Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes,Journal of the American Chemical Society

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Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes
Journal of the American Chemical Society ( IF 14.4 ) Pub Date : 2021-05-20 , DOI: 10.1021/jacs.0c13235
Sioned F Jones _{1,

2} , Himanshu Joshi ₃ , Stephen J Terry _{2,

4} , Jonathan R Burns ₁ , Aleksei Aksimentiev ₃ , Ulrike S Eggert ₂ , Stefan Howorka ₁

Affiliation

Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA–membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA–bilayer interactions will guide the rational design of membrane-targeting nanostructures.

中文翻译：

DNA 双链体与合成膜和生物膜之间的疏水相互作用

为 DNA 配备疏水锚能够实现与脂质双层的有针对性的相互作用，适用于生物物理学、细胞生物学和合成生物学的应用。了解 DNA 与膜的相互作用对于合理设计功能性 DNA 至关重要。在这里，我们结合实验和原子分子动力学 (MD) 模拟来研究疏水标记 DNA 与合成膜和细胞膜的相互作用。 DNA 双链体通过与末端胆固醇锚结合或通过化学合成电荷中和的烷基硫代磷酸酯 (PPT) 带而呈现疏水性。胆固醇-DNA 与不同脂质成分和电荷的脂质囊泡相连，而 PPT DNA 结合强烈依赖于烷基长度、带位置和头基电荷。缓冲液中的二价阳离子也会影响结合。我们的 MD 模拟直接揭示了脂质膜内 PPT DNA 的复杂结构和能量学，证明较长的烷基 PPT 链提供最稳定的膜锚定，但可能会破坏溶液中的 DNA 碱基配对。在细胞上进行测试时，胆固醇-DNA 均匀分布在细胞表面，而烷基-PPT DNA 则在质膜上以簇状结构积累。通过核酸酶和鞘磷脂酶消化测定，将束缚在细胞膜外部的 DNA 与跨膜的 DNA 区分开来。对 DNA-双层相互作用的基本了解将指导膜靶向纳米结构的合理设计。

更新日期：2021-06-09

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