Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration

Area of Science:

• Molecular Biology
• Nanotechnology
• Computational Chemistry

Background:

• Single-stranded DNA (ssDNA) migration between DNA overhangs is fundamental to dynamic DNA nanotechnology.
• Migration speed, influenced by specific gaits, limits the performance of DNA nanodevices like nanowalkers.

Purpose of the Study:

• To classify all possible ssDNA inter-overhang migration gaits based on symmetry.
• To computationally investigate migration pathways and estimate migration rates.
• To provide a framework for optimizing ssDNA migration in DNA nanotechnology.

Main Methods:

• Exhaustive classification of ssDNA migration gaits into four categories based on symmetry.
• Systematic computational study using the oxDNA package to identify lowest-energy pathways.
• Application of first passage time theory to estimate migration rates from free-energy profiles.

Main Results:

• Identified and classified four fundamental ssDNA migration gait categories based on intrinsic symmetry.
• Determined lowest-energy pathways and generated 1D free-energy profiles for each category.
• Estimated migration rates, revealing potential for significant speed improvements in DNA nanowalkers (exceeding 1 μm/min).

Conclusions:

• Symmetry-based analysis provides a unified framework for understanding and optimizing ssDNA migration.
• Distinct symmetric patterns in free-energy profiles dictate migration kinetics, trapping, and directional bias.
• This approach enables enhanced structural design and kinetic control for advanced DNA nanotechnology applications.