Inferring the in vivo looping properties of DNA

Details Inferring the in vivo looping properties of DNA Inferring the in vivo looping properties of DNA

2005-12-20

arxiv.org/abs/q-bio/0512036v1

Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005)

Biology

Quantitative Biology

Biomolecules

20 pages, 4 figures

Scientific paper

10.1073/pnas.0505693102

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.

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