Structural interconversion of alternating purine-pyrimidine inverted repeats cloned in supercoiled plasmids.
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.
Klysik
J
J
Department of Bioorganic Chemistry, Polish Academy of Sciences, Lodz.
Zacharias
W
W
Galazka
G
G
Kwinkowski
M
M
Uznanski
B
B
Okruszek
A
A
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
D004278:DNA, Superhelical; D004214:Distamycins; D044503:5-Methylcytosine; C030000:stallimycin; D003596:Cytosine; D004247:DNA