Tag: USC-F0.3-k0.3

Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides

Ceramides are central intermediates of sphingolipid metabolism that also function as potent messengers in stress signaling and apoptosis. Progress in understanding how ceramides execute their biological roles is hampered by a lack of methods to manipulate their cellular levels and metabolic fate with appropriate spatiotemporal precision.*

In the article “Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides” Matthijs Kol, Ben Williams, Henry Toombs-Ruane, Henri G Franquelim, Sergei Korneev, Christian Schroeer, Petra Schwille, Dirk Trauner, Joost CM Holthuis and James A Frank report on clickable, azobenzene-containing ceramides, caCers, as photoswitchable metabolic substrates to exert optical control over sphingolipid production in cells.*

They combine atomic force microscopy on model bilayers with metabolic tracing studies in cells, and demonstrate that light-induced alterations in the lateral packing of caCers lead to marked differences in their metabolic conversion by sphingomyelin synthase and glucosylceramide synthase. These changes in metabolic rates are instant and reversible over several cycles of photoswitching. The findings described in the article disclose new opportunities to probe the causal roles of ceramides and their metabolic derivatives in a wide array of sphingolipid-dependent cellular processes with the spatiotemporal precision of light.*

The High-speed AFM in AC mode described in the article was done with NanoWorld Ultra-Short Cantilevers USC-F0.3-k0.3 with a typical stiffness of 0.3 N/m. The AFM cantilever oscillation was tuned to a frequency of 100–150 kHz and the amplitude kept below 10 nm. The scan rate was set to 25–150 Hz. Images were acquired at 256 × 256 pixel resolution. All measurements were performed at room temperature. The force applied on the sample was minimized by continuously adjusting the set point and gain during imaging. Height, error, deflection and phase-shift signals were recorded and images were line-fitted as required.*

Figure 2 b from “ Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides “ by Matthijs Kol et al. :
Photo-isomerization of caCers affects membrane fluidity and lipid domain structure in supported lipid bilayers.
(b) Atomic force microscopy of supported lipid bilayers ( SLBs )prepared as in (a). Isomerization of caCer-3 (top) and caCer-4 (bottom) to cis with UV-A light (365 nm) resulted in a fluidification inside the Lo domains, as indicated by the appearance of small fluid Ld lakes and an increased Ld/Lo area ratio. This effect was reversed on isomerization back to trans with blue light (470 nm), marked by a drop in the Ld/Lo area ratio. Scale bars, 2 μm. (c) Time-course plotting the normalized Lo area over multiple 365/470 nm irradiation cycles for caCer-3 (top) and caCer-4 (bottom).
Please refer to https://doi.org/10.7554/eLife.43230.007 for the full figure.

*Matthijs Kol, Ben Williams, Henry Toombs-Ruane, Henri G Franquelim, Sergei Korneev, Christian Schroeer, Petra Schwille, Dirk Trauner, Joost CM Holthuis, James A Frank
Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides
eLife 2019;8:e43230
DOI: 10.7554/eLife.43230
https://doi.org/10.7554/eLife.43230.001
https://doi.org/10.7554/eLife.43230.007

Please follow this external link to read the full article: https://elifesciences.org/articles/43230

Open Access The article “Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides “ by Matthijs Kol, Ben Williams, Henry Toombs-Ruane, Henri G Franquelim, Sergei Korneev, Christian Schroeer, Petra Schwille, Dirk Trauner, Joost CM Holthuis and  James A Frank 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/.

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions.*

In their article “Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability” Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin , Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller investigate the effect of long-term storage of the employed staple strands on DNA origami assembly and stability.*

Atomic force microscopy (AFM) under liquid and dry conditions was employed to characterize the structural integrity of Rothemund triangles assembled from different staple sets that have been stored at −20 °C for up to 43 months.*

NanoWorld Ultra-Short Cantilevers USC-F0.3-k0.3 were the AFM probes that were used for the AFM measurements under liquid conditions.*

Figure 1. from “Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability” by Charlotte Kielar et al.
(a) Schematic illustration of the Rothemund triangle DNA origami. AFM images of DNA origami triangles assembled from staple sets aged for (b) 2–7 months, (c) 11–16 months, (d) 22–27 months, and (e) 38–43 months. Measurements were performed either in liquid (left column) or dry conditions after gently dipping the sample into water (central column) or after harsh rinsing (right column). Scale bars represent 250 nm. Height scales are given in the individual images. The insets show zooms of individual DNA origami triangles.

*Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin , Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller
Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
Molecules 2019, 24(14), 2577
doi: https://doi.org/10.3390/molecules24142577

Please follow this external link to the full article: https://www.mdpi.com/1420-3049/24/14/2577/htm

Open Access: The article « Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability » by Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin , Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller 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/.

Membrane sculpting by curved DNA origami scaffolds

In the article “Membrane sculpting by curved DNA origami scaffolds” the authors show that “dependent on curvature, membrane affinity and surface density, DNA origami coats can indeed reproduce the activity of membrane-sculpting proteins such as BAR, suggesting exciting perspectives for using them in bottom-up approaches towards minimal biomimetic cellular machineries.”*

The AFM images for this article were taken in high-speed AC mode using NanoWorld Ultra-Short Cantilevers of the USC-F0.3-k0.3 type.

Supplementary Figure 5 b from Membrane sculpting by curved DNA origami scaffolds: Characterization of folded DNA origami nanoscaffolds. ( a ) Assembly of the folded bare origami structures L, Q, H was initially assessed via agarose gel (2%) electrophoresis analysis. Lanes containing marker DNA ladder (1kb) and M13 single - stranded p7249 sc affold (Sc) were also included. ( b ) Structure of folded bare origami L, Q and H was further validated using negative - stain transmission electron microscopy (TEM ; scale bar s : 100 nm ) and atomic force microscopy (AFM ; scale bar s : 200nm ).
Supplementary Figure 5 b from “Membrane sculpting by curved DNA origami scaffolds”:
Characterization of folded DNA origami nanoscaffolds.
b) Structure of folded bare origami L, Q and H was further validated using negative-stain transmission electron microscopy (TEM; scale bars: 100 nm) and atomic force microscopy (AFM; scale bars: 200nm).

*Henri G. Franquelim, Alena Khmelinskaia, Jean-Philippe Sobczak, Hendrik Dietz, Petra Schwille
Membrane sculpting by curved DNA origami scaffolds
Nature Communicationsvolume 9, Article number: 811 (2018)
DOI: https://doi.org/10.1038/s41467-018-03198-9

Please follow this link to the full article: https://rdcu.be/8zZi

Open Access: The article “Membrane sculpting by curved DNA origami scaffolds” by Franquelim et. al 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/.