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Nucleic Acids Research, 1990, Vol. 18, No. 23 6981-6987
© 1990

Articles

DNA rotational positioning in a regulatory nucleosome is determined by base sequence. An algorithm to model the preferred superhelix

Benjamin Piña1,2,+, Mathias Truss1, Heiko Ohlenbusch3, Johan Postma2 and Miguel Beato1,*

1Institut für Molekularbiologie und Tumorforschung Emil-Mannkopff-Straße 2, D-3550 Marburg 2EMBL Computer Graphics, Meyerhofstrasse 1, Postfach 102209 D-6900 Heidelberg, FRG 3Université Louis Pasteur de Strasbourg, Faculté de Médicine, Institut de Physique Biologique 4 rue Kirschleger, F-67085 Strasbourg Cedex, France

* To whom correspondence should be addressed

Received August 7, 1990. Revised October 26, 1990. Accepted October 26, 1990.

MMTV-LTR sequences –190/–45 position a histone octamer both In vivo and In vivo. Experimental evidence suggested that nucleosome rotational positioning is determined by the DNA sequence itself. We developed an algorithm that is able to predict the most favorable path of a given DNA sequence over a histone octamer, based on rotational preferences of different dinucleotides. Our analysis shows that these preferences are sufficient for explaining the observed rotational positioning of the MMTV-LTR nucleosome, at one base pair accuracy level. Computer-generated 3-D models of the experimentally calculated and predicted MMTV-LTR nucleosome show that the predicted orientation is fully compatible with the urrently available data in terms of accessibility of relevant sequences to regulatory proteins

+Present address: Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA


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