Height drift correction in non-raster atomic force microscopy

Meyer, Travis R.; Ziegler, Dominik; Brüne, Christoph; Chen, Alex; Farnham, Rodrigo; Huynh, Nen; Chang, Jen-Mei; Bertozzi, Andrea L.; Ashby, Paul D.

doi:10.1016/j.ultramic.2013.10.014

Cited by 28 publications

(13 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All reported resolutions are based on the gold standard FSC-0.143 criterion 57 and FSC-curves were corrected for the convolution effects of a soft mask using high-resolution noise-substitution 58 in RELION 3.1 as well as in cryoSPARC v3. All reconstructions were sharpened by applying a negative B -factor that was estimated using automated procedures 59 .…”

Section: Methodsmentioning

confidence: 99%

Structural basis for allosteric regulation of Human Topoisomerase IIα

et al. 2021

View full text Add to dashboard Cite

The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, structural information on this large dimeric assembly is limited to the catalytic domains, hindering the exploration of allosteric mechanism governing the enzyme activities and the contribution of its non-conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human Topo IIα nucleoprotein complex in different conformations solved at subnanometer resolutions (3.6–7.4 Å). Our data unveils the molecular determinants that fine tune the allosteric connections between the ATPase domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA-binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in modulating the enzyme’s activities and opens perspective for the analysis of post-translational modifications.

show abstract

Section: Methodsmentioning

confidence: 99%

Structural basis for allosteric regulation of Human Topoisomerase IIα

et al. 2021

View full text Add to dashboard Cite

show abstract

“…It must be noted that no tilt correction was applied to the presented images. The quality of the data obtained by the rotational scanning could be further improved by applying tilt correction for non-raster scanning trajectories [24] and sensor inpainting [13].…”

Section: Resultsmentioning

confidence: 99%

Rotational scanning atomic force microscopy

Ulčinas

Vaitekonis²

2017

Nanotechnology

View full text Add to dashboard Cite

A non-raster scanning technique for atomic force microscopy (AFM) imaging which combines rotational and translational motion is presented. The use of rotational motion for the fast scan axis allows us to significantly increase the scanning speed while imaging a large area (diameter > 30 μm). An image reconstruction algorithm and the factors influencing the resolution of the technique are discussed. The experimental results show the potential of the rotational scanning technique for high-throughput large area AFM investigation.

show abstract

“…Conversely, constructing a vertically symmetrical AFM instrument is difficult; thus, the vertical drift becomes larger than the horizontal drift. Therefore, several previous studies were aimed at correcting the vertical drift [4,5,11]. The other requirement is that the cross section around the reference profile should be uniform within the area of supposed drift, during the measurement, along the slow-scan axis.…”

Section: Methodsmentioning

confidence: 99%

“…(3) The height drift is corrected using self-intersecting scan paths to distinguish the drift from the surface topography. Observing the height differences when passing the same position at different times enables reconstruction of a continuous function for the drift [11].…”

Section: Introductionmentioning

confidence: 99%

A reference-scan-based method for correcting the nonlinear drift of atomic force microscopy at sub-nanometer precision

Kizu¹,

Misumi²,

Hirai³

et al. 2020

Meas. Sci. Technol.

View full text Add to dashboard Cite

A known fundamental issue with atomic force microscopy (AFM) is that drift occurs during an AFM measurement, distorting the AFM image. In this study, a method for correcting this nonlinear drift in two dimensions (the vertical axis and one of the two horizontal axes) is proposed and demonstrated. A normal AFM measurement is accomplished with many fast-scan profiles, using the raster scan method. In the proposed drift-correction method, the first-scanned profile is set as the reference profile, and the scan at the first-scanned location is inserted periodically during the normal profile scans. The normal scanned profiles are used to construct a normal AFM image, which is distorted by the drift. The time-dependent drift distance can be estimated by a series of the scanned reference profiles, and the distorted AFM image is corrected using this estimated distance. It is shown, experimentally, that the drift correction in two dimensions has both high resolution and repeatability at the sub-nanometer scale.

show abstract

Height drift correction in non-raster atomic force microscopy

Cited by 28 publications

References 20 publications

Structural basis for allosteric regulation of Human Topoisomerase IIα

Structural basis for allosteric regulation of Human Topoisomerase IIα

Rotational scanning atomic force microscopy

A reference-scan-based method for correcting the nonlinear drift of atomic force microscopy at sub-nanometer precision

Contact Info

Product

Resources

About