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Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation
ACS Environmental Au Pub Date : 2022-07-24 , DOI: 10.1021/jasms.2c00122
Fabrice Saintmont 1, 2 , Sébastien Hoyas 1, 2 , Frédéric Rosu 3 , Valérie Gabélica 3, 4 , Patrick Brocorens 2 , Pascal Gerbaux 1
Affiliation  

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4+ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4+ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

中文翻译:

真空中树枝状化合物的结构表征:联合离子迁移率/分子动力学研究

首次证明了离子淌度质谱和分子动力学模拟之间的结合,以提供关于含有 ds-DNA 和低代树枝状聚合物的树枝状聚合物在从溶液转移到气相时所经历的结构变化的有价值信息。使用质谱实验鉴定呈现 1:1 和 2:1 化学计量的 Dendriplex 离子,并使用漂移时间离子迁移率实验测量 1:1 离子的碰撞截面 (CCS)。使用分子动力学 (MD) 模拟的结构预测表明,当模拟全局电喷雾过程(包括溶剂分子蒸发)时,会生成气相相关结构,即实验和理论 CCS 之间的良好匹配,而不是突然将离子从溶液转移到气相。铵基团的逐步迁移(无论是 NH4 +从缓冲液或树枝状大分子的质子化胺)进入 DNA 的小沟和大沟,在整个蒸发过程中显示通过静电和氢键相互作用压缩 DNA 结构。随后的质子从铵(NH 4 +或质子化氨基)转移到 DNA 磷酸基团允许在紧密结构内产生质子化磷酸/磷酸氢键。MD 模拟显示了溶液中和气相中树枝状结构之间的主要结构差异,这不仅是由于溶剂的损失,还由于质子转移以及溶液和气相电荷状态之间的巨大差异。
更新日期:2022-07-24
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