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. 1991 Jul 1;88(13):5699–5703. doi: 10.1073/pnas.88.13.5699

Specificity of the Mnt protein determined by binding to randomized operators.

G D Stormo 1, M Yoshioka 1
PMCID: PMC51945  PMID: 2062848

Abstract

The relative binding affinities of Mnt protein from bacteriophage P22 are determined for each possible base pair at position 17 of the operator. These are determined from the partitioning of randomized operators into bound and unbound fractions; quantitation is provided by restriction enzyme analysis. Mnt protein is found to have an unusual specificity at this position: a C.G base pair (the wild-type operator) has the highest affinity, a G.C base pair has the lowest affinity, and both orientations of A.T base pairs are intermediate and nearly equivalent. A specific binding constant and specific binding free energy are defined and shown to be directly related to the information content of the operator sequences bound to the protein, taking into account the quantitative differences in binding affinities.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Berg O. G. Selection of DNA binding sites by regulatory proteins: the LexA protein and the arginine repressor use different strategies for functional specificity. Nucleic Acids Res. 1988 Jun 10;16(11):5089–5105. doi: 10.1093/nar/16.11.5089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berg O. G., von Hippel P. H. Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol. 1988 Apr 20;200(4):709–723. doi: 10.1016/0022-2836(88)90482-2. [DOI] [PubMed] [Google Scholar]
  3. Berg O. G., von Hippel P. H. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol. 1987 Feb 20;193(4):723–750. doi: 10.1016/0022-2836(87)90354-8. [DOI] [PubMed] [Google Scholar]
  4. Bowie J. U., Sauer R. T. TraY proteins of F and related episomes are members of the Arc and Mnt repressor family. J Mol Biol. 1990 Jan 5;211(1):5–6. doi: 10.1016/0022-2836(90)90004-6. [DOI] [PubMed] [Google Scholar]
  5. Knight K. L., Bowie J. U., Vershon A. K., Kelley R. D., Sauer R. T. The Arc and Mnt repressors. A new class of sequence-specific DNA-binding protein. J Biol Chem. 1989 Mar 5;264(7):3639–3642. [PubMed] [Google Scholar]
  6. Knight K. L., Sauer R. T. DNA binding specificity of the Arc and Mnt repressors is determined by a short region of N-terminal residues. Proc Natl Acad Sci U S A. 1989 Feb;86(3):797–801. doi: 10.1073/pnas.86.3.797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Knight K. L., Sauer R. T. Identification of functionally important residues in the DNA binding region of the mnt repressor. J Biol Chem. 1989 Aug 15;264(23):13706–13710. [PubMed] [Google Scholar]
  8. Sarai A., Takeda Y. Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6513–6517. doi: 10.1073/pnas.86.17.6513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Schneider T. D., Stormo G. D. Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Res. 1989 Jan 25;17(2):659–674. doi: 10.1093/nar/17.2.659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Schneider T. D., Stormo G. D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986 Apr 5;188(3):415–431. doi: 10.1016/0022-2836(86)90165-8. [DOI] [PubMed] [Google Scholar]
  11. Staacke D., Walter B., Kisters-Woike B., von Wilcken-Bergmann B., Müller-Hill B. How Trp repressor binds to its operator. EMBO J. 1990 Jun;9(6):1963–1967. doi: 10.1002/j.1460-2075.1990.tb08324.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Stormo G. D. Computer methods for analyzing sequence recognition of nucleic acids. Annu Rev Biophys Biophys Chem. 1988;17:241–263. doi: 10.1146/annurev.bb.17.060188.001325. [DOI] [PubMed] [Google Scholar]
  13. Stormo G. D. Consensus patterns in DNA. Methods Enzymol. 1990;183:211–221. doi: 10.1016/0076-6879(90)83015-2. [DOI] [PubMed] [Google Scholar]
  14. Stormo G. D., Schneider T. D., Gold L. Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res. 1986 Aug 26;14(16):6661–6679. doi: 10.1093/nar/14.16.6661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Takeda Y., Sarai A., Rivera V. M. Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc Natl Acad Sci U S A. 1989 Jan;86(2):439–443. doi: 10.1073/pnas.86.2.439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Vershon A. K., Liao S. M., McClure W. R., Sauer R. T. Bacteriophage P22 Mnt repressor. DNA binding and effects on transcription in vitro. J Mol Biol. 1987 May 20;195(2):311–322. doi: 10.1016/0022-2836(87)90652-8. [DOI] [PubMed] [Google Scholar]
  17. Vershon A. K., Youderian P., Susskind M. M., Sauer R. T. The bacteriophage P22 arc and mnt repressors. Overproduction, purification, and properties. J Biol Chem. 1985 Oct 5;260(22):12124–12129. [PubMed] [Google Scholar]
  18. Youderian P., Vershon A., Bouvier S., Sauer R. T., Susskind M. M. Changing the DNA-binding specificity of a repressor. Cell. 1983 Dec;35(3 Pt 2):777–783. doi: 10.1016/0092-8674(83)90110-1. [DOI] [PubMed] [Google Scholar]

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