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Copyright © 1996 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 70, Issue 2, 917-923, 1 February 1996
doi:10.1016/S0006-3495(96)79634-0
Research Article
Structural prediction of A- and B-DNA duplexes based on coordinates of the phosphorus atoms
C.S. Tung and D.M. Soumpasis
Abstract
The sequence-dependent structure of DNA double helices was studied extensively during the past 10 years. How the backbone structure correlates with the base structure in a duplex conformation is still an important yet open question. Using a set of reduced coordinates and a least-squares fitting procedure, we have developed a method to predict structures for B-DNA duplexes based on coordinates of the phosphorus atoms. This method can be used to predict all-atom structures for both bent and straight molecules. We estimated the accuracies of the predictions by studying a set of 10 oligonucleotides with their structures available from the Protein Data Bank. We used this method to construct a modeled structure for the bacteriophage lambda cro operator for which the phosphorus coordinates were known from 3.5-angstrum resolution crystal data (4CRO).
