Imaging of Unstained DNA Origami Triangles with Electron Microscopy
Abstract
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). Here, 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. 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 stainingmore »
- Authors:
-
[1]
- Ames Lab., Ames, IA (United States)
- Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States)
- 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 Volume: 3; Journal Issue: 12; 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. https://doi.org/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. https://doi.org/10.1002/smtd.201900393. https://www.osti.gov/servlets/purl/1557787.
@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 = {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). Here, 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. 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 = 12,
volume = 3,
place = {United States},
year = {Tue Aug 13 00:00:00 EDT 2019},
month = {Tue Aug 13 00:00:00 EDT 2019}
}
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Figures / Tables:
Figure 1: AFM images of DNA origami triangle nanostructures on (a) mica, and (b) silicon. A similar approach can be used for AFM imaging of DNA origami triangles deposited on thin electron transparent substrates, such as (c) ultrathin amorphous carbon film on a lacey carbon supported Cu TEM grid. Scalemore »
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