Trapping a Knot into Tight Conformations by Intra-Chain Repulsions

Area of Science:

• Biophysics
• Polymer Physics
• Computational Biology

Background:

• Knots are observed in biopolymers like DNA and peptides.
• Previous research indicated long-range repulsions unexpectedly tighten polymer knots.

Purpose of the Study:

• To investigate knot trapping into tight conformations using insights from previous studies.
• To explore the phenomenon of "knot breathing" in biopolymers.
• To determine the conditions for knot trapping and breathing in charged biopolymers.

Main Methods:

• Utilizing Langevin dynamics simulations to model knot behavior.
• Employing a Yukawa potential to represent screened electrostatic interactions.
• Tuning intra-chain repulsion strength to achieve weak knot trapping.

Main Results:

• Demonstrated that long-range repulsions can create a potential well, trapping knots in tight conformations.
• Observed "knot breathing": thermal fluctuations drive knots to escape and re-enter traps, switching between tight and loose states.
• Determined the minimal screened length and repulsion strength required for knot trapping in charged biopolymers.

Conclusions:

• Knot trapping and breathing are achievable in biopolymers through controlled intra-chain repulsions.
• Coulomb-induced knot trapping is feasible in single-stranded DNA and peptides under typical ionic conditions.
• The findings offer insights into the conformational dynamics of knotted biopolymers.