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Nucleic Acids Research, Vol 26, Issue 6 1503-1508, Copyright © 1998 by Oxford University Press

ARTICLES

Non-complementary DNA helical structure induced by positive torsional stress

AV Vologodskii, X Yang and NC Seeman
Department of Chemistry, New York University, New York, NY 10003, USA.

We have induced a local conformational transition by positive torsional stress in small synthetic circular DNA molecules containing cruciforms with immobile or tetramobile branched junctions. The immobile species correspond to the extruded and intruded extrema of the tetramobile junction. Under normal conditions the sequences of all the branched species prevent them from being re-absorbed into the circle. We have induced positive stress by addition of ethidium to the circle, in a low ionic strength medium. Alterations in gel electrophoretic mobility under increasing concentrations of ethidium suggest that the cruciforms undergo a transition under torsional stress. The product of this transition contains mispaired nucleotides, but interwound backbones. By comparing the electrophoretic mobilities of circles containing these structures with that of a completely complementary circle of the same length, we conclude that the twist in the mispairing region is similiar to that of completely paired species.
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