Nucleic Acids Research, 1977, Vol. 4, No. 5 1579-1594
© 1977
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Binding of E.coli lac repressor to non-operator DNA*
Institute of Molecular Biology and Department of Chemistry, University of Oregon Eugene, OR 97403, USA
Received January 17, 1977.
It is shown by melting profile analysis of lac repressor-DNA complexes that repressor binds tightly and preferentially (relative to single-stranded DNA) to double-stranded non-operator DNA. This binding stabilizes the DNA against melting and the repressor against thermal denaturation. Analysis of the extent of stabilization and the rate of dissociation of repressor from non-operator DNA as a function of sodium ion concentration shows, in confirmation of other studies,3,4 that the binding constant (KRD) is very ionic strength dependent; KRD increases from {small tilde} 106 M–1 at {small tilde}0.1 M Na+ to values in excess of 1010 M–1 at 0.002 M Na+. Repressor bound to non-operator DNA is not further stabilized against thermal denaturation by inducer binding, indicating that the inducer and DNA binding sites probably represent separately stabilized local conformations. Transfer melting experiments are used to measure the rate of dissociation of repressor from operator DNA. These experiments show that most of the ionic strength dependence of the binding constant is in the dissociation process; the estimated dissociation rate constant decreases from greater than 10–1 sec–1 at [Na+]
0.02 M to less than 10–4 sec–1 at [Na+] 
0.002 M. Competition melting experiments are used to show that at 0.02 to 0.002 M Na+ the affinity of lac repressor for various natural DNAs and synthetic double-stranded polynucleotides (including poly[d(m6A-T)], which carries a methyl group in the large groove) are approximately independent of base composition, except that the affinity of repressor for poly[d(A-T)] is {small tilde} 2- to 3-fold greater than for the other DNAs tested. The affinity for single-stranded polynucleotides is at least 50-fold less than for the double-helical forms.
*Dedicated to the memory of Jerome Vinograd. These studies were supported in part by USPHS Research Grants GM-l5792 and GM-15423, as well as by a USPHS post-doctoral fellowship (GM-55928) to A.R., and a pre-doctoral traineeship (from USPHS Training Grant GM-OO715) to A.P.B. We are grateful to Ms. Ying Kao Huang and Ms. Pamela O'Conner for preparing much of the repressor used in these studies.
1Present address: Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824.
2Present address: Division of Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830.3
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