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Research Article

Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping

  • Yongli Zhang mail,

    To whom correspondence should be addressed. E-mail: sdlevene@utdallas.edu

    Affiliation: Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America

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  • Abbye E. McEwen,

    Affiliation: Institute of Biomedical Sciences and Technology, University of Texas at Dallas, Richardson, Texas, United States of America

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  • Donald M. Crothers,

    Affiliation: Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America

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  • Stephen D. Levene mail

    To whom correspondence should be addressed. E-mail: sdlevene@utdallas.edu

    Affiliations: Institute of Biomedical Sciences and Technology, University of Texas at Dallas, Richardson, Texas, United States of America, Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas, United States of America

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  • Published: December 27, 2006
  • DOI: 10.1371/journal.pone.0000136

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Figure S1

Posted by Bonnie_Real on 19 Jan 2007 at 01:18 GMT

(see Figure S1)
http://plosone.org/article/info:doi/10.1371/journal.pone.0000136#article1.body1.sec2.sec2.p2

Due to a PLoS error, this figure is presented as the final figure in the paper (doi:10.1371/journal.pone.0000136.g008) rather than in Supporting Information. The legend was also omitted, it is as follows:

Dependence of the J factor and ΔGloop on the dihedral angle, τPP, between LacR dimers in the v-shaped tetramer conformation. All calculations were done for the case of a rigid LacR tetramer assembly. Loop topoisomers were labeled as (-) or (+) depending on whether the total loop twist was respectively less than or greater than that for a relaxed loop. (A) J factor and ΔGloop as functions of τPP for 163-bp (torsionally in-phase) and 179-bp (torsionally out-of-phase) loops in the LB conformation. In the case of the 179-bp LB loop, values for both (+) and (-) loop topoisomers as well as their sum are shown. The 163-bp LB loop is only very slightly underwound and therefore contributions from the (+) topoisomer are negligible. (B) J factor and ΔGloop as functions of τPP for 179-bp (torsionally in-phase) and 163-bp (torsionally out-of-phase) WA loops. Individual contributions from (+) and (-) loop topoisomers as well as totals are shown for the 163-bp loop. (C) J-factor and ΔGloop dependence on τPP for 179-bp (torsionally in-phase) and 165-bp (partially out-of-phase) WT loops. Solutions for mechanical-equilibrium conformations failed to converge near the expected J-factor minimum (163-bp), most likely because of high strain energy in strongly under- and overwound WT conformations. Interestingly, there is only slight asymmetry present in the nearly parabolic dependence on dihedral angle.