title: Parallel-stranded DNA under topological stress: rearrangement of (dA)15.(dT)15 to a d(A.A.T)n triplex.
abstract: DNA oligonucleotides with appropriate sequences can form a stable duplex in which the two strands are paired in a parallel orientation instead of as the conventional antiparallel double helix of B-DNA. In parallel-stranded DNA (ps-DNA) base pairing is noncanonical with the glycosidic bonds in a trans orientation. The two grooves are equivalent. We have synthesized DNA duplexes consisting of a central parallel-stranded (dA)15.(dT)15 tract flanked by normal antiparallel regions, and ligated them into the pUC18 plasmid. The effect of negative supercoiling on the covalently closed circular molecules was studied by two-dimensional agarose gel electrophoresis and by chemical modification with OsO4-pyridine (Os,py) and diethylpyrocarbonate (DEPC). The following results were obtained: (i) The ps insert, and by inference ps-DNA in general, adopts a right handed helical form. (ii) Upon increasing the negative superhelix density (-sigma) to greater than 0.03 the 15 bp ps insert undergoes a major transition leading to a relaxation corresponding to a reduction in twist of approximately 2.5 helical turns. The transition free surgery is approximately kcal/mol. (iii) The chemical modification pattern of the resulting structure suggests that the purine strand folds back and associates with the pyrimidine strand, forming a novel intramolecular triplex structure consisting of d(A.A.T) base triplets. A model for the triplex conformation is proposed and its thermodynamic properties are analyzed by statistical mechanics.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, FRG.
authors.forename: J
authors.initials: J
authors.lastname: Klysik
authors.forename: K
authors.initials: K
authors.lastname: Rippe
authors.forename: T M
authors.initials: TM
authors.lastname: Jovin
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004270:DNA, Circular / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D004047:Diethyl Pyrocarbonate / Q000737:chemistry; D004587:Electrophoresis, Agar Gel; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009993:Osmium Tetroxide / Q000737:chemistry; D010957:Plasmids / Q000235:genetics; D011067:Poly dA-dT / Q000737:chemistry*; D013053:Spectrophotometry
chemical_list: D004270:DNA, Circular; D004278:DNA, Superhelical; D011067:Poly dA-dT; D004047:Diethyl Pyrocarbonate; D009993:Osmium Tetroxide