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Nucleic Acids Research, 1988, Vol. 16, No. 12 5473-5490
© 1988

Articles

Intermediate range effects in DNA I: low pH/stress induced conformational changes in the vicinity of an extruded d(AT)n·d(AT)n cruciform

J. N. Mark Glover, David B. Haniford and David E. Pulleyblank

Department of Biochemistry, University of Toronto Toronto, Ontario, M5S 1A8, Canada

Received February 8, 1988. Revised May 19, 1988. Accepted May 19, 1988.

A family of plasmids which contain d(AT)n cruciforms are sensitive to "single strand specific" (SS) endonucleases and a variety of chemical probes in a "random sequence" region centered 10–30 residues away from the cruciform junction. The SS nuclease sensitive structures are dependent on the presence of the extruded cruciform and exhibit a degree of sequence independence. Their appearance depends upon the combined effects of slightly lower than neutral pH and superhelical coiling above the minimum required to drive the extrusion of the d(AT)n cruciform arms. The nuclease sensitive structure is therefore underwound with respect to the B conformation and contains protonated bases.


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