Parallel-stranded DNA under topological stress: rearrangement of (dA)15.(dT15to a d(A.A.T)ntriplex

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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 plasm Id. The effect of negative supercoiling on the covalently closed circular molecules was studied by two-dimensional agarose gel electrophoresls and by chemical modification with OsO4-pyridlne (Os,py) and dlethylpyrocarbonate (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 (-σ) to > 0.03 the 15 bp ps Insert undergoes a major transition leading to a relaxation corresponding to a reduction in twist of ∼ 2.5 helical turns. The transition free energy is ∼10 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.
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