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. Author manuscript; available in PMC: 2013 Jul 18.
Published in final edited form as: Int J Non Linear Mech. 2008 Dec;43(10):1082–1093. doi: 10.1016/j.ijnonlinmec.2008.07.003

Table 3.

Calculated energy (in kT) and configurational parameters for O3*-O1 LacR-mediated DNA loops with bound CAP.†

Loop α β Lk Ψ Φ GLacR GDNA ΔGDNA
A1e 34 33 9 65.6 76.2 – 154.4 70.2
A1f 34 33 10 48.4 72.6 – 133.6 49.4
A2e 34 33 8 65.2 74.9 – 153.0 68.8
A2f 34 33 9 23.0 72.8 – 108.1 23.9
P1e 34 33 9 90.6 80.6 – 183.2 99.0
P1f 34 33 10 54.8 75.7 – 142.5 58.3
P2c 34 33 10 35.4 73.9 – 122.4 38.2
Ee 61 2 9 54.4 73.7 2.8±1 144.0±1 59.8±1
Free – – – 0 70.5 – 84.2
†

Loops denoted by labels in Figure 6; α, β, Lk, Ψ, Φ, GLacR, GDNA are as in Table 1. “Free” refers to the unbound, linear DNA chain of the (O3*-O1) sequence: AAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATT. Here the O3* and O1 sequences are shown in boldface and the CAP binding site is underlined.