Computer graphics and the generation of DNA confirmations for intercalation studies

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Abstract

We report a series of structures for double-stranded DNA that is in the process of opening up to admit an intercalating drug such as ethidium. Using the method of damped least-squares (suggested by Vitek) to provide ring closure across the base pairs, we obtained backbone confirmations for parallel base planes at various specified separations. Conformational energies were then calculated, taking into account solution effects, and the minimum energy was chosen. The resulting confirmations can ba viewed on an interactive display or drawn with high precision as simulated CPK models in color, with shading and high lights.

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    This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48 (N.L.M.) and supported by the National Cancer Institute under contract No. N01-CP-75927 and the National Science Foundation under grant No. ENV77-24061 (D.M. and A.J.H.)

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