Structural prediction of A- and B-DNA duplexes based on coordinates of the phosphorus atoms.
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).
Tung
C S
CS
Theoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico 87545, USA. cst@tensor.lanl.gov
Soumpasis
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DM
D010582:Bacteriophage lambda / Q000737:chemistry / Q000235:genetics; D055592:Biophysical Phenomena; D001703:Biophysics; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D004268:DNA-Binding Proteins; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D010758:Phosphorus / Q000737:chemistry; D012097:Repressor Proteins / Q000235:genetics; D012984:Software; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D004279:DNA, Viral; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D010758:Phosphorus; D004247:DNA