Theoretical Analysis of DNA Low-Frequency Phonon Modes
Abstract
Low frequency phonon modes of a helical DNA olygomers- were calculated and compared. The customized program -cages JiMA and UGAND (developed in Dr. Laverys group lBPc. Paris) were was adopted for IBM PC and employed to minimize potential energy and to calculate vibrational frequencies of a molecule. The initial geometry for the B-helix oligonucleotides d(TATATATATATA)d(ATATATATATA) and d(A AAAAAAAAAAA)d(TTTTTTTTTTTT) was created by program JUMNA. The energy of interatomic interactions was calculated using a Semiempiric force field FLEX. The conformational energy was minimized in the space of internal coordinates of a molecule (i.e. daedral and valnoe angles for all the covalent bonds). Vibrational frequencies were calculated using second derivative of the conformational energy with the program LIGAND. 360 normal modes with vibrational frequencies ranging from 0 to 900 cm-1 were found. A new method for the analysis of optical activity for each normal mode was developed. The essence of the method is to calculate oscillator strengths from vibrations of the dipole moment of a molecule. All the modes were analyzed for their ability for the infrared absorption. For this purpose we calculated the motions of the DNA molecule along each modes and analyzed the deviations of dipole moments. The described calculations clearly demonstrated that (1) DNA double helix has at least hundreds of vibrational modes in far infrared region: and (2) theses normal modes may differ many folds in their ability for the radiation absorption. The dependent of absorption coefficient on the wave length was calculated and compared for the two molecules under the study. We have demonstrated that the differences in nucleotide sequence produce significant differences in the absorption spectra. The calculated positions of the resonance peaks were found to be in an excellent agreement with those known from the experiment.
Document Details
- Document Type
- Technical Report
- Publication Date
- Sep 24, 1999
- Accession Number
- ADA379532
Entities
People
- Maria Bykhovskaia
Organizations
- University of Virginia