Multifunctional molecules were designed to produce microgels with specific structures. Both static light scattering and dynamic light scattering were employed to determine the fractal dimension of the microgels. The protein, avidin, was strongly bound to four biotin moieties. Biotin was attached covalently to specifically engineered peptide nucleic acid (PNA) oligomers. Three designed DNA oligomers self-assembled to produce a trifunctional three-way junction (TWJ) with single-stranded ends that were complementary to the PNA sequence. The sizes of the supramolecular aggregates were characterized by dynamic light scattering. The fractal dimension was obtained from the angular dependence of the scattered intensity when the microgels were large enough. When the microgels were formed via cooling from a temperature above the melting point of the PNA-DNA helices, reversible structures with a fractal dimension of approximately 1.86 were formed, which is consistent with a cluster-cluster aggregation mechanism. When the microgels were formed by the slow addition of biotinylated PNA bound to the TWJ to a solution of avidin at room temperature, the observed fractal dimension approached 2.6, which is consistent with a point-cluster aggregation mechanism. (C) 2003 Wiley Periodicals, Inc.