Subdomain structure of the matrix attachment region located within the mouse immunoglobulin kappa gene intron

Using the matrix attachment region (MAR) derived from Ig kappa gene intron, we assessed the importance of internal subregions required for the specific binding to the nuclear matrix. Relative affinities of MAR subfragments were compared in an in vitro binding reaction with isolated matrix. Cleavage at the near-centric MboII site generated two subfragments retaining a significant binding affinity. Dimerization of these subfragments greatly increased the affinity. Only a partial segment (130 bp) of the 3' fragment was necessary to restore the binding. The dimerization effect was lost when the monomer units were separated by nonMAR spacers of 500 bp <. This bipartite organization of Ig kappa MAR could be a general feature of AT-rich MARs, regardless of their genomic locations.