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

Yoones Kabiri, Alessandro Angelin, Ishtiaq Ahmed, Hatice Mutlu, Jens Bauer, Christof M. Niemeyer, Henny Zandbergen, Cees Dekker

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)
102 Downloads (Pure)

Abstract

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.

Original languageEnglish
Pages (from-to)822-830
JournalChemBioChem
Volume20
Issue number6
DOIs
Publication statusPublished - 2019

Keywords

  • contrast agents
  • DNA
  • intercalation
  • scanning transmission electron microscopy
  • single-molecule studies

Fingerprint Dive into the research topics of 'Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level'. Together they form a unique fingerprint.

  • Cite this