title: Structural interconversion of alternating purine-pyrimidine inverted repeats cloned in supercoiled plasmids.
abstract: Two self complementary oligonucleotides, T(GC)4AT(GC)4ACATG and C(GC)2(AT)5 (GC)3ATG, were synthesized and cloned into plasmids. Negative supercoiling causes a structural transition in the primary helix of both inserts. The first sequence converts into the left-handed helix, whereas the second sequence undergoes a transition into a cruciform or a Z-type structure depending on the experimental conditions employed. This has been deduced from the mapping of S1 nuclease sensitive sites, OsO4-sensitive sites, DEP modification pattern and relaxation studies. In addition, the differential effect of 5-cytosine methylation and binding of the AT-specific drug distamycin on these transitions further supports this interpretation. Thus, it is demonstrated, that the same sequence which is both inverted repeat and alternating purine-pyrimidine type may adopt either the left-handed conformation or the cruciform structure in response to the superhelical stress. Formation of the Z-type helix can be transmitted through the d(AT)n region which is 10 bp in length.
authors.affiliation: Department of Bioorganic Chemistry, Polish Academy of Sciences, Lodz.
authors.forename: J
authors.initials: J
authors.lastname: Klysik
authors.forename: W
authors.initials: W
authors.lastname: Zacharias
authors.forename: G
authors.initials: G
authors.lastname: Galazka
authors.forename: M
authors.initials: M
authors.lastname: Kwinkowski
authors.forename: B
authors.initials: B
authors.lastname: Uznanski
authors.forename: A
authors.initials: A
authors.lastname: Okruszek
mesh_terms: D044503:5-Methylcytosine; D003596:Cytosine / Q000031:analogs & derivatives; D004247:DNA; D004278:DNA, Superhelical; D004214:Distamycins / Q000494:pharmacology; D006860:Hydrogen Bonding; D008745:Methylation; D009690:Nucleic Acid Conformation / Q000187:drug effects; D010957:Plasmids; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004278:DNA, Superhelical; D004214:Distamycins; D044503:5-Methylcytosine; C030000:stallimycin; D003596:Cytosine; D004247:DNA