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Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD

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RNA Nanostructures

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2709))

Abstract

Structural characterization of nucleic acid nanoparticles (NANPs) in solution is critical for validation of correct assembly and for quantifying the size, shape, and flexibility of the construct. Small-angle X-ray scattering (SAXS) is a well-established method to obtain structural information of particles in solution. Here, we present a procedure for the preparation of NANPs for SAXS. This procedure outlines the steps for a successful SAXS experiment and the use of SAXS-driven molecular dynamics to generate an ensemble of structures that best explain the data observed in solution. We use an RNA NANP as an example, so the reader can prepare the sample for data collection, analyze the results, and perform SAXS-driven MD on similar NANPs.

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Acknowledgments

The LIX beamline is part of the Center for BioMolecular Structure (CBMS), which is primarily supported by the National Institutes of Health, by the National Institute of General Medical Sciences (NIGMS) through a P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). LIX also received additional support from NIH Grant S10 OD012331. As part of NSLS-II, a national user facility at Brookhaven National Laboratory, work performed at the CBMS is supported in part by the US Department of Energy, Office of Science, Office of Basic Energy Sciences Program under contract number DE-SC0012704. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM139587 (to K.A.A.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors would like to thank Dr. Robert Sweet for insightful comments and suggestions for this chapter. KC is supported by Brookhaven National Laboratory LDRD (21-038). The authors would like to thank Dr. Hubertus JJ van Dam for setting up GROMACS-SWAXS on the institute cluster.

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Authors and Affiliations

  1. Brookhaven National Laboratory, Upton, NY, USA

    James Byrnes, Kriti Chopra, Shirish Chodankar & Lin Yang

  2. University of North Carolina at Charlotte, Charlotte, NC, USA

    Lewis A. Rolband, Leyla Danai & Kirill A. Afonin

Authors
  1. James Byrnes
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  2. Kriti Chopra
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  3. Lewis A. Rolband
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  4. Leyla Danai
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  5. Shirish Chodankar
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  6. Lin Yang
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  7. Kirill A. Afonin
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Corresponding author

Correspondence to James Byrnes .

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Editors and Affiliations

  1. Department of Chemistry, UNC Charlotte, Charlotte, NC, USA

    Kirill A. Afonin

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Byrnes, J. et al. (2023). Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD. In: Afonin, K.A. (eds) RNA Nanostructures. Methods in Molecular Biology, vol 2709. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3417-2_4

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  • DOI: https://doi.org/10.1007/978-1-0716-3417-2_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3416-5

  • Online ISBN: 978-1-0716-3417-2

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