Aspects of protein–DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ

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• 作者：Peter D. Munro ; Gary K. Ackers ; Keith E. Shearwin
• 关键词：Synthetic biology ; Mathematical model ; lac repressor ; Lambda CI repressor ; Escherichia coli expression system
• 刊名：Biophysical Reviews
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：8
• 期：4
• 页码：331-345
• 全文大小：
• 刊物类别：Physics and Astronomy
• 刊物主题：Biochemistry, general; Biological and Medical Physics, Biophysics; Cell Biology; Membrane Biology; Biological Techniques; Nanotechnology;
• 出版者：Springer Berlin Heidelberg
• ISSN：1867-2469
• 卷排序：8

文摘

Protein–DNA interactions are central to the control of gene expression across all forms of life. The development of approaches to rigorously model such interactions has often been hindered both by a lack of quantitative binding data and by the difficulty in accounting for parameters relevant to the intracellular situation, such as DNA looping and thermodynamic non-ideality. Here, we review these considerations by developing a thermodynamically based mathematical model that attempts to simulate the functioning of an Escherichia coli expression system incorporating two of the best characterised prokaryotic DNA binding proteins, Lac repressor and lambda CI repressor. The key aim was to reproduce experimentally observed reporter gene activities arising from the expression of either wild-type CI repressor or one of three positive-control CI mutants. The model considers the role of several potentially important, but sometimes neglected, biochemical features, including DNA looping, macromolecular crowding and non-specific binding, and allowed us to obtain association constants for the binding of CI and its variants to a specific operator sequence.