Salt-induced conformational switching of a flat rectangular DNA origami structure

Area of Science:

• DNA nanotechnology
• Nanobiotechnology
• Structural DNA nanotechnology

Background:

• Rectangular DNA origami structures are widely utilized in DNA nanotechnology.
• Understanding structural dynamics is crucial for advancing DNA nanodevices.

Purpose of the Study:

• To investigate structural changes in rectangular DNA origami.
• To reveal cation-induced reversible rolling-up phenomena.
• To develop and apply novel assays for studying DNA nanostructure transitions.

Main Methods:

• Utilized one-color and two-color superresolution DNA-PAINT to visualize structural changes.
• Employed protruding strands along DNA origami edges to detect rolling-up.
• Integrated gold nanoparticles and dye molecules for distance-dependent fluorescence quenching measurements.

Main Results:

• Observed a single-line signal in DNA-PAINT assays, indicating rolling-up at increased salt concentrations.
• Identified distinct conformations with parallel and angled edges using two-color DNA-PAINT.
• Demonstrated preferential rolling-up along the diagonal of the DNA origami structure via fluorescence quenching.

Conclusions:

• Bivalent cations (Mg2+, Ca2+) induce a reversible rolling-up of rectangular DNA origami.
• The developed assays are effective for studying dynamic structural transitions in DNA nanostructures.
• Findings contribute to validating DNA structural models and advancing DNA nanotechnology applications.