New smoothly connecting open curves for modeling nucleosome-decorated DNA

TL;DR

This paper presents a new analytical method for smoothly connecting open DNA curves to model nucleosome-decorated DNA minicircles, enabling detailed analysis of their configurations and energies.

Contribution

The authors introduce a general mathematical approach to connect open curves, applied here to model DNA with nucleosomes, capturing various configurations and energy states.

Findings

Predicted stable DNA configurations match experimental observations.

Method effectively models DNA supercoiling and nucleosome arrangements.

Energy calculations reveal effects of salt conditions on DNA stability.

Abstract

We introduce an analytical method to generate the pathway of a closed protein-bound DNA minicircle. This is a general method which can be used to connect any two open curves with well defined mathematical definitions as well as pairs of discrete systems found experimentally. We used this method to describe the configurations of torsionally relaxed, 360-base pair DNA rings with two evenly-spaced, ideal nucleosomes. We considered superhelical nucleosomal pathways with different levels of DNA wrapping and allowed for different inter-nucleosome orientations. We completed the DNA circles with the smooth connectors and studied the associated bending and electrostatic energies for different configurations in the absence and presence of salt. The predicted stable states bear close resemblance to reconstituted minicircles observed under low and high salt conditions.