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/.

In Situ Molecular-Level Observation of Methanol Catalysis at the Water–Graphite Interface

“Methanol occupies a central role in chemical synthesis and is considered an ideal candidate for cleaner fuel storage and transportation. It can be catalyzed from water and volatile organic compounds, such as carbon dioxide, thereby offering an attractive solution for reducing carbon emissions.”*

In “In Situ Molecular-Level Observation of Methanol Catalysis at the Water–Graphite Interface” the authors show that graphite immersed in ultrapure water is able to spontaneously catalyze methanol from volatile organic compounds in ambient conditions. Using single-molecule resolution atomic force microscopy (AFM) in liquid, they directly observe the formation and evolution of methanol–water nanostructures at the surface of graphite.*
The findings described in this article could have a significant impact on the development of organic catalysts and on the function of nanoscale carbon devices

NanoWorld ARROW-UHFAuD AFM probes were used for the Atomic Force Microscopy imaging in liquid.

Figure 1 from “In Situ Molecular-Level Observation of Methanol Catalysis at the Water–Graphite Interface” by W. Foster et al.: High-resolution amplitude modulation AFM imaging of HOPG immersed in initially ultrapure water. (a) A solid-like patch formed by the self-assembly of molecules (dashed white outline) nucleates from an atomic step at the HOPG surface (dashed black line). The molecular self-assembly is observed here in situ as it progressively grows across the HOPG surface over a period of 9 min, with the patch edges moving away from the step. Rowlike structures with a periodicity of 4.30 ± 0.28 nm as visible within the patch. (b) Sub-nanometer imaging of other structures reveals detailed features (0.79 ± 0.08 nm periodicity, red arrows) perpendicular to the main rows (periodicity 2.45 ± 0.08 nm, white arrow). The exact molecular arrangement is not known, but strongly reminiscent of the alternated water–methanol nanoribbons recently reported by our group.(22) The white scale bars are 100 nm in (a) and 1 nm in (b). The purple color scale bar represents a topographic variation of 20 Å in (a) and 1 Å nm in (b). The blue scale bar represents a phase variation of 20° in (a) and 10° in (b). In (a) the time lapse between the first and second frames is 1 min and then 4 min elapses between the subsequent frames. NanoWorld Arrow-UHFAuD AFM probes were used.
Figure 1 from “In Situ Molecular-Level Observation of Methanol Catalysis at the Water–Graphite Interface” by W. Foster et al.: High-resolution amplitude modulation AFM imaging of HOPG immersed in initially ultrapure water. (a) A solid-like patch formed by the self-assembly of molecules (dashed white outline) nucleates from an atomic step at the HOPG surface (dashed black line). The molecular self-assembly is observed here in situ as it progressively grows across the HOPG surface over a period of 9 min, with the patch edges moving away from the step. Rowlike structures with a periodicity of 4.30 ± 0.28 nm as visible within the patch. (b) Sub-nanometer imaging of other structures reveals detailed features (0.79 ± 0.08 nm periodicity, red arrows) perpendicular to the main rows (periodicity 2.45 ± 0.08 nm, white arrow). The exact molecular arrangement is not known, but strongly reminiscent of the alternated water–methanol nanoribbons recently reported by our group.(22) The white scale bars are 100 nm in (a) and 1 nm in (b). The purple color scale bar represents a topographic variation of 20 Å in (a) and 1 Å nm in (b). The blue scale bar represents a phase variation of 20° in (a) and 10° in (b). In (a) the time lapse between the first and second frames is 1 min and then 4 min elapses between the subsequent frames

*William Foster, Juan A. Aguilar, Halim Kusumaatmaja, Kislon Voϊtchovsky
In Situ Molecular-Level Observation of Methanol Catalysis at the Water–Graphite Interface
ACS Appl. Mater. Interfaces, 2018, 10 (40), pp 34265–34271
DOI: 10.1021/acsami.8b12113

Please follow this external link for the full article: https://pubs.acs.org/doi/full/10.1021/acsami.8b12113

Open Access The article “In Situ Molecular-Level Observation of Methanol Catalysis at the Water–Graphite Interface” by William Foster, Juan A. Aguilar, Halim Kusumaatmaja and Kislon Voϊtchovsky 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/.

Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid

Researchers from the Physics Department at Durham University demonstrate an imaging technique using Atomic Force Microscopy in their JoVE Engineering publication.

For each step, the authors have explained the scientific rationale behind their choices to facilitate the adaptation of the methodology to every user’s specific system.

The NanoWorld Arrow-UHF AFM probe for high speed AFM is also mentioned in this publication.

Ethan J. Miller, William Trewby, Amir Farokh Payam, Luca Piantanida, Clodomiro Cafolla, Kislon  Voïtchovsky, Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid (2016), JoVE, 1940-087X, doi:10.3791/54924

https://www.jove.com/video/54924/sub-nanometer-resolution-imaging-with-amplitude-modulation-atomic

AM-AFM images of hard samples in fluid solutions
AM-AFM images of hard samples in fluid solutions. – figure from Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid Jove.com – please refer to link above for the full article

 

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