Energy minimized structures of base displacement in an AAF modified B-DNA dodecamer are presented. A rational search strategy, beginning with a global search of the conformation space of the modified deoxydinucleoside monophosphate, together with model building by computer graphics, has been employed. A number of different minimum energy conformations have been located which reveal base displaced structures. These show fluorene interstrand stacking, fluorene inter- and intrastrand stacking, and non-stacked fluorene situated in the denatured bulge. The local helix axis is bent to various extents in the different forms, and one or two base pairs are fully denatured. One structure of especial interest offers a molecular view that suggests how AAF can induce the -2 deletion mutation observed in AAF modified E. coli (18).
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