7YWH

Six DNA Helix Bundle nanopore - State 1

Summary for 7YWH

• Entry DOI: 10.2210/pdb7ywh/pdb
• EMDB information: 14342
• Descriptor: DNA (50-MER), ... (6 entities in total)
• Functional Keywords: dna origami, nanopore., dna
• Biological source: DNA molecule; More
• Total number of polymer chains: 6
• Total formula weight: 92191.03

Authors

Javed, A.,Ahmad, K.,Lanphere, C.,Coveney, P.,Howorka, S.,Orlova, E.V. (deposition date: 2022-02-14, release date: 2023-05-24, Last modification date: 2024-07-17)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (8 Å)