Divalent Cations Induce Rigid and Compact Structures in Underwound DNA

Abstract

Negative supercoiling (underwinding) of DNA plays a vital role in regulating genome organization and gene expression. These processes often depend on the DNA structure, yet the influence of ionic strength on supercoiled DNA structure is still not well understood. Here, we develop an approach to extract detailed insight into the mechanical properties of underwound DNA from force–distance measurements. Using this approach, we demonstrate that low concentrations (2 mM) of divalent cations are sufficient to induce substantial increases in DNA persistence length at high superhelical densities. This is consistent with the formation of Z-DNA, a rigid, left-handed conformation, and suggests that Z-DNA-like structures can be more readily formed than is often assumed. We also show that divalent cations can induce extensive sawtooth-like behavior in force–extension curves of underwound DNA, revealing unexpectedly strong stabilization of secondary structures. Together, these findings demonstrate how divalent salt can sensitively modulate the stability of different underwound structures.