Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

TL;DR

This study uses Atomic Force Microscopy to analyze the structural properties of DNA molecules across all biologically relevant supercoiling states, revealing significant differences between positive and negative supercoiling.

Contribution

It provides a comprehensive AFM-based analysis of DNA supercoiling, covering the full spectrum of topologies, which was previously lacking especially for positively supercoiled DNA.

Findings

Distinct structural behaviors of positively and negatively supercoiled DNA

Differences observed under various observation conditions

Enhanced understanding of DNA topology effects on structure

Abstract

Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.