Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site

Figure 1

(Top) structure of the dodecamer containing the HhaI target GCGC sequence (red) in the protein-DNA complex (protein removed), showing the extrahelical deoxycytidine. (Bottom) sequence of the target DNA; residues highlighted in red are labeled at the 5′/5″ position. Residues highlighted in green are labeled at the 2″ position.