Fig. 5.
Comparison of the calculated DNase I cutting patterns of different 74-bp LacR-mediated loops formed from the pHK74 construct with the observed protection pattern (20): AATTGTGAGC GCTCACAATT CCACACACTC TAGCAACTAG TGAGCTTGGC TGCAGGTCGA CGGATCCCCCTAGA AATTGTGAGC GCTCACAATT. The high-affinity symmetrized LacR binding sites are shown in boldface, and the sites of enhanced and diminished DNase I activity are underlined by double and single lines, respectively. (A) Plots of free energy of DNA loops, GDNA, versus enzyme binding location n for A1 (green line), A2 (cyan line), P1 (blue line), and P1E (red line) loop types. (The number n denotes the distance of bound enzyme from the center of the first operator.) In each case the dotted line corresponds to the free energy of the pHK74 loop in the absence of DNase I: A1, 77.5 kT; A2, 87.4 kT; P1, 109.4 kT; P1E, 70.5 kT. (B) The predicted sites of enhanced (“x”) and diminished (“o”) DNase I sensitivity correspond, respectively, to the valleys and peaks in the plots of GDNA versus n in A. (The valleys for which the minimum value of GDNA is larger than the free energy of the pHK74 loop in the absence of DNase I, and hence where no enhancement is expected, are marked with a lightly shaded “x.”) The experimentally observed sites (20) are noted by the label pHK74.