7YWH

Six DNA Helix Bundle nanopore - State 1

7YWH の概要

• エントリーDOI: 10.2210/pdb7ywh/pdb
• EMDBエントリー: 14342
• 分子名称: DNA (50-MER), ... (6 entities in total)
• 機能のキーワード: dna origami, nanopore., dna
• 由来する生物種: DNA molecule; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 92191.03

構造登録者

Javed, A.,Ahmad, K.,Lanphere, C.,Coveney, P.,Howorka, S.,Orlova, E.V. (登録日: 2022-02-14, 公開日: 2023-05-24, 最終更新日: 2024-07-17)

主引用文献

Ahmad, K.,Javed, A.,Lanphere, C.,Coveney, P.V.,Orlova, E.V.,Howorka, S.
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.
Nat Commun, 14:3630-3630, 2023

PubMed Abstract: 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.

PubMed: 37336895
DOI: 10.1038/s41467-023-38681-5

実験手法

ELECTRON MICROSCOPY (8 Å)