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| Title | Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. |
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| Journal, issue, pages | Nat Commun, Vol. 14, Issue 1, Page 3630, Year 2023 |
| Publish date | Jun 19, 2023 |
 Authors | Katya Ahmad / Abid Javed / Conor Lanphere / Peter V Coveney / Elena V Orlova / Stefan Howorka /   |
| 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 ...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. |
 External links | Nat Commun / PubMed:37336895 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 8.0 Å |
| Structure data | EMDB-14342, PDB-7ywh: EMDB-14343, PDB-7ywi: EMDB-14344, PDB-7ywl: EMDB-14345, PDB-7ywn: EMDB-14346, PDB-7ywo: |
| Source |
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 Keywords | DNA / DNA origami / nanopore. / nanopore |
