Interactions of molecules with nucleic acids. VII. Evaluation and presentation of steric contours and molecules in bonding sites

A technique to generate steric contours is developed and applied to the presentation of molecules that interact with DNA. The contours are generated by a Taylor's expansion in an extrapolation procedure designed to avoid infinite derivatives and correct for reversal in the direction of the drawing of the curve. A solution to the hidden line problem in computer graphics is presented for the case of steric contours ordered in parallel planes. The techniques developed in this article are demonstrated with stereographic orthographic projections for B-DNA, for intercalation complexes of lucanthone and actinomycin-D with DNA, and for the binding of benzo[a]pyrene diol epoxides (BPDEs) to guanine. The latter example illustrates the value of steric contours in demonstrating the lack of fit of BPDEs to B-DNA and by the need to unwind DNA to accommodate this molecule. Electrostatic contours in planes may be generated by this same procedure.