Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots

Area of Science:

• Biophysics
• Polymer Physics
• Nanotechnology

Background:

• DNA knotting is crucial for packaging and biological functions.
• Controlling DNA knot topology, particularly handedness, is a significant challenge.

Purpose of the Study:

• To investigate the use of helical nano-channels as 'knot-factories' for producing DNA knots with preferred handedness.
• To explore the effects of confinement strength and compressive forces on DNA topology within helical channels.

Main Methods:

• Molecular dynamics simulations of DNA polymer chains.
• Confining DNA within helical nano-channels under varying compression levels.
• Analyzing DNA knottedness, writhe, and knot handedness.

Main Results:

• DNA topology in helical channels differs significantly from cylindrical channels, affecting knottedness and writhe.
• Helical geometry influences the handedness of DNA knots formed.
• Knot chirality can be controlled by selecting the appropriate channel handedness.

Conclusions:

• Helical nano-channels offer a promising approach for producing DNA knots with controlled chirality.
• The study demonstrates a method for engineering DNA knot handedness using geometric confinement.