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

James Byrnes; Kriti Chopra; Lewis A Rolband; Leyla Danai; Shirish Chodankar; Lin Yang; Kirill A Afonin

doi:10.1007/978-1-0716-3417-2_4

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

Methods Mol Biol. 2023:2709:65-94. doi: 10.1007/978-1-0716-3417-2_4.

Authors

James Byrnes¹, Kriti Chopra², Lewis A Rolband³, Leyla Danai³, Shirish Chodankar², Lin Yang², Kirill A Afonin³

Affiliations

¹ Brookhaven National Laboratory, Upton, NY, USA. jbyrnes@bnl.gov.
² Brookhaven National Laboratory, Upton, NY, USA.
³ University of North Carolina at Charlotte, Charlotte, NC, USA.

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.

Keywords: Molecular dynamics; RNA; SAXS; SAXS-driven molecular dynamics; WAXS.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Molecular Dynamics Simulation
Nanoparticles*
Nucleic Acids*
Scattering, Small Angle
X-Ray Diffraction

Substances

Nucleic Acids

Abstract

Publication types

MeSH terms

Substances

Grants and funding