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Understanding DNA Looping Through Cre-Recombination Kinetics

  • Massa J. ShouraEmail author
  • Stephen D. Levene
Chapter
Part of the Natural Computing Series book series (NCS)

Abstract

The interior of a cell is a crowded and fluctuating environment where DNA and other biomolecules are both highly constrained and subject to many mechanical forces. The extensive compaction of DNA in living cells is a challenge to many critical biological functions. An evolutionary solution to this challenge may be the juxtaposition of cis-acting elements such that multimeric protein complexes simultaneously interact with two or more protein-binding sites. This mode of biological activity involves the formation of looped DNA structures, which, by themselves, are thermodynamically unfavorable. Our knowledge about the roles of DNA bending, twisting, and their respective energetics in DNA looping has come mainly from analyses of ligase-dependent DNA cyclization experiments, which are quantitatively described by the Jacobson–Stockmayer, or J, factor. In this chapter, we discuss a novel quantitative approach to measuring the probability of DNA loop formation in solution using ensemble Förster resonance energy transfer (FRET) measurements of intramolecular and intermolecular Cre-recombination kinetics. Because the mechanism of Cre recombinase does not conform to a simple kinetic scheme, we employ numerical methods to extract rate constants for fundamental steps that pertain to Cre-mediated loop closure.

Keywords

Extract Rate Constant Intermolecular Reaction Transcription Factor Interaction Intramolecular Recombination Repeat loxP Site 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank Andreas Hanke and Stefan Giovan for calculations of J theor. This work was supported by a grant from the NIH/NSF Joint Program in Mathematical Biology (DMS-0800929 from the National Science Foundation) to SDL.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.The University of Texas at DallasRichardsonUSA

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