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© IRL Press Limited

Analysis of dynamics trajectories of DNA and DNA - drug complexes

Andrzej Galat

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 250 Longwood Avenue, Boston, MA 02115, USA

A FORTRAN-77 program is described which was applied for analysis of optimized structures and computer-generated dynamics trajectories of DNA and DNA -drug complexes. The CORDAN program (coordinates analysis) also can be used for various manipulations of DNA-drug complexes, i.e. inversion of asymmetric sites or rebuilding the structure of the intercalator, among others. These procedures can find application in drug design. Analysis of dynamics trajectory of neocarzinostatin antibiotic (NCS) intercalated to the A-DNA form of 5'GGATGGGAG: 5'CTCCCATCC is presented. The procedures described can be used for detailed analysis of dynamics structures of DNA and their complexes with intercalating drugs.

Received on December 20, 1988; accepted on June 27, 1989

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