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Cryopreservation of DNA Origami Nanostructures

Although DNA origami nanostructures have found their way into numerous fields of fundamental and applied research, they often suffer from rather limited stability when subjected to environments that differ from the employed assembly conditions, that is, suspended in Mg2+-containing buffer at moderate temperatures.*

In the article “Cryopreservation of DNA Origami Nanostructures” Yang Xin, Charlotte Kielar, Siqi Zhu, Christoph Sikeler, Xiaodan Xu, Christin Möser, Guido Grundmeier, Tim Liedl, Amelie Heuer-Jungemann, David M. Smith and Adrian Keller investigate means for efficient cryopreservation of 2D and 3D DNA origami nanostructures and, in particular, the effect of repeated freezing and thawing. It is found that, while the 2D DNA origami nanostructures maintain their structural integrity over at least 32 freeze–thaw cycles, ice crystal formation makes the DNA origami gradually more sensitive toward harsh sample treatment conditions. *

The cryoprotectants glycerol and trehalose are found to efficiently protect the DNA origami nanostructures against freeze damage at concentrations between 0.2 × 10−3and 200 × 10−3m and without any negative effects on DNA origami shape. This work thus provides a basis for the long-term storage of DNA origami nanostructures, which is an important prerequisite for various technological and medical applications. *

NanoWorld Ultra-Short Cantilevers for High-Speed AFM USC-F0.3-k0.3 were used for the AFM imaging in liquid of the DNA origami sample described in this article.

Figure 2 from “Cryopreservation of DNA Origami Nanostructures” by Yang Xin et al.:

AFM images of triangular DNA origami nanostructures after 32 freeze–thaw cycles measured a) in air and b) in liquid. AFM images of triangular DNA origami nanostructures assembled from scaffold and staple strands that were subjected to 32 freeze–thaw cycles measured c) in air and d) in liquid. Images have a size of 1.5 × 1.5 μm2 and height scales are 2.3 nm. — Figure 2 from “*Cryopreservation of DNA Origami Nanostructures*” by Yang Xin et al.:

AFM images of triangular DNA origami nanostructures after 32 freeze–thaw cycles measured a) in air and b) in liquid. AFM images of triangular DNA origami nanostructures assembled from scaffold and staple strands that were subjected to 32 freeze–thaw cycles measured c) in air and d) in liquid. Images have a size of 1.5 × 1.5 μm2 and height scales are 2.3 nm.

*Yang Xin, Charlotte Kielar, Siqi Zhu, Christoph Sikeler, Xiaodan Xu, Christin Möser, Guido Grundmeier, Tim Liedl, Amelie Heuer-Jungemann, David M. Smith and Adrian Keller
Cryopreservation of DNA Origami Nanostructures
Small 2020, 16, 1905959
DOI: 10.1002/smll.20190595

Please follow this external link to read the full article: https://onlinelibrary.wiley.com/doi/pdf/10.1002/smll.201905959

Open Access The article “ Cryopreservation of DNA Origami Nanostructures “ by Yang Xin, Charlotte Kielar, Siqi Zhu, Christoph Sikeler, Xiaodan Xu, Christin Möser, Guido Grundmeier, Tim Liedl, Amelie Heuer-Jungemann, 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/.

Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas

Dietary fibers have been shown to exert immune effects via interaction with pattern recognition receptors (PRR) such as toll-like receptors (TLR) and nucleotide-binding oligomerization domain (NOD)-like receptors. Pectin is a dietary fiber that interacts with PRR depending on its chemical structure. Papaya pectin retains different chemical structures at different ripening stages. How this influences PRR signalling is unknown.*

The aim of the article “Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas” by Samira B. R. Prado, Martin Beukema, Eva Jermendi, Henk A. Schols, Paul de Vos and João Paulo Fabi was to determine how ripening influences pectin structures and their ability to interact with TLR2, 3, 4, 5 and 9, and NOD1 and 2.*

Papaya ripening is an enzymatic, biochemically driven process that occurs over a short period of time (five days) and involves the mobilization of pectin and the alteration of its chemical composition.

The authors evaluated the interaction of the water-soluble fractions rich in pectin extracted from unripe to ripe papayas. The pectin extracted from ripe papayas activated all the TLR and, to a lesser extent, the NOD receptors. The pectin extracted from unripe papayas also activated TLR2, 4 and 5 but inhibited the activation of TLR3 and 9.*

During papaya ripening, profound changes in pectin structures lead to differences in the biological effects. The data presented in the paper show that papaya pectin extracted from fruit pulp at different ripening points differently interacted with PRR in a ripening-dependent way. The longer chains of HG from unripe papayas pectin, which were less methyl-esterified, inhibited the activation of TLR3 and 9 and activated TLR2 and 4, in contrast to the ripe papaya’s pectin, which have smaller HG chains with medium methyl esterification thus activating TLR2, 3, 4, 5 and 9.*

This variation may represent new biological features of papaya pectin structures in addition to anticancer activities, possibly creating new and cost-effective approaches to extracting papaya pectin with desirable structural and biological features.*

These findings might lead to selection of ripening stages for tailored modulation of PRR to support or attenuate immunity in consumers.*

The changes in Molecular weight ( Mw ) can also be visualized by Atomic Force Microscopy (see Fig. 1C in the paper.)

