Exchange between stacking conformers in a four-Way DNA junction

Biochemistry
R J GraingerD M Lilley

Abstract

Four-way DNA junctions undergo metal ion-induced folding by means of pairwise coaxial stacking of helical arms in one of two possible conformers that depend on the choice of stacking partners. For most such junctions there is a significant bias toward one conformer over the other. In this study we have characterized a four-way DNA junction in which there is rapid exchange between equal populations of the two possible stacking conformers. Analysis of the global conformation using comparative gel electrophoresis gives results consistent with either a tetrahedral disposition of the four arms or an equilibrium between equal populations of the two alternative stacked X-structures. Protection of bases at the center of the junction against attack by osmium tetroxide indicates that base stacking is preserved through the point of strand exchange. Cleavage across the point of strand exchange by the restriction enzyme MboII is consistent with pairwise coaxial stacking of helical arms. Taken together, these indicate that the junction adopts the stacked X-structure, but unusually there appears to be little bias for one stacking conformer over the other. Complete digestion of junctions by MboII demonstrates that all the molecules in solution...Continue Reading

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