使用小角 X 射线散射（SAXS）和 SAXS 驱动的 MD 对核酸纳米粒子进行结构表征。
Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD.
机构信息
Brookhaven National Laboratory, Upton, NY, USA.
University of North Carolina at Charlotte, Charlotte, NC, USA.
出版信息
Methods Mol Biol. 2023;2709:65-94. doi: 10.1007/978-1-0716-3417-2_4.
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.
摘要
在溶液中对核酸纳米颗粒（NANP）进行结构表征对于验证正确的组装和量化构建体的大小、形状和柔韧性至关重要。小角度 X 射线散射（SAXS）是一种成熟的方法，可用于获得溶液中颗粒的结构信息。在这里，我们介绍了一种用于 SAXS 的 NANP 制备方法。该程序概述了成功进行 SAXS 实验的步骤，以及使用 SAXS 驱动的分子动力学生成最佳解释溶液中观察到的数据的结构集合。我们以 RNA NANP 为例，因此读者可以为数据收集准备样品，分析结果，并对类似的 NANP 进行 SAXS 驱动的 MD。
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