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Updated: Feb 13, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack
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Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes.

Pi Liu1,2, Yan Zhao3, Xiaoguo Liu3

  • 1State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China.

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|March 13, 2018
PubMed
Summary

Charge neutralization controls DNA nanotube shape. Ions like Mg2+ and Na+ dictate whether the 6-helix bundle (6HB) DNA nanostructure adopts a compact or expanded state, offering insights into biological channel gating.

Keywords:
DNA nanotechnologySAXSmolecular channelsmolecular dynamicsshape reconfiguration

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Area of Science:

  • Biomimetic Nanotechnology
  • Structural Biology
  • Computational Biophysics

Background:

  • Understanding the gating mechanisms of biological ion channels is crucial but challenging due to difficulties in observing subtle structural changes.
  • Biomimetic DNA nanostructures offer model systems to study channel-like behaviors and structural dynamics.

Purpose of the Study:

  • To investigate how charge neutralization influences the structural reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB).
  • To explore the role of electrostatic and hydrophobic forces in controlling the shape of DNA nanostructures for potential biomedical applications.

Main Methods:

  • Molecular dynamics (MD) simulations to model structural changes.
  • Small-angle X-ray scattering (SAXS) for structural characterization.
  • Förster resonance energy transfer (FRET) to probe conformational states.

Main Results:

  • Charge neutralization by Mg2+ ions induced a compact state in the 6HB DNA nanotube.
  • Na+ ions induced an expanded state, demonstrating ion-dependent shape control.
  • Chemical modification of DNA backbone charges resulted in a compact, ion-insensitive state, highlighting the interplay of electrostatic and hydrophobic forces.

Conclusions:

  • Charge neutralization is a key factor driving the shape reconfiguration of 6HB DNA nanotubes.
  • This DNA nanostructure system serves as a valuable platform for understanding biological channel structure-function relationships.
  • Provides design principles for controlling DNA nanostructure shape in biomedical contexts.