Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.
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DOI：
10.1038/s41467-023-38681-5
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发表时间：
2023-06-19
影响因子：
16.6
通讯作者：
Howorka, Stefan
中科院分区：
文献类型：
--
作者：
Ahmad, Katya;Javed, Abid;Lanphere, Conor;Coveney, Peter V.;Orlova, Elena V.;Howorka, Stefan
DNA可以折叠成合理设计的、独特的和功能性的材料。为了充分发挥这些DNA材料的潜力，有必要对其结构和动力学进行基本了解，无论是在简单溶剂中还是在更复杂和多样化的各向异性环境中。在这里，我们分析了一个典型的六重DNA纳米结构与单粒子低温电子显微镜和分子动力学模拟溶剂中的可调离子强度和各向异性环境中的生物膜。在脂质双层外，六重束缺乏设计的对称桶型结构。相反，双链体以非六边形的方式排列，并且错位以形成更宽、更少伸长的结构。然而，插入到脂质膜中，由于双层的侧向双重压缩，恢复了预期的桶形。考虑到带负电荷的双链体之间的可调静电排斥，盐浓度对插入的桶形DNA纳米孔的稳定性具有剧烈影响。通过协同实验和模拟相结合，我们增加了对广泛使用的纳米体系结构的环境依赖性结构动力学的基本理解。这一见解将为未来的工程和生物传感应用铺平道路。DNA可以折叠成合理设计的、独特的和功能性的材料。在这里，作者分析了一个原型的DNA纳米结构与单粒子冷冻电子显微镜和分子动力学模拟。
DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications. DNA can be folded into rationally designed, unique, and functional materials. Here the authors analyse an archetypal DNA nanoarchitecture with single particle cryo-electron microscopy and molecular dynamics simulations.
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影响因子：
16.6
作者：
Burns, Jonathan R.;Goepfrich, Kerstin;Wood, James W.;Thacker, Vivek V.;Stulz, Eugen;Keyser, Ulrich F.;Howorka, Stefan
通讯作者：
Howorka, Stefan
DOI：
10.1107/s2059798318009324
发表时间：
2018-09-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
通讯作者：
Urzhumtsev A
影响因子：
16.6
作者：
Burns, Jonathan R.;Al-Juffali, Noura;Janes, Sam M.;Howorka, Stefan
通讯作者：
Howorka, Stefan
影响因子：
17.1
作者：
Arulkumaran, Nishkantha;Lanphere, Conor;Howorka, Stefan
通讯作者：
Howorka, Stefan
影响因子：
38.3
作者：
Burns, Jonathan R.;Seifert, Astrid;Howorka, Stefan
通讯作者：
Howorka, Stefan