The AFM images presented in the paper were acquired in tapping mode using an NanoWorld Pointprobe® NCHR AFM probe with a typical spring constant of 42 N/m and typically 320 kHz resonance frequency. The scan speed and scanning resolution were 0.5 Hz and 512 × 512 points, respectively.*

Figure 1 C from “Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas” by Samira B. R. Prado et al. 2020:
(C) Representative topographical AFM images of Un-1-WSF and R-2-WSF. White arrow indicates linear structures, black arrow aggregates and grey arrow the smaller structure from the R-2-WSF. Un-1-WSF: unripe – papaya from 1st day after harvest – water-soluble fraction; Un-2-WSF: unripe – papaya from 2nd day after harvest – water-soluble fraction; I-WSF: intermediate ripening time point – papaya from 3rd day after harvest – water-soluble fraction; R-1-WSF: ripe – papaya from 4th day after harvest – water-soluble fraction; R-2-WSF: ripe – papaya from 5th day after harvest – water-soluble fraction. Please have a look at the full article for the full figure.

*Samira B. R. Prado, Martin Beukema, Eva Jermendi, Henk A. Schols, Paul de Vos and João Paulo Fabi
Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas
Nature Scientific Reports volume 10, Article number: 1690 (2020)
DOI: https://doi.org/10.1038/s41598-020-58311-0

Please follow this external link to read the full article htt ps://rdcu.be/b3Fnb .

Open Access The article “ Pectin Interaction with Immune Receptors is Modulated by Ripening Process in Papayas “ by Samira B. R. Prado, Martin Beukema, Eva Jermendi, Henk A. Schols, Paul de Vos and João Paulo Fabi 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/.

KPFM surface photovoltage measurement and numerical simulation

Kelvin Probe Force Microscopy ( KPFM ) is a scanning probe microscopy technique. It is a combination of the Kelvin probe and of Atomic Force Microscopy methods. The technique consists in evaluating the difference in work function between two conducting materials, by using a nanometer scale tip ( the “KPFMtip”), and placing it close to the material to be characterised, where a difference in work function leads to an electrostatic force developing between the two, which is translated as an oscillation of the tip’s cantilever. A bia sapplied via an external circuit is varied until the force and hence the electrostatic field between sample and KPFM tip is cancelled.*

In the article “KPFM surface photovoltage measurement and numerical simulation” Clément Marchat, James P. Connolly, Jean-Paul Kleider, José Alvarez, Lejo J. Koduvelikulathu and Jean Baptiste Puel present a method for the analysis of Kelvin probe force microscopy (KPFM) characterization of semiconductor devices.
It enables evaluation of the influence of defective surface layers. The model is validated by analysing experimental KPFM measurements on crystalline silicon samples of contact potential difference (VCPD) in the dark and under illumination, and hence the surface photovoltage (SPV). It is shown that the model phenomenologically explains the observed KPFM measurements. It reproduces the magnitude of SPV characterization as a function of incident light power in terms of a defect density assuming Gaussian defect distribution in the semiconductor bandgap. This allows an estimation of defect densities in surface layers of semiconductors and therefore increased exploitation of KPFM data.*

The KPFM measurements were performed using NanoWorld ARROW-EFM conductive AFM tips with a PtIr coating.
The tip work function didn’t require calibration because only SPV measurement were performed and studied. Measurements were performed in the KPFM amplitude modulation (AM)mode rather than the frequency modulation (FM) one. The AM mode was chosen because lateral resolution was not a problem on the homogeneous bulk samples studied, allowing focus on the superior surface potential resolution that can be achieved with the AM mode.*

Fig. 1 from “*KPFM surface photovoltage measurement and numerical simulation*” by Clément Marchat et al:
Kelvin probe force microscopy setup schematic. The conducting cantilever carrying the KPFM tip is scanned over a surface while AC + DC potential is applied. The AC signal is a sinusoid whose frequency matches the mechanical resonance of the cantilever. The four-quadrant detector provides feedback in order to minimise cantilever oscillation by varying the DC signal thereby yielding the sample work function compared to the tip one.

*Clément Marchat, James P. Connolly, Jean-Paul Kleider, José Alvarez, Lejo J. Koduvelikulathu and Jean Baptiste Puel
KPFM surface photovoltage measurement and numerical simulation
EPJ Photovoltaics10, 3 (2019)
DOI: https://doi.org/10.1051/epjpv/2019002

Please follow this external link to read the full article: https://www.epj-pv.org/articles/epjpv/abs/2019/01/pv180014/pv180014.html

Open Access The article “KPFM surface photovoltage measurement and numerical simulation “ by Clément Marchat, James P. Connolly, Jean-Paul Kleider, José Alvarez, Lejo J. Koduvelikulathu and Jean Baptiste Puel 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/.