Structure of the four-way DNA junction and its interaction with proteins

Abstract

The four-way DNA junction is an important intermediate in recombination processes; it is, the substrate for different enzyme activities. In solution, the junction adopts a right-handed, antiparallel-stacked X-structure formed by the pairwise coaxial-stacking of helical arms. The stereochemistry is determined by the juxtaposition of grooves and backbones, which is optimal when the smaller included angle is 60 degrees. The antiparallel structure has two distinct sides with major and minor groove-characteristics, respectively. The folding process requires the binding of metal cations, in the absence of which, the junction remains extended without helix-helix stacking. The geometry of the junction can be perturbed by the presence of certain base-base mispairs or phosphodiester discontinuities located at the point of strand exchange. The four-way DNA junction is selectively cleaved by a number of resolving enzymes. In a number of cases, these appear to recognize the minor groove face of the junction and are functionally divisible into activities that recognize and bind the junction, and a catalytic activity. Some possible mechanisms for the recognition of branched DNA structure are discussed.

Characterization of the structural and protein recognition properties of hybrid PNA–DNA four-way junctions

“…In low ionic strength solutions (≤ 100 μM Mg +2 ), the open-x or unstacked conformer is favored 22–28 . In high ionic strength solutions (≥ 100 μM Mg +2 ), the helical arms of each duplex stack coaxially to generate a cruciform or stacked-x structure 28–31 . Several research labs have confirmed that the stacked-x conformer possesses greater structural heterogeneity than the open-x conformer; these studies show that the stacked-x conformer can fold into the two isomers (I/II and III/IV) displayed in Figure 1B 32–35 .…”