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(Received for publication, February 20, 1996, and in revised form, May 9, 1996)
From the Similar imperfect purine/pyrimidine mirror repeat
(PMR) elements have previously been identified upstream of the human
MUC1 mucin and CFTR genes. These elements
confer S1 nuclease sensitivity on isolated plasmid DNA at low pH. We
now present a detailed characterization of the non-B DNA structure
responsible for S1 nuclease sensitivity upstream of the
MUC1 gene. A ~90-base pair (bp) DNA fragment containing a
32-bp PMR element termed M-PMR3 was subcloned into a recombinant
vector. This fragment conferred S1 nuclease sensitivity on the
resulting supercoiled plasmid. High resolution mapping of sites
reactive to S1 and P1 nucleases demonstrates that cleavage occurs
within the M-PMR3 element. High resolution mapping with chemical agents
selective for non-B DNA provides evidence that M-PMR3 adopts an H-DNA
structure (intramolecular triple helix) in the less common H-y5 isomer
at low pH. This result is observed in the presence or absence of
Mg2+. Mutation of the native M-PMR3 element to create
perfect homopurine/homopyrimidine mirror symmetry alters the preferred
folding to the more common H-y3 triplex DNA isomer. These results
demonstrate that imperfections in mirror symmetry can alter the
relative stabilities of different H-DNA isomers.
Volume 271, Number 30,
Issue of July 26, 1996
pp. 18061-18067
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
,
,
and
Eppley Institute for Research in Cancer and
Allied Diseases, University of Nebraska Medical Center, Omaha,
Nebraska 68198-6805 and the § Department of Biochemistry
and Molecular Biology, Mayo Foundation, Rochester,
Minnesota 55905
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