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. 1988 Jul 25;16(14B):6915–6933. doi: 10.1093/nar/16.14.6915

Structural interconversion of alternating purine-pyrimidine inverted repeats cloned in supercoiled plasmids.

J Klysik 1, W Zacharias 1, G Galazka 1, M Kwinkowski 1, B Uznanski 1, A Okruszek 1
PMCID: PMC338342  PMID: 3405754

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.

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