Cargando…

Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level

Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator mo...

Descripción completa

Detalles Bibliográficos
Autores principales: Kabiri, Yoones, Angelin, Alessandro, Ahmed, Ishtiaq, Mutlu, Hatice, Bauer, Jens, Niemeyer, Christof M., Zandbergen, Henny, Dekker, Cees
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6470888/
https://www.ncbi.nlm.nih.gov/pubmed/30501011
http://dx.doi.org/10.1002/cbic.201800638
_version_ 1783411900098281472
author Kabiri, Yoones
Angelin, Alessandro
Ahmed, Ishtiaq
Mutlu, Hatice
Bauer, Jens
Niemeyer, Christof M.
Zandbergen, Henny
Dekker, Cees
author_facet Kabiri, Yoones
Angelin, Alessandro
Ahmed, Ishtiaq
Mutlu, Hatice
Bauer, Jens
Niemeyer, Christof M.
Zandbergen, Henny
Dekker, Cees
author_sort Kabiri, Yoones
collection PubMed
description Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis‐acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two‐dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide‐field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single‐molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA–dye association constants, number of dye molecules bound per base pair, and the electron‐scattering capacity of the metal‐containing ligands. These findings pave the way for the future development of electron dyes with specific DNA‐binding motifs for high‐resolution TEM imaging.
format Online
Article
Text
id pubmed-6470888
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-64708882019-04-19 Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level Kabiri, Yoones Angelin, Alessandro Ahmed, Ishtiaq Mutlu, Hatice Bauer, Jens Niemeyer, Christof M. Zandbergen, Henny Dekker, Cees Chembiochem Full Papers Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis‐acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two‐dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide‐field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single‐molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA–dye association constants, number of dye molecules bound per base pair, and the electron‐scattering capacity of the metal‐containing ligands. These findings pave the way for the future development of electron dyes with specific DNA‐binding motifs for high‐resolution TEM imaging. John Wiley and Sons Inc. 2019-02-07 2019-03-15 /pmc/articles/PMC6470888/ /pubmed/30501011 http://dx.doi.org/10.1002/cbic.201800638 Text en © 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Papers
Kabiri, Yoones
Angelin, Alessandro
Ahmed, Ishtiaq
Mutlu, Hatice
Bauer, Jens
Niemeyer, Christof M.
Zandbergen, Henny
Dekker, Cees
Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level
title Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level
title_full Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level
title_fullStr Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level
title_full_unstemmed Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level
title_short Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level
title_sort intercalating electron dyes for tem visualization of dna at the single‐molecule level
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6470888/
https://www.ncbi.nlm.nih.gov/pubmed/30501011
http://dx.doi.org/10.1002/cbic.201800638
work_keys_str_mv AT kabiriyoones intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT angelinalessandro intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT ahmedishtiaq intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT mutluhatice intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT bauerjens intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT niemeyerchristofm intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT zandbergenhenny intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel
AT dekkercees intercalatingelectrondyesfortemvisualizationofdnaatthesinglemoleculelevel