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Nucleic Acids Research, 1991, Vol. 19, No. 23 6527-6532
© 1991

MOLECULAR BIOLOGY

H-DNA and Z-DNA in the mouse c-Ki-ras promoter

Dmitri G. Pestov, Andrey Dayn, Elena Yu. Siyanova, Donna L. George1 and Sergei M. Mirkin*

Department of Genetics, University of Illinois at Chicago Chicago, IL 60612 1Department of Human Genetics and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine Philadelphia, PA 19104-6145, USA

*To whom correspondence should be addressed

Received August 6, 1991. Accepted November 5, 1991.

The mouse c-Ki-ras protooncogene promoter contains a homopurine-homopyrimidine domain that exhibits S1 nuclease sensitivity in vitro. We have studied the structure of this DNA region in a supercoiled state using a number of chemical probes for non-B DNA conformations including diethyl pyrocarbonate, osmium tetroxide, chloroacetaldehyde, and dimethyl sulfate. The results demonstrate that two types of unusual DNA structures formed under different environmental conditions. A 27-bp homopurinehomopyrimidine mirror repeat adopts a triple-helical HDNA conformation under mildly acidic conditions. This H-DNA seems to account for the S1 hypersensitivity of the promoter in vitro, since the observed pattern of S1 hypersensitivity at a single base level fits well with the H-DNA formation. Under conditions of neutral pH we have detected Z-DNA created by a (CG)5-stretch, located adjacent to the homopurine-homopyrimidine mirror repeat. The ability of the promoter DNA segment to form non-B structures has implications for models of gene regulation.


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