Modulation of DNA conformation in electrolytic nanodroplets

Area of Science:

• Biophysics and Molecular Engineering
• Computational Biology and Nanotechnology

Background:

• Deoxyribonucleic acid (DNA) behavior in confined environments is critical for bioengineering and medical applications.
• Understanding DNA conformation transitions is essential for manipulating genetic material at the nanoscale.

Purpose of the Study:

• To investigate the conformational transitions of double-strand DNA (dsDNA) within electrolytic nanodroplets.
• To elucidate the physical mechanisms governing dsDNA behavior under nanoscale confinement and varying ionic concentrations.

Main Methods:

• All-atom molecular dynamics simulations were employed to model dsDNA within nanodroplets.
• Analysis of dsDNA characteristics including overcharging, end-to-end distance, and radius of gyration.
• Numerical results were used to understand the interplay between confinement and electrostatic forces.

Main Results:

• Observed three distinct dsDNA conformations: C-shaped, folded S-shaped, and double C-shaped.
• Conformation transitions are attributed to polymer buckling under nanodroplet compression, modulated by ionic concentration.
• Persistence length increases with nanodroplet radii due to the competition between confinement and electrostatic effects.

Conclusions:

• Nanoscale confinement and electrostatic effects dynamically influence dsDNA conformation in nanodroplets.
• A non-dimensional elasto-capillary number (μ) is proposed to classify dsDNA conformations.
• Findings provide insights into controlling DNA behavior for nanoscale applications.