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

Abstract

We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement strength and compressive forces in a range covering weak, intermediate and strong confinement together with weak and strong compressive forces. The results find that while the common metrics of polymer chain in cylindrical and helical channels are very similar, the DNA in helical channels exhibits greatly different topology in terms of chain knottedness, writhe and handedness of knots. The results show that knots with a preferred chirality in terms of average writhe can be produced by using channels with a chosen handedness.

Keywords

• polymer
• DNA
• chirality
• topology
• knots
• molecular dynamics