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Proceedings Paper

Thermally induced coherent vibrations in DNA
Author(s): Kim O Rasmussen; George Kalosakas; N. K. Voulgarakis; Alan R Bishop; C. H. Choi; A. Usheva
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Paper Abstract

We compare numerical calculations and experimental data showing that large, slow thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating a bacteriophage DNA gene promoter segment, we find that the large opening tends to occur at the transcription start site. Other probable large openings appear to be related to other regulatory sites. Sequence specificity, nonlinearity and entropy, are the basic elements for controlling coherent dynamics. To further characterize the dynamics related to the bubble formation we investigate the temperature dependence on the dynamic structure factor. A distinct feature in the dynamics structure factor is identified and attributed to the denaturation bubbles.

Paper Details

Date Published: 25 May 2004
PDF: 7 pages
Proc. SPIE 5467, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II, (25 May 2004); doi: 10.1117/12.548416
Show Author Affiliations
Kim O Rasmussen, Los Alamos National Lab. (United States)
George Kalosakas, Max-Planck-Institut für Physik komplexer Systeme (Germany)
N. K. Voulgarakis, Univ. of Crete (Greece)
FORTH (Greece)
Alan R Bishop, Los Alamos National Lab. (United States)
C. H. Choi, Harvard Medical School (United States)
A. Usheva, Harvard Medical School (United States)

Published in SPIE Proceedings Vol. 5467:
Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II
Derek Abbott; Sergey M. Bezrukov; Andras Der; Angel Sanchez, Editor(s)

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