Cruciform structures in palindromic DNA are favored by DNA supercoiling

Abstract

A totally palindromic circular DNA has been prepared by head-to-head ligation of a restriction fragment of plasmid pBR322 DNA. When negatively supercoiled, this DNA readily converts to a cruciform structure, as seen by either electron microscopy or gel electrophoresis. If the DNA is further supercoiled by DNA gyrase after hairpin formation has been initiated, as much as 80% of the molecular length can be extruded into hairpins. The rate of formation of the cruciform structure is strongly temperature-dependent; it is at least five-fold slower at 25 °C than at 35 °C. The palindromic DNA, although it contains all the necessary genetic information, is unable to transform Escherichia coli. We suggest that the intracellular formation of large cruciform structures is incompatible with survival of the DNA species.