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Title: Imaging of Unstained DNA Origami Triangles with Electron Microscopy

Abstract

Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy of samples immobilized on bulk substrates. Less commonly used are electron microscopy techniques, typically carried out after negative staining of DNA structures or by using cryo-transmission electron microscopy (TEM). In this work, direct imaging of unstained DNA origami on common electron-transparent substrates with utilizing high angular annular dark field scanning transmission electron microscopy (HAADF-STEM) is reported. This approach establishes a method for depositing and imaging intact DNA triangles with mass-thickness contrast sufficient to measure the scaffold-to-scaffold distances and the length of the triangle's seam. The signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness is measured on three types of commercially available TEM grids. This allows for edge detection of ≈1 nm height DNA triangles on carbon substrates as thick as ≈25 nm. Observations on the effect on SNR with the imaging modes are discussed. The effect of cation concentration used for pretreating the grid on the image resolution is also explored. Finally, this work presents proof-of-concept results demonstrating that electron microscopy can be used to resolve key elements of the DNA origami triangle without the usemore » of staining protocols.« less

Authors:
 [1];  [2];  [2];  [2];  [3];  [2];  [2]; ORCiD logo [1]
  1. Ames Lab., Ames, IA (United States)
  2. Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States)
  3. Univ. of Pittsburgh, PA (United States)
Publication Date:
Research Org.:
Ames Laboratory (AMES), Ames, IA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division; USDOE
OSTI Identifier:
1557787
Alternate Identifier(s):
OSTI ID: 1557006
Report Number(s):
IS-J-9972
Journal ID: ISSN 2366-9608
Grant/Contract Number:  
AC02‐07CH11358; DE‐AC02‐07CH11358
Resource Type:
Accepted Manuscript
Journal Name:
Small Methods
Additional Journal Information:
Journal Name: Small Methods; Journal ID: ISSN 2366-9608
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; atomic force microscopy; DNA origami; scanning transmission electron microscopy; signal‐to‐noise ratio; unstained DNA

Citation Formats

Londono‐Calderon, Alejandra, Hossen, Md Mir, Palo, Pierre E., Bendickson, Lee, Vergara, Sandra, Nilsen‐Hamilton, Marit, Hillier, Andrew C., and Prozorov, Tanya. Imaging of Unstained DNA Origami Triangles with Electron Microscopy. United States: N. p., 2019. Web. doi:10.1002/smtd.201900393.
Londono‐Calderon, Alejandra, Hossen, Md Mir, Palo, Pierre E., Bendickson, Lee, Vergara, Sandra, Nilsen‐Hamilton, Marit, Hillier, Andrew C., & Prozorov, Tanya. Imaging of Unstained DNA Origami Triangles with Electron Microscopy. United States. doi:10.1002/smtd.201900393.
Londono‐Calderon, Alejandra, Hossen, Md Mir, Palo, Pierre E., Bendickson, Lee, Vergara, Sandra, Nilsen‐Hamilton, Marit, Hillier, Andrew C., and Prozorov, Tanya. Tue . "Imaging of Unstained DNA Origami Triangles with Electron Microscopy". United States. doi:10.1002/smtd.201900393.
@article{osti_1557787,
title = {Imaging of Unstained DNA Origami Triangles with Electron Microscopy},
author = {Londono‐Calderon, Alejandra and Hossen, Md Mir and Palo, Pierre E. and Bendickson, Lee and Vergara, Sandra and Nilsen‐Hamilton, Marit and Hillier, Andrew C. and Prozorov, Tanya},
abstractNote = {Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy of samples immobilized on bulk substrates. Less commonly used are electron microscopy techniques, typically carried out after negative staining of DNA structures or by using cryo-transmission electron microscopy (TEM). In this work, direct imaging of unstained DNA origami on common electron-transparent substrates with utilizing high angular annular dark field scanning transmission electron microscopy (HAADF-STEM) is reported. This approach establishes a method for depositing and imaging intact DNA triangles with mass-thickness contrast sufficient to measure the scaffold-to-scaffold distances and the length of the triangle's seam. The signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness is measured on three types of commercially available TEM grids. This allows for edge detection of ≈1 nm height DNA triangles on carbon substrates as thick as ≈25 nm. Observations on the effect on SNR with the imaging modes are discussed. The effect of cation concentration used for pretreating the grid on the image resolution is also explored. Finally, this work presents proof-of-concept results demonstrating that electron microscopy can be used to resolve key elements of the DNA origami triangle without the use of staining protocols.},
doi = {10.1002/smtd.201900393},
journal = {Small Methods},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {8}
}

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