J. Med. Chem. 1991,34, 1998-2003
1998
material). Reminimization was then done in AMBER. The octanucleotide duplex d(GATGCAT02was constructed and minimized in AMBER using Amott's B DNA geometry.% Figure 3 shows a schematic for this sequence. Minimized saframycin A species were docked onto it near G4 using MIDAS. In many cases, it was obvious that certain orientations would give unsatisfactory models. For protonated saframycin A hydroquinone the covalent models were made in both the 3' and 5' direction. Subsequent models were made only in the 3' direction. Coordinates of the docked models were captured and the structures were refined in AMBER to a root mean square value of
