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. 2014 Aug 5;107(3):700–710. doi: 10.1016/j.bpj.2014.06.023

Figure 7.

Figure 7

ATTO-DNA systems simulated by MD in the course of this work. (A) DNA duplex modeling the product of the Cre-recombination reaction in (42), in which donor and acceptor fluorophores are conjugated to C5 positions of adjacent thymine residues on opposing strands. (B) A fluorophore-labeled Cre-mediated synapse of DNA duplexes based on the PDB cocrystal structure 5CRX (46,60). (C) The Cre HJ intermediate complex based on the PDB cocrystal structure 3CRX (45,46,60) with fluorophore labels at sites corresponding to the positions used in Shoura et al. (42). Integrated positions of donor (green) and acceptor (red) centers of mass over the course of complete trajectories in aqueous solution are shown. See also Movie S2. (Two columns, 6.5″ W × 5.19″ H.) To see this figure in color, go online.