characterization

Real-time multistep asymmetrical disassembly of nucleosomes and chromatosomes visualized by high-speed atomic force microscopy

During replication, expression, and repair of the eukaryotic genome, cellular machinery must access the DNA wrapped around histone proteins forming nucleosomes. These octameric protein·DNA complexes are modular, dynamic, and flexible and unwrap or disassemble either spontaneously or by the action of molecular motors. Thus, the mechanism of formation and regulation of subnucleosomal intermediates has gained attention genome-wide because it controls DNA accessibility.*

In the article “Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy” Bibiana Onoa, César Díaz-Celis, Cristhian Cañari-Chumpitaz, Antony Lee and Carlos Bustamante describe how they imaged nucleosomes and their more compacted structure with the linker histone H1 (chromatosomes) using high-speed atomic force microscopy to visualize simultaneously the changes in the DNA and the histone core during their disassembly when deposited on mica.*

Furthermore, Bibiana Onoa et al. trained a neural network and developed an automatic algorithm to track molecular structural changes in real time. *

The authors’ results show that nucleosome disassembly is a sequential process involving asymmetrical stepwise dimer ejection events. The presence of H1 restricts DNA unwrapping, significantly increases the nucleosomal lifetime, and affects the pathway in which heterodimer asymmetrical dissociation occurs. *

Bibiana Onoa et al. observe that tetrasomes are resilient to disassembly and that the tetramer core (H3·H4)2 can diffuse along the nucleosome positioning sequence. Tetrasome mobility might be critical to the proper assembly of nucleosomes and can be relevant during nucleosomal transcription, as tetrasomes survive RNA polymerase passage. These findings are relevant to understanding nucleosome intrinsic dynamics and their modification by DNA-processing enzymes. *

To characterize the nucleosomes dynamics in 2D, individual molecules were observed in buffer using an Ando-type high speed atomic force microscope together with NanoWorld Ultra-Short Cantilevers for HS-AFM of the USC-F1.2-K0.15 AFM probe type ( typical spring constant 0.15 N/m, typical resonance frequency in air 1200 kHz, resonance frequency 500–600 kHz in liquid). *

The AFM data presented in the article allow the authors to directly visualize the dynamics of DNA and histones during nucleosome and chromatosome disassembly, providing a simultaneous observation of DNA unwrapping and histone dissociation. *

The experimental and analytical strategy presented shows that real-time HS-AFM is a robust and powerful tool for studying single nucleosomes and chromatin dynamics. *

graphical abstract from Bibiana Onoa et al 2024 "Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy" - NanoWorld Ultra-Short Cantilevers of the USC-F1.2-k0.15 AFM probe type were used for the high-speed atomic force microscopy — graphical abstract from Bibiana Onoa et al 2024 “Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy”

*Bibiana Onoa, César Díaz-Celis, Cristhian Cañari-Chumpitaz, Antony Lee and Carlos Bustamante
Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy
ACS Central Science 2024, 10, 1, 122–137
DOI: https://doi.org/10.1021/acscentsci.3c00735

Open Access The article “Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy” by Bibiana Onoa, César Díaz-Celis, Cristhian Cañari-Chumpitaz, Antony Lee and Carlos Bustamante is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Kinetic-controlled Crystallization of α-FAPbI3 Inducing Preferred Crystallographic Orientation Enhances Photovoltaic Performance

Physical properties of the polycrystalline materials are mostly determined by their microstructure. As the crystallization process can determine the microstructure, the nucleation, and growth can also control whether the materials will be resulted in single crystalline or polycrystalline. Along with the morphological changes, anisotropic properties of the materials can also be controlled. *

As a result, preferential orientation with advanced optoelectronic properties can enhance the photovoltaic devices’ performance. *

Although incorporation of additives is one of the most studied methods to stabilize the photoactive α-phase of formamidinium lead tri-iodide (α-FAPbI3), no studies focus on how the additives affect the crystallization kinetics. *

In the article “Kinetic-Controlled Crystallization of α-FAPbI3 Inducing Preferred Crystallographic Orientation Enhances Photovoltaic Performance” along with the role of methylammonium chloride (MACl) as a “stabilizer” in the formation of α-FAPbI3, Sooeun Shin, Seongrok Seo, Seonghwa Jeong, Anir S. Sharbirin, Jeongyong Kim, Hyungju Ahn, Nam-Gyu Park and Hyunjung Shin point out the additional role as a “controller” in the crystallization kinetics. *

With microscopic observations, for example, electron backscatter diffraction and selected area electron diffraction, it is examined that higher concentration of MACl induces slower crystallization kinetics, resulting in larger grain size and [100] preferred orientation. *

Optoelectronic properties of [100] preferentially oriented grains with less non-radiative recombination, a longer lifetime of charge carriers, and lower photocurrent deviations in between each grain induce higher short-circuit current density (Jsc) and fill factor. *

Resulting MACl40 mol% attains the highest power conversion efficiency (PCE) of 24.1%.

