Apparent Persistence Length Renormalization of Bent DNA

TL;DR

This paper develops a theoretical model for DNA with loops and defects, revealing an apparent reduction in persistence length, supported by simulations and applicable to various experimental setups.

Contribution

It introduces an analytical approach to quantify how loops and defects affect DNA's mechanical properties, extending to multiple experimental contexts.

Findings

Sliding loops cause a significant apparent reduction in DNA persistence length.

Analytical force-extension relations are derived for various loop and boundary configurations.

MD simulations confirm the theoretical predictions.

Abstract

We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in quantum mechanical tunneling problems. The results reveal a remarkable feature of sliding loops - an apparent strong reduction of the persistence length. We generalize these results to several other experimentally interesting situations ranging from rigid DNA-protein loops to the problem of anchoring deflections in AFM stretching of semiflexible polymers. Expressions relating the force-extension measurements to the underlying loop/boundary deflection geometry are provided and applied to the case of the GalR-loop complex. The theoretical predictions are complemented and quantitatively confirmed by MD simulations.