Effect of magnesium ions and temperature on the sequence-dependent curvature of DNArestriction fragments

Abstract

Transient electric birefringence has been used to quantify the curvature of two DNArestriction fragments, a 199-base-pair fragment taken from the origin of replication of theM13 bacteriophage and a 207-base-pair fragment taken from the VP1 gene inthe SV40 minichromosome. Stable curvature in the SV40 and M13 restrictionfragments is due to a series of closely spaced A tracts, runs of 4–6 contiguousadenine residues located within 40 or 60 base pair ‘curvature modules’ near thecenter of each fragment. The M13 and SV40 restriction fragments exhibit bends of ∼ 45° in solutions containing monovalent cations and ∼ 60° in solutionscontaining Mg2 + ions. The curvature is not localized at a single site but is distributed over the various Atracts in the curvature modules. Thermal denaturation studies indicate that thecurvature in the M13 and SV40 restriction fragments remains constant up to30 °C in solutions containing monovalent cations, and up to40 °C in solutionscontaining Mg2 + ions, before beginning to decrease slowly with increasing temperature. Hence, stable curvaturein these DNA restriction fragments exists at the biologically important temperature of37 °C.