The results provide observations of a direct correlation between the crystallographic orientation and device performance as it highlights the importance of crystallization kinetics resulting in desirable microstructures for device engineering. *

The electrical characterizations with atomic force microscopy (AFM) and conductive atomic force microscopy ( C-AFM) were done to measure the local conductance of FAPbI3 films. All measurements were performed under illumination (green LED) with a 1.3 V bias using a Pt-coated C-AFM probe (NanoWorld PlatinumIridium coated Pointprobe® CONTPt ). FTO was used for the conductive substrates. *

Conductive atomic force microscopy (C-AFM) indicated much more homogeneous photocurrent generation along the surface of (100) preferentially oriented layers. *

Figure 4 from Sooeun Shin et al. 2023 “Kinetic-Controlled Crystallization of α-FAPbI3 Inducing Preferred Crystallographic Orientation Enhances Photovoltaic Performance”:
Electrical properties of (100)-oriented α-FAPbI3 thin films. a,b) Surface topography and photocurrent measurement by C-AFM of MACl10% and MACl40%. Measurements were taken under illumination (green LED) with a 1.3 V bias. Current images indicate that photocurrents were induced grain by grain, as each grain showed a distinct photocurrent. The photocurrent deviation for each grain is larger in MACl10% than in MACl40%, which shows a similar photocurrent grain by grain. c,d) Current line profile extracted from the current image (a and b). The standard deviation calculated from the magnitude of the photocurrent in each grain is displayed in the inset (0.019 and 0.014 nA for MACl10% and MACl40%, respectively). A low photocurrent was exhibited at the grain boundaries in both MACl10% and MACl40%. The dark areas measured within the current images are most likely distributed between grain edges. This may be caused by the formation of PbI2 or the loss of contact between the grain and the conducting substrate.

*Sooeun Shin, Seongrok Seo, Seonghwa Jeong, Anir S. Sharbirin, Jeongyong Kim, Hyungju Ahn, Nam-Gyu Park and Hyunjung Shin
Kinetic-Controlled Crystallization of α-FAPbI3 Inducing Preferred Crystallographic Orientation Enhances Photovoltaic Performance
Advanced Science, Volume 10, Issue 14, May 17, 2023, 2300798
DOI: https://doi.org/10.1002/advs.202300798

Open Access The article “Kinetic-Controlled Crystallization of α-FAPbI3 Inducing Preferred Crystallographic Orientation Enhances Photovoltaic Performance” Sooeun Shin, Seongrok Seo, Seonghwa Jeong, Anir S. Sharbirin, Jeongyong Kim, Hyungju Ahn, Nam-Gyu Park and Hyunjung Shin is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Electrically and mechanically driven rotation of polar spirals in a relaxor ferroelectric polymer

Flux-closure structures, vortices/antivortices, skyrmions, and merons in oxides, metals and polymers represent non-trivial topologies in which a local polar/magnetic order undergoes quasi-continuous spatial variations in a host crystal lattice. These structures are now extensively studied due to emergent functionalities, but the application of electrical/mechanical fields has so far only served to destroy the polar topologies of interest. *

Topology created by quasi-continuous spatial variations of a local polarization direction represents an exotic state of matter, but field-driven manipulation has been hitherto limited to creation and destruction. *In the article “Electrically and mechanically driven rotation of polar spirals in a relaxor ferroelectric polymer” Mengfan Guo, Erxiang Xu, Houbing Huang, Changqing Guo, Hetian Chen, Shulin Chen, Shan He, Le Zhou, Jing Ma, Zhonghui Shen, Ben Xu, Di Yi, Peng Gao, Ce-Wen Nan, Neil. D. Mathur and Yang Shen report that relatively small electric or mechanical fields can drive the non-volatile rotation of polar spirals in discretized microregions of the relaxor ferroelectric polymer poly(vinylidene fluoride-ran-trifluoroethylene).*

These polar spirals arise from the asymmetric Coulomb interaction between vertically aligned helical polymer chains, and can be rotated in-plane through various angles with robust retention. *

Given also that their manipulation of topological order can be detected via infrared absorption, Mengfan Guo et al.’s work suggests a new direction for the application of complex materials. *

Mengfan Guo et al. produced a 100-nm-thick monolayer of face-on lamellae with vertically aligned polymer chains by melt-recrystallizing spin-coated thin films of P(VDF-TrFE).

The resulting melt-recrystallized thin film of the relaxor ferroelectric polymer was characterized by the authors using a commercial atomic force microscope for in-plane piezo-response force microscopy (IP-PFM).

NanoWorld Platinum Iridium coated Arrow-CONTPt AFM probes (typical resonant frequency: 14 kHz, typical force constant: 0.2 N/m, typical AFM tip radius 25 nm) were used for the in-plane (IP) PFM tests and the PFM lithography tests.

For piezo-response force microscopy (PFM) imaging, Vector mode was used where AFM tips were modulated at around 240 kHz for IP imaging, with the AC voltage set at 2 V. The images obtained by Vector Mode were double checked by using dual AC resonance tracking (DART) mode and the patterns could be reproduced. *

For angle-resolved IP-PFM tests, the rotation of sample was controlled by a protractor. To ensure identical position was imaged after rotating the sample, the authors made cross-scratches as a mark on the sample surface in advance. This method was applied to locate the scanning position in other situations if Mengfan Guo et al. had to move the sample in between the scanning probe microscopic studies.

