroscopic approaches…”

Section: Transmission Electron Microscopymentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

View full text Add to dashboard Cite

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

show abstract

“…Advancements in electronics, miniaturization of cantilevers, and improvement in piezoelectric scanner design have contributed to the continuous development of high-speed atomic force microscopy (HS-AFM) over the past two decades 1 . With its ~ 1000-fold higher imaging speed compared to conventional AFM and video-rate imaging capabilities up to 20 frames per seconds, HS-AFM permits visualizing conformational changes of proteins in real time 1 , 2 . HS-AFM is now routinely used to investigate the structural dynamics of biological molecules using different in vitro model system.…”

Section: Introductionmentioning

confidence: 99%

An ultra-wide scanner for large-area high-speed atomic force microscopy with megapixel resolution

Marchesi

Umeda

Komekawa

et al. 2021

Sci Rep

View full text Add to dashboard Cite

High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualizing the dynamics of individual biomolecules. However, in single-molecule HS-AFM imaging applications, x,y-scanner ranges are typically restricted to a few hundred nanometers, preventing overview observation of larger molecular assemblies, such as 2-dimensional protein crystal growth or fibrillar aggregation. Previous advances in scanner design using mechanical amplification of the piezo-driven x,y-positioning system have extended the size of HS-AFM image frames to several tens of micrometer, but these large scanners may suffer from mechanical instabilities at high scan speeds and only record images with limited pixel numbers and comparatively low lateral resolutions (> 20–100 nm/pixel), complicating single-molecule analysis. Thus, AFM systems able to image large sample areas at high speeds and with nanometer resolution have still been missing. Here, we describe a HS-AFM sample-scanner system able to record large topographic images (≤ 36 × 36 µm2) containing up to 16 megapixels, providing molecular resolution throughout the image frame. Despite its large size, the flexure-based scanner features a high resonance frequency (> 2 kHz) and delivers stable operation even at high scans speeds of up to 7.2 mm/s, minimizing the time required for recording megapixel scans. We furthermore demonstrate that operating this high-speed scanner in time-lapse mode can simultaneously identify areas of spontaneous 2-dimensional Annexin A5 crystal growth, resolve the angular orientation of large crystalline domains, and even detect rare crystal lattice defects, all without changing scan frame size or resolution. Dynamic processes first identified from overview scans can then be further imaged at increased frame rates in reduced scan areas after switching to conventional HS-AFM scanning. The added ability to collect large-area, high-resolution images of complex samples within biological-relevant time frames extends the capabilities of HS-AFM from single-molecule imaging to the study of large dynamic molecular arrays. Moreover, large-area HS-AFM scanning can generate detailed structural data sets from a single scan, aiding the quantitative analysis of structurally heterogenous samples, including cellular surfaces.

show abstract

Biological physics by high-speed atomic force microscopy

Cited by 23 publications

References 131 publications

DNA Manipulation and Single-Molecule Imaging

DNA Manipulation and Single-Molecule Imaging

DNA Studies: Latest Spectroscopic and Structural Approaches

An ultra-wide scanner for large-area high-speed atomic force microscopy with megapixel resolution

Contact Info

Product

Resources

About