The instability of plasmid DNAs that contained various numbers of repeated CAG units in Escherichia coli was examined. Synthetic [5'-P-32](CAG)(15) and [5'-P-32](GTG)(15) oligonucleotides were incubated with plasmid DNA. A minor fraction of the plasmid DNA formed a stable complex with either the repeated CAG or the repeated CTG oligonucleotide when the number of CAG repeats in the plasmid DNA was more than 30, regardless of the polarity of replication. The formation of the complexes appeared to occur by the normal hybridization process. The DNA that formed stable complexes could be purified with a biotinylated fragments of CAG repeats and avidin-coated beads. In addition, in the case of the DNA containing CAG repeats derived from the IT15 gene of a patient with Huntington's disease, there seemed to be an unusual product that contained a partially replicated product that extended only from the origin of replication to the CAG-repeated region. The formation of this product was observed when replication started downstream of IT15 gene. (C) 1997 Academic Press.