Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques

Yoones Kabiri,Ute Kaiser,Henny Zandbergen,Allard J Katan,Raimond B G Ravelli,Haoyuan Qi,Peter J Peters,Cees Dekker,Tibor Lehnert,Natascha Roest

doi:10.1038/s41598-019-43687-5

Yoones Kabiri, Ute Kaiser + Show 8 more

Open Access

https://doi.org/10.1038/s41598-019-43687-5

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Journal: Scientific Reports	Publication Date: May 10, 2019
Citations: 10	License type: open-access

Affiliation: University of Ulm, Maastricht University

Abstract

Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form has remained extremely challenging. Here, we present high-contrast images of unstained single-layer DNA nanostructures that were obtained using advanced in-focus phase contrast TEM techniques. These include sub-Ångstrom low voltage electron microscopy (SALVE), the use of a volta-potential phase plate (VPP), and dark-field (DF) microscopy. We discuss the advantages and drawbacks of these techniques for broad applications in structural biology and materials science.

Highlights

transmission electron microscopy (TEM) imaging of DNA, in its native unstained form, is crucial for various applications across life sciences, it has remained extremely difficult to obtain such images
Whereas conventional TEM (CTEM) renders poor contrast, we find that a chromatic and spherical aberration corrected (Cc + Cs) SALVE microscopy, or the cosine-type phase shift induced by the volta-potential phase plate (VPP) technology, resulted in an overall visibility of the DNA nanostructures, without the need of labelling
We were unable to detect sufficient contrast of DNA origami plates supported on commercial carbon membranes using the normal CTEM at 200–300 kV acceleration voltages, even with large defocus values for the objective lens and even when the micrographs were acquired by a direct detector camera

Summary

Introduction

TEM imaging of DNA, in its native unstained form, is crucial for various applications across life sciences, it has remained extremely difficult to obtain such images. Whereas CTEM renders poor contrast, we find that a chromatic and spherical aberration corrected (Cc + Cs) SALVE (sub-Ångstrom low voltage electron) microscopy, or the cosine-type phase shift induced by the VPP technology, resulted in an overall visibility of the DNA nanostructures, without the need of labelling. This enabled the particle picking and class averaging algorithms in the SPA workflow. We discuss the prospect of SALVE and VPP techniques in terms of in-focus SPA workflow

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