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J. Biol. Chem., Vol. 278, Issue 15, 12955-12960, April 11, 2003
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From the Department of Biological Sciences, University at Buffalo,
Buffalo, New York 14260-1300
The sequence of non-contacted bases at the center
of the 434 repressor binding site affects the strength of the
repressor-DNA complex by influencing the structure and flexibility of
DNA (Koudelka, G. B., and Carlson, P. (1992) Nature
355, 89-91). We synthesized 434 repressor binding sites that differ in
their central sequence base composition to test the importance of minor
groove substituents and/or the number of base pair hydrogen bonds
between these base pairs on DNA structure and strength of the
repressor-DNA complex. We show here that the number of base pair
H-bonds between the central bases apparently has no role in determining
the relative affinity of a DNA site for repressor. Instead we find that
the affinity of DNA for repressor depends on the absence or presence the N2-NH2 group on the purine bases at the binding site
center. The N2-NH2 group on bases at the center of the 434 binding site appears to destabilize 434 repressor-DNA complexes by
decreasing the intimacy of the specific repressor-DNA contacts, while
increasing the reliance on protein contacts to the DNA phosphate
backbone. Thus, the presence of an N2-NH2 group on the
purines at the center of a binding site globally alters the precise
conformation of the protein-DNA interface.
The Role of the Minor Groove Substituents in Indirect Readout of
DNA Sequence by 434 Repressor*
*
The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence should be addressed: Dept. of Biological
Sciences, University at Buffalo (SUNY), Cooke Hall, North Campus,
Buffalo, NY 14260-1300. Tel.: 716-645-2363, Ext. 158; Fax:
716-645-2975; E-mail: koudelka@acsu.buffalo.edu.
Copyright © 2003 by The American Society for Biochemistry and Molecular Biology, Inc.
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