For electric-field-induced manipulations using PFM lithography, the DC voltage on AFM tip was previously edited in the software. The scan speed was set at 1.95 Hz and no AC voltage was applied during the scanning. The DC voltage was divided by film thickness (100 nm) to obtain the electric field value. And an electric field with downward direction is defined with a positive sign.

For stress-induced manipulations, the deflection value of the PFM cantilever, which is a signal from photodetector, was preset to control the stress/force applied onto the sample. The difference in deflection value between a pressed AFM cantilever and a free AFM cantilever reflects how hard the AFM tip and sample surface are pressed to each other.*

To obtain the force value F, Mengfan Guo et al. first calibrated the AFM tips by the thermal noise method, and obtain the inverse optical lever sensitivity (InvOLS) and the spring constant k of the AFM tips.

The authors also conducted a polarization analysis based on their PFM measurements. *

To obtain the nominal toroidal order evaluated by the local curvature, the obtained IP-PFM amplitude image was firstly divided into 33 × 33 arrays, and each region was then subjected to a recognition of potential domain walls and measurement of an averaged curvature radius. *

To obtain polarization maps, angle-resolved IP-PFM images were first aligned to correct spatial distortion in nanoscale measurement. Positions with specific morphological characteristics were selected as reference points to determine the coordinate. After the correction, improved angle-resolved IP-PFM phase images would be divided into 64 × 64 arrays for deriving polarization maps. *

Fig. 1 from Mengfan Guo et al. (2024) “Electrically and mechanically driven rotation of polar spirals in a relaxor ferroelectric polymer”:Observation of a microregion containing an in-plane polar spiral. a Morphology of a melt-recrystallized thin film of the relaxor ferroelectric polymer. The scale bar is 2 μm. IP-PFM phase (b) and amplitude (c) images of the same area in a exhibiting concentric ring-shaped domains in curly stripe domains. d Distribution of domain wall curvatures in the same area in a–c evidencing nominal toroidal order. It is assumed that the local polarization is parallel to the nearest domain wall so that larger curvature (denoted red) reflects stronger toroidal order. IP-PFM phase images of identical concentric ring-shaped domains with the axis along vertical (e) and horizontal (f) measurement directions. The scale bar is 0.3 μm. The curl (g) and the divergence (h) of local polarization in the same area as e and f, revealing the polar spiral topology. i Schematic stereoscopic view of a CCW polar spiral, arrows represent regions of polarization. The red/blue arrows denote the polar source/sink that spirals in/out. The white arrows represent Néel rotation along the radial direction, as shown in more detail via the inset. NanoWorld Platinum Iridium coated Arrow-CONTPt AFM probes (typical resonant frequency: 14 kHz, typical force constant: 0.2 N/m, typical AFM tip radius 25 nm) were used for the in-plane (IP) PFM tests and the PFM lithography tests. — Fig. 1 from Mengfan Guo et al. (2024) “Electrically and mechanically driven rotation of polar spirals in a relaxor ferroelectric polymer”:
Observation of a microregion containing an in-plane polar spiral.
a Morphology of a melt-recrystallized thin film of the relaxor ferroelectric polymer. The scale bar is 2 μm. IP-PFM phase (b) and amplitude (c) images of the same area in a exhibiting concentric ring-shaped domains in curly stripe domains. d Distribution of domain wall curvatures in the same area in a–c evidencing nominal toroidal order. It is assumed that the local polarization is parallel to the nearest domain wall so that larger curvature (denoted red) reflects stronger toroidal order. IP-PFM phase images of identical concentric ring-shaped domains with the axis along vertical (e) and horizontal (f) measurement directions. The scale bar is 0.3 μm. The curl (g) and the divergence (h) of local polarization in the same area as e and f, revealing the polar spiral topology. i Schematic stereoscopic view of a CCW polar spiral, arrows represent regions of polarization. The red/blue arrows denote the polar source/sink that spirals in/out. The white arrows represent Néel rotation along the radial direction, as shown in more detail via the inset.

*Mengfan Guo, Erxiang Xu, Houbing Huang, Changqing Guo, Hetian Chen, Shulin Chen, Shan He, Le Zhou, Jing Ma, Zhonghui Shen, Ben Xu, Di Yi, Peng Gao, Ce-Wen Nan, Neil. D. Mathur and Yang Shen
Electrically and mechanically driven rotation of polar spirals in a relaxor ferroelectric polymer
Nature Communications volume 15, Article number: 348 (2024)
DOI: https://doi.org/10.1038/s41467-023-44395-5

The article “Electrically and mechanically driven rotation of polar spirals in a relaxor ferroelectric polymer” by Mengfan Guo, Erxiang Xu, Houbing Huang, Changqing Guo, Hetian Chen, Shulin Chen, Shan He, Le Zhou, Jing Ma, Zhonghui Shen, Ben Xu, Di Yi, Peng Gao, Ce-Wen Nan, Neil. D. Mathur and Yang Shen is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third-party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.