Principal component analysis of DNA oligonucleotide structural data.
The microstructure of a DNA helix is characterized by several base pair and base step parameters such as twist, rise, roll, propeller twist, etc., in addition to conformational parameters such as the backbone and the glycosidic torsion angles. Among these only a few, which are independent of all others and of each other, may be used to precisely characterize the helix. The problem however is to identify these independent parameters. We have used principal component analysis to identify a relatively small set of independent parameters, with which to characterize each DNA helix. We show that these principal components clearly discriminate between A and B DNA helical types. The calculations further suggest that the microstructure of a DNA helix is better characterized using dinucleotides.
Bharanidharan
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D
Department of Crystallography and Biophysics, University of Madras, Chennai 600 025, India.
Gautham
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N
D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000032:analysis / Q000737:chemistry*; D030541:Databases, Genetic; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000032:analysis / Q000737:chemistry*; D025341:Principal Component Analysis; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013329:Structure-Activity Relationship
D009841:Oligonucleotides; D004247:DNA