Molecular Models

It is generally valuable to prepare molecular models of the final device designs. This is often quite difficult because structural information on the proteins involved may be unavailable. For designs involving well-characterized structures, models have been constructed in Insight II (Accelrys, San Diego, CA). In those cases [15,27] a model of the DNA scaffold (linear DNA or Y-junction) was constructed, and the DNA present in the three dimensional structure of the bacterial methyl-transferase-DNA complex [28,29] was spliced into the DNA model at the appropriate site. After constraining the protein and the DNA at the protein binding sites, the structures were then minimized in molecular mechanics using the Dreiding force field in Biograf (MSI, San Diego, CA) or the AMBER force field in Insight II until the RMS force was less that 0.1 (kcal/mol) /A, followed by 1000 steps of simple dynamics. Models of the M-EcoRII containing devices have not yet been prepared, however inspection of the homology models of this protein [30] suggests that the parameters used in the construction of the devices containing M-HhaI [1,27] would carry over to the devices described here.

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