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Nucleic Acids Research, 1988, Vol. 16, No. 18 8999-9015
© 1988

Articles

A molecular model for proflavine-DNA intercalation

S. Neidle*, L.H. Pearl, P. Herzyk** and Helen M. Berman1

Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research Sutton, Survey SM2 5PX, UK 1Institute for Cancer Research, Fox Chase Cancer Center 7701 Burholme Avenue, Philadelphia, PA 19111, USA

*To whom correspondence should be addressed

Received July 4, 1988. Revised August 22, 1988. Accepted August 22, 1988.

A molecular model has been derived for the intercalation of proflavine into the CpG site of the decamer duplex of d(GATACGATAC). The starting geometry of the intercalation site was taken from previous crystallographic studies on the d(CpG)-proflavine complex, and molecular mechanics used to obtain a stereocheracally acceptable structure. This has widened grooves compared to standard A- or B- double helices, as well as distinct conformational, roll, twist and tilt features.

**On leave from the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-532 Warsaw


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