STRUCTURAL PREDICTION OF A-DNA AND B-DNA DUPLEXES BASED ON COORDINATES OF THE PHOSPHORUS ATOMS

The sequence-dependent structure of DNA double helices was studied ext ensively during the past 10 years. How the backbone structure correlat es with the base structure in a duplex conformation is still an import ant yet open question. Using a set of reduced coordinates and a least- squares fitting procedure, we have developed a method to predict struc tures 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 availa ble from the Protein Data Bank. We used this method to construct a mod eled structure for the bacteriophage lambda cro operator for which the phosphorus coordinates were known from 3.5-Angstrom, resolution cryst al data (4CRO).