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(Received for publication, April 12, 1995; and in revised form, June 21, 1995) The binding of DNA topoisomerase III (Topo III) to a
single-stranded DNA substrate containing a strong cleavage site has
been examined. The minimal substrate requirement for Topo III-catalyzed
cleavage has been determined to consist of 7 bases: 6 bases 5` to the
cleavage site and only 1 base 3` to the site. Nuclease P1 protection
experiments indicate that the enzyme also binds to its substrate
asymmetrically, protecting
Volume 270,
Number 40,
Issue of October 06, pp. 23700-23705, 1995
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
12 bases 5` to the cleavage site and
only 2 bases 3` to the cleavage site. A catalytically inactive mutant
of Topo III shows the same protection pattern as the active
polypeptide, indicating that Topo III is a site-specific binding
protein as well as a topoisomerase. Consistent with this view, an
oligonucleotide containing a cleavage site is a more effective
inhibitor and is bound more efficiently by Topo III than an
oligonucleotide without a cleavage site.
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