Document Detail

Vibrational local modes in DNA polymer.
MedLine Citation:
PMID:  7946063     Owner:  NLM     Status:  MEDLINE    
Where the translational symmetry of a long polymer chain is interrupted, characteristic vibrations of the molecule are possible in which only those atoms at or relatively near the defect site partake of the motion. This contrasts with the more common vibrational states in which the motion propagates along the chain as a sound wave. Examples of readily producible local defects include broken bonds, missing atoms or groups, and extra links as are found, e.g., in thymine dimers. For each different defect, the spectrum of local mode frequencies is characteristic of its structure. Hence the local modes give direct information about the nature of the defect and can serve as a diagnostic signature of the polymer chain lesion. We have developed and are using algorithms and fortran code to predict the existence and nature of local modes based on their atomic structures. We have studied examples of different defects and found their eigen-frequencies and eigenvectors. For the simplest case of a broken hydrogen bond in a single A-T unit in a long homopolymer dA.dT chain, we display stereo views of the vibrating unit side-by-side with the undisturbed molecule for the three local modes occurring below 300 cm-1 in frequency.
L L Van Zandt; V K Saxena
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Journal of biomolecular structure & dynamics     Volume:  11     ISSN:  0739-1102     ISO Abbreviation:  J. Biomol. Struct. Dyn.     Publication Date:  1994 Apr 
Date Detail:
Created Date:  1994-12-06     Completed Date:  1994-12-06     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8404176     Medline TA:  J Biomol Struct Dyn     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  1149-59     Citation Subset:  IM    
Dept of Physics, Purdue University, W. Lafayette, IN 47907.
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MeSH Terms
DNA / chemistry*,  genetics
Hydrogen Bonding
Models, Molecular
Poly dA-dT / chemistry*,  genetics
Spectrum Analysis, Raman
Reg. No./Substance:
26966-61-0/Poly dA-dT; 9007-49-2/DNA

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