Single-Molecule Nucleic Acid Detection with a Reconfigurable Rotating DNA Origami Nanodevice

Area of Science:

• Nanotechnology
• Biotechnology
• Molecular Biology

Background:

• DNA nanodevices offer programmable platforms for nanoscale engineering.
• Macroscopic machines inspire the design of dynamic nanodevices with specialized functions.

Purpose of the Study:

• To develop a DNA origami-based rotating nanodevice for continuous nucleic acid sensing.
• To demonstrate the reversibility and regeneration capabilities of the nanodevice for multiple detection rounds.
• To design single-mode and dual-mode nanodevices for Förster Resonance Energy Transfer (FRET) and multiplexed measurements.

Main Methods:

• Utilized DNA origami for precise nanoscale construction.
• Employed toehold-mediated strand displacement for reversible target detection.
• Applied ensemble and single-molecule techniques to analyze nanodevice dynamics and conformational changes.
• Designed single-mode (FRET) and dual-mode (FRET/quenched) systems for varied detection strategies.

Main Results:

• Achieved a detection limit in the low nanomolar range for nucleic acid sensing.
• Demonstrated successful regeneration of the nanodevice for multiple detection cycles.
• Obtained high-resolution insights into dynamic conformational changes at the single-molecule level.
• Successfully implemented multiplexed measurements using the dual-mode nanodevice.

Conclusions:

• The developed DNA origami nanodevice enables continuous and reversible nucleic acid sensing.
• Single-molecule analysis provides valuable insights into the dynamic behavior of nanodevices.
• The programmable nature of DNA origami allows for versatile sensor design, including multiplexed detection.
• This work offers a foundation for optimizing DNA nanodevice design for enhanced sensing applications.