Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping 1 1Edited by R. Ebright

Tsodikov, Oleg V.; Saecker, Ruth M.; Melcher, Sonya E.; Levandoski, Mark M.; Frank, Diane E.; Michael, W.; Record, M. Thomas

doi:10.1006/jmbi.1999.3283

Cited by 37 publications

(41 citation statements)

References 69 publications

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“…Based on DNA wrapping in LacI-DNA interactions, the parallel mode was suggested as a general model of DNA loop formation (Tsodikov et al 1999). However, in AFM studies of the Gal repressosome, the parallel geometry of DNA loop was not observed (Virnik et al 2003).…”

Section: Discussionmentioning

confidence: 99%

“…The structure of the GalR tetramer allows the operators in the loop to be either parallel (wrapping mode; Friedman et al 1995;Tsodikov et al 1999) or antiparallel (looping mode; Geanacopoulos et al 2001). In each mode the DNA loop can have two alternative trajectories, which differ in the relative stacking arrangements of the two operator-bound GalR dimers (see Fig.…”

mentioning

confidence: 99%

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DNA trajectory in the Gal repressosome

Semsey¹,

Tolstorukov²,

Virnik³

et al. 2004

Genes Dev.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

DNA trajectory in the Gal repressosome

Semsey¹,

Tolstorukov²,

Virnik³

et al. 2004

Genes Dev.

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“…We treat the bead as a sphere, the wall as a plane and the steric exclusion between them as a hard-wall interaction. We neglect nonspecific DNA–protein interactions (‘wrapping’ [20]).…”

Section: Introductionmentioning

confidence: 99%

First-principles calculation of DNA looping in tethered particle experiments

et al. 2009

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We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in tethered particle motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the ‘looping J factor’ (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on TPM, and then compare to our model’s predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our first-principles predictions for the looping free energy change are confirmed to within about 1 kBT, for loops of length around 300 basepairs. More significantly, our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical ‘open’ conformation of the LacI tetramer.

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“…The availability of crystallographic structures for the repressor alone and in complex with two DNA oligonucleotides [19,20], together with studies of the thermodynamic and kinetic stabilities of Lac repressor–DNA looped complexes in vitro [7,21–25], have led to the proposal of a variety of different structural models for looped protein–DNA complexes [1,19,20,24,26–28]. Most of these models are based on the crystallographic repressor–oligonucleotide model and a smoothly bent interoperator DNA segment.…”

Section: Introductionmentioning

confidence: 99%

Interconvertible Lac Repressor–DNA Loops Revealed by Single-Molecule Experiments

et al. 2008

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At many promoters, transcription is regulated by simultaneous binding of a protein to multiple sites on DNA, but the structures and dynamics of such transcription factor-mediated DNA loops are poorly understood. We directly examined in vitro loop formation mediated by Escherichia coli lactose repressor using single-molecule structural and kinetics methods. Small (∼150 bp) loops form quickly and stably, even with out-of-phase operator spacings. Unexpectedly, repeated spontaneous transitions between two distinct loop structures were observed in individual protein–DNA complexes. The results imply a dynamic equilibrium between a novel loop structure with the repressor in its crystallographic “V” conformation and a second structure with a more extended linear repressor conformation that substantially lessens the DNA bending strain. The ability to switch between different loop structures may help to explain how robust transcription regulation is maintained even though the mechanical work required to form a loop may change substantially with metabolic conditions.

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Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping 1 1Edited by R. Ebright

Cited by 37 publications

References 69 publications

DNA trajectory in the Gal repressosome

DNA trajectory in the Gal repressosome

First-principles calculation of DNA looping in tethered particle experiments

Interconvertible Lac Repressor–DNA Loops Revealed by Single-Molecule Experiments

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