Analysis of DNA Origami Nanostructures Using Capillary Electrophoresis

Area of Science:

• Nanotechnology
• Biomedical Engineering
• Analytical Chemistry

Background:

• DNA origami nanostructures offer customizable, biocompatible properties for medicine and biocomputing.
• A key challenge for DNA origami application is achieving pure, well-folded structures.
• Rapid purity analysis methods are crucial for advancing DNA origami development.

Purpose of the Study:

• To develop and optimize capillary electrophoresis (CE) as an analytical tool for DNA origami nanostructures.
• To evaluate both capillary zone electrophoresis (CZE) and capillary transient isotachophoresis (ctITP) modes for DNA origami analysis.
• To assess the potential of SYBR dyes for on-column labeling and laser-induced fluorescence detection.

Main Methods:

• Investigated capillary electrophoresis (CE) in both CZE and ctITP modes.
• Optimized CE conditions for separating folded DNA origami from excess staple strands.
• Employed SYBR Gold, Green I, and Green II dyes for noncovalent on-column labeling and laser-induced fluorescence detection.

Main Results:

• Achieved baseline resolved separations of folded DNA origami from excess staple strands using CE.
• Demonstrated superior performance of ctITP with high resolution (Rs = 2.05 ± 0.3), efficiency (N = 12,200 ± 230), and symmetry (As = 1.29 ± 0.032).
• Successfully applied ctITP to various DNA origami shapes and for differentiating DNA origami aggregates.

Conclusions:

• Capillary electrophoresis, particularly ctITP, is an effective analytical method for assessing DNA origami purity.
• The developed CE method provides rapid, high-resolution separation crucial for advancing DNA origami research and applications.
• On-column labeling with SYBR dyes enables sensitive detection of DNA origami nanostructures.