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. 2012 May 16;102(10):2331–2338. doi: 10.1016/j.bpj.2012.04.013

Table 2.

Relative free energy (kcal/mol) of HMGB1a binding to Cp versus Ox

Sequence (reference) KD ratio ΔΔGbind from KD ratio ΔΔGdeform,2D
AGGC (6) 2.6 −0.56 0.10
CGGA (6) 3.2 −0.69 −0.13
TGGA (5) 55.1 −2.39 −0.87
TGGT (6) 1.8 −0.35 −0.39

Values are calculated from experimental binding affinity data (ΔΔGbind from KD ratio) and from 2D deformability umbrella sampling calculations (ΔΔGdeform,2D). ΔΔG is the difference in 2D deformation energy between Ox and Cp, i.e., a negative value indicates that deforming Cp-DNA is easier than deforming Ox-DNA.