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Type: Journal article
Title: Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements
Author: Hao, N.
Sneppen, K.
Shearwin, K.
Dodd, I.
Citation: Nucleic Acids Research, 2017; 45(9):5074-5085
Publisher: Oxford University Press
Issue Date: 2017
ISSN: 0305-1048
Statement of
Nan Hao, Kim Sneppen, Keith E. Shearwin, Ian B. Dodd
Abstract: Genes are frequently regulated by interactions between proteins that bind to the DNA near the gene and proteins that bind to DNA sites located far away, with the intervening DNA looped out. But it is not understood how efficient looping can occur when the sites are very far apart. We develop a simple theoretical framework that relates looping efficiency to the energetic cost and benefit of looping, allowing prediction of the efficiency of single or multiple nested loops at different distances. Measurements of absolute loop efficiencies for Lac repressor and ╬╗ CI using gene expression reporters in Escherichia coli cells show that, as predicted by the model, long-range DNA looping between a pair of sites can be strongly enhanced by the use of nested DNA loops or by the use of additional protein-binding sequences. A combination of these approaches was able to generate efficient DNA looping at a 200 kb distance.
Keywords: Infarction; lacunar; DNA; escherichia coli; tissue factor pathway inhibitor
Rights: The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
DOI: 10.1093/nar/gkx069
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