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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 2.

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
A1c 34 33 9 38.2 71.2 – 121.9 42.2
A1d 34 33 10 50.1 70.0 – 132.1 52.4
A2c 34 33 8 76.5 73.7 – 162.6 82.9
A2d 34 33 9 80.6 73.6 – 167.0 87.3
P1c 34 33 9 44.5 72.9 – 128.2 48.5
P1d 34 33 10 82.8 73.9 – 167.7 88.0
Ec 110 18 8 35.6 68.9 2.8±1 120.1±1 40.4±1
Ed 108 −50 9 24.3 67.2 2.8±1 105.9±1 26.2±1
Free – – – 0 67.0 – 79.7
†

Loops denoted by labels in Figure 4; α, β, Lk, Ψ, Φ, GLacR, GDNA are as in Table 1. ΔGDNA: free energy difference between loop and “free” DNA with bound CAP and LacR dimers. Sequence: GGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATT. Here the O3 and O1 sequences are shown in boldface and the CAP binding site is underlined.