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Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility

Author

Listed:
  • Jeroen F. Dyck

    (University of Antwerp)

  • Jonathan R. Burns

    (University College London)

  • Kyle I. P. Huray

    (University of Leeds)

  • Albert Konijnenberg

    (University of Antwerp
    Thermo Fisher Scientific)

  • Stefan Howorka

    (University College London)

  • Frank Sobott

    (University of Antwerp
    University of Leeds)

Abstract

Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.

Suggested Citation

  • Jeroen F. Dyck & Jonathan R. Burns & Kyle I. P. Huray & Albert Konijnenberg & Stefan Howorka & Frank Sobott, 2022. "Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31029-5
    DOI: 10.1038/s41467-022-31029-5
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    References listed on IDEAS

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    1. Anton Kuzyk & Robert Schreiber & Zhiyuan Fan & Günther Pardatscher & Eva-Maria Roller & Alexander Högele & Friedrich C. Simmel & Alexander O. Govorov & Tim Liedl, 2012. "DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response," Nature, Nature, vol. 483(7389), pages 311-314, March.
    2. Adrien Marchand & Martin F. Czar & Elija N. Eggel & Jérôme Kaeslin & Renato Zenobi, 2020. "Studying biomolecular folding and binding using temperature-jump mass spectrometry," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    3. Xiao Wang & Eman Alnabati & Tunde W. Aderinwale & Sai Raghavendra Maddhuri Venkata Subramaniya & Genki Terashi & Daisuke Kihara, 2021. "Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
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