title: Normal mode calculation of a netropsin-DNA complex: effect of structural deformation on vibrational spectrum.
abstract: Calculations of the normal mode spectrum of a netropsin-DNA complex, an isolated DNA helix of the same sequence, and a free netropsin molecule were carried out and compared with observations. We find that the frequency of modes of the complex that are primarily vibrations localized to the helix are relatively unchanged from the frequencies found for similar modes of the isolated helix. On the other hand, the frequencies of thosemodes of the complex that are found to be primarily in the netropsin are found to change significantly in the complex from that of the free netropsin. Further analysis indicates that the changes in the "netropsin modes" are primarily due to the conformational deformation induced in the netropsin by formation of the complex. All the frequencies and shifts in frequency are in good agreement with recent Raman measurements.
authors.affiliation: Department of Physics, Purdue University, West Lafayette University, Indiana.
authors.forename: Y Z
authors.initials: YZ
authors.lastname: Chen
authors.forename: E W
authors.initials: EW
authors.lastname: Prohofsky
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D008433:Mathematics; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009429:Netropsin / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011089:Polydeoxyribonucleotides / Q000737:chemistry*; D011487:Protein Conformation; D012091:Repetitive Sequences, Nucleic Acid; D013059:Spectrum Analysis, Raman
chemical_list: D009838:Oligodeoxyribonucleotides; D011089:Polydeoxyribonucleotides; D009429:Netropsin; D004247:DNA