Inferring the in vivo looping properties of DNA

Abstract

The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of the loop and found that, in addition to the intrinsic periodicity of the DNA double helix, the free energy has an oscillatory component with about half the helical period. Moreover, the oscillations have such an amplitude that the effects of regulatory molecules become strongly dependent on their precise DNA positioning and yet easily tunable by their cooperative interactions. These unexpected results can confer to the physical properties of DNA a more prominent role at shaping the properties of gene regulation than previously thought.

arXiv comment20 pages, 4 figures

References in corpus (1)

• DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise

Cited by in corpus (18)

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• Multilevel Deconstruction of the In Vivo Behavior of Looped DNA-Protein Complexes
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• DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation
• Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system
• Control of gene expression by modulated self-assembly
• Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension
• In vivo evidence of alternative loop geometries in DNA-protein complexes
• Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy
• Efficiency and versatility of distal multisite transcription regulation
• Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation
• Colloidal particle motion as a diagnostic of DNA conformational transitions
• Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression