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. 2012 Nov 7;41(1):156–166. doi: 10.1093/nar/gks1011

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

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Figure 4. — Repression data and fits to thermodynamic model for loops with upstream (A and B) versus downstream (C–F) auxiliary O_sym operators. Reporter activity is shown as E' (A, C and E) where the shaded envelope in (A) indicates behavior of upstream loop constructs under induced (open symbols, dashed fit curve) or repressed (filled symbols, solid fit curve) conditions with fits to thermodynamic model. Blue symbols for spacings closer than the vertical line at 41 bp (C–F) indicate constructs that do not show a canonical looping pattern. Panels (B, D and F) show RR data and fits to the thermodynamic model (see Supplementary Figure S3). Filled triangles and dashed fits indicate RR data for strains containing only an auxiliary O_sym operator in the absence of a proximal operator. Grey fits in panels (D) and (F) indicate RR behaviour of upstream loops from (B). Green symbols and fits in panels (E) and (F) show data obtained in the absence of functional Lac repressor (LacI Y282D). Data and fit in magenta (panel F) show the modified RR for downstream loop constructs where the numerator reflects reporter expression in the absence of functional repressor (LacI Y282D) and the denominator reflects repressed reporter expression in the presence of wild-type Lac repressor.