STRUCTURE OF THE 4-WAY DNA JUNCTION AND ITS INTERACTION WITH PROTEINS

The four-way DNA junction is an important intermediate in recombinatio n processes; it is, the substrate for different enzyme activities. In solution, the junction adopts a right-handed, antiparallel-stacked X-s tructure formed by the pairwise coaxial-stacking of helical arms. The stereochemistry is determined by the juxtaposition of grooves and back bones, which is optimal when the smaller included angle is 60 degrees. The antiparallel structure has two distinct sides with major and mino r groove-characteristics, respectively. The folding process requires t he binding of metal cations, in the absence of which, the junction rem ains extended without helix-helix stacking. The geometry of the juncti on can be perturbed by the presence of certain base-base mispairs or p hosphodiester discontinuities located at the point of strand exchange. The four-way DNA junction is selectively cleaved by a number of resol ving enzymes. In a number of cases, these appear to recognize the mino r groove face of the junction and are functionally divisible into acti vities that recognize and bind the junction, and a catalytic activity. Some possible mechanisms for the recognition of branched DNA structur e are discussed.