Fractal Dimension and Localization of DNA Knots

TL;DR

This study investigates the scaling behavior and localization of DNA knots using atomic force microscopy, revealing how different adsorption protocols affect their conformational properties and knot localization.

Contribution

It provides new insights into the fractal dimension and localization of DNA knots under different surface adsorption conditions, highlighting the effects of kinetic trapping and relaxation.

Findings

Gyration radius scales with Flory exponent ~0.58 under strong binding

Gyration radius scales with Flory exponent ~0.66 under weak binding

Evidence of knot crossing localization in 2D

Abstract

The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the three-dimensional (3D) configuration, and of (ii) weak binding, that permits (partial) relaxation on the surface. In (i) the gyration radius of the adsorbed DNA knot scales with the 3D Flory exponent $\nu\approx 0.58$ within error. In (ii), we find $\nu\approx 0.66$, a value between the 3D and 2D ($\nu=3/4$) exponents, indicating an incomplete 2D relaxation or a different polymer universality class. Compelling evidence is also presented for the localization of the knot crossings in 2D.