. 2009 Jun 9;37(14):4707–4722. doi: 10.1093/nar/gkp475

Table 1.

Predicted (F_pred) and measured (F_exp) free energies of computationally designed and control sequences

	F_pred (arb.units)	F_exp (kcal/mol)
B71S1	−20.09	−1.57 ± 0.41
B71S2	−20.10	−1.51 ± 0.27
601S1	−0.49	−2.99 ± 0.55
601S2	−1.74	−2.46 ± 0.18
W147S	15.26	0.09 ± 0.23
X147	5.92	0.75 ± 0.29
X146	6.86	0.45 ± 0.91

Experimental free energies are shown relative to the reference sequence from the Lumbriculus variegatus 5S rRNA gene. Histone binding is dominated by the contribution from the H3₂H4₂ tetramer with the 71 bp binding site (25). The best binder was created by using simulated annealing to introduce mutations and thus minimize the energy of a 71 bp DNA molecule. B71S1 and B71S2 have different sequences flanking the 71 bp designed site (whose contribution dominates the total free energy). 601S1 and 601S2 consist of the 71-bp site from the center of the 601 sequence (27) and flanking sequences from B71S1 and B71S2, respectively. W147S is a 147 bp sequence whose free energy (with contributions from multiple H3₂H4₂ binding sites) was maximized by simulated annealing. X146 and X147 are 146 and 147 bp DNA sequences from nucleosome crystal structures 1aoi (10) and 1kx5 (2).