Magnesium concentration effects on cruciform extrusion in supercoiled DNA examined by atomic force microscopy

Cruciform structures can form in DNA sequences with inverted repeats or palindromic symmetry under unwinding torsional stress. DNA repeats are widespread in the genomes of eukaryotes and prokaryotes, and their extrusion into cruciform structures may be involved in various genetic processes, including transcription and replication. Intracellular Mg2+ may change the free energy of supercoiling to provide the driving force for cruciform extrusion. We have used atomic force microscopy (AFM) to image the effects of magnesium concentrations on cruciform extrusions in supercoiled DNA. Mg2+ concentration dependent cruciform extrusions were observed in the supercoiled topoisomer of the pPR-PARP plasmid (〈σ〉=−0.065). These data show an application of AFM imaging to demonstrate that the presence of Mg2+ results in increased extrusions and promotes compact cruciform conformation.