GENOMIC SIMPLE REPETITIVE DNAS ARE TARGETS FOR DIFFERENTIAL BINDING OF NUCLEAR PROTEINS

The biological meaning of abundant simple repetitive DNA sequences in eukaryote genomes is obscure. Therefore, (GAA)(n), (GT)(n), and compos ite (GT)(n)(GA)(m) blocks were characterized for protein binding in th e repeat and flanking sequences of cloned genomic DNA fragments. In ge l mobility shift and competition assays the binding of nuclear protein s to the repeats was specific (including some flanking single copy seq uences). DNase footprinting revealed the target sequences within and a djacent to the repeats. Chemical modifications (OsO4, DEPC) demonstrat ed non-B DNA structures in the polypurine blocks. The binding of nucle ar proteins in and around simple repeat sequences refute biological in significance of all of these ubiquitously interspersed elements.