Like HMGB1a, the MAEL HMG box Pravastatin sodium domain does not bind to dsDNA, but unlike HMGB1a, only a single complex is formed with the DNA4WJ. A possible explanation for this is that the ��hook�� and ��propeller�� regions are accommodated at the open center of the junction, PMSF however, their bulkiness prevents accommodation of the second protein. The above results suggest that MAELHMG-box domain prefers RNA hairpins with completely base-paired stems with adjacent loops larger than 4 bases to ones with disrupted double-stranded regions and smaller hairpins. MAEL HMG-box domain interacts better with RNA4WJ than with other RNA tested earlier. However, unlike with DNA4WJ, it forms a large complex. Furthermore, instead of being titrated away, this complex became predominant with additional RNA in the reaction. A description of identical RNA 4WJ by others suggests a possible explanation for the presence of these larger complexes. Unlike a DNA4WJ that primarily exists in the open conformation, the RNA counter part is more dynamic, under going multiple structural transitions. Therefore, its ensemble is largely composed of structures with dsRNA arms that are adjacent to each other either in parallel or antiparallel orientations. It is thus possible that RNA helices in proximity to each other form a structurally unique region that accommodates multiple MAEL HMG box domains at once. This mode of binding is supported by the arginine-rich sequence and the structure of MAEL HMG-box domain. These positive residues in the “hook” and the “propeller” regions are distributed such that they span almost 270 degrees, providing sufficient rotational freedom for the rest of the domain to be accommodated in multiple ways. Arginine-rich peptides are enriched in other RNA-binding motifs and, have previously been implicated in facilitating complex protein-RNA interactions through ��arginine-fork�� phenomena. Therefore, formation of large complexes with RNA4WJ may be due to the interaction of arginine-rich regions of MAEL HMG-box domain with the closed portion of 4WJ ensemble. In the presence of additional RNA4WJ in the reaction, the ensemble of the structures effectively changes to favor closed conformations.