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Understanding DNA Looping Through Cre-Recombination Kinetics

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Discrete and Topological Models in Molecular Biology

Part of the book series: Natural Computing 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.

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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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Authors and Affiliations

  1. The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, TX, 75080, USA

    Massa J. Shoura & Stephen D. Levene

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  1. Massa J. Shoura
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  2. Stephen D. Levene
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Correspondence to Massa J. Shoura .

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Editors and Affiliations

  1. Dept. Mathematics & Statistics, University of South Florida, Tampa, Florida, USA

    Nataša Jonoska

  2. Dept. Mathematics & Statistics, University of South Florida, Tampa, Florida, USA

    Masahico Saito

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Shoura, M.J., Levene, S.D. (2014). Understanding DNA Looping Through Cre-Recombination Kinetics. In: Jonoska, N., Saito, M. (eds) Discrete and Topological Models in Molecular Biology. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40193-0_19

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  • DOI: https://doi.org/10.1007/978-3-642-40193-0_19

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