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J Biol Chem, Vol. 273, Issue 36, 23558-23566, September 4, 1998
From the Department of Biological Sciences, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213
We report the effects of depurination and
prenicking at various positions of the phage
Stimulation of Open Complex Formation by Nicks and Apurinic Sites
Suggests a Role for Nucleation of DNA Melting in Escherichia
coli Promoter Function
prmup-1
265 promoter DNA on the rate of open complex
formation. We have found that depurination and prenicking at positions
around the 
10 region strongly stimulated the rate of open complex
formation. Since nicking and depurination are known to destabilize DNA
helical structure, our observations indicate that the instability of
the 10 region is important for open complex formation. We further
infer that (i) the nucleation of DNA melting, which occurs during the
isomerization from the closed complex into the open complex,
contributes to the rate of open complex formation; (ii) the nucleation
of melting occurs around the 10 region; and (iii) the propagation of
DNA melting from the nucleation region is not rate-limiting. In
addition, we have found that depurination at several positions
inhibited open complex formation. We used dimethyl sulfate modification protection studies to show that most of the guanine bases that are
among these positions are in contact with RNA polymerase in the open
complex.
Copyright © 1998 by The American Society for Biochemistry and Molecular Biology, Inc.
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