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Identifying and interpreting spectral features of dissolved poly(dA)-poly(dT) DNA polymer in the high-microwave range

Identifying and interpreting spectral features of dissolved poly(dA)-poly(dT) DNA polymer in the... The vibrational modes involving the hydrogen-bond fluctuations in B conformation of poly(dA)-poly(dT) DNA homopolymer dissolved in aqueous solution have been theoretically studied within the recently developed effective-field model, including longitudinal as well as radial fields, and a properly frequency-dependent dielectric constant for the surrounding water. We have analyzed the vibrational eigenvectors to characterize two types of motions involving hydrogen bonds, namely, propeller twist and hydrogen-bond breathing. We ran our analysis for five different sets of partial atomic charges, and found that the major mode frequencies are essentially independent of the choice of partial charges. Since hydrogen-bond strength changes with temperature, we simulated the effect of temperature on the hydrogen bonds by varying the hydrogen-bond force constants. Our calculations indicate that a mode near 42 cm - 1 with strong propeller twist motion is to be expected. Around 63 cm - 1 , another mode with strong hydrogen-bond breathing character should be found. We discuss the expected variations of these resonances with temperature as a guide to spectral identification. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Physical Review A American Physical Society (APS)

Identifying and interpreting spectral features of dissolved poly(dA)-poly(dT) DNA polymer in the high-microwave range

Saxena, V. K
Physical Review A , Volume 43 (8) – Apr 15, 1991
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Publisher
American Physical Society (APS)
Copyright
Copyright © 1991 The American Physical Society
ISSN
1094-1622
DOI
10.1103/PhysRevA.43.4510
Publisher site
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Abstract

The vibrational modes involving the hydrogen-bond fluctuations in B conformation of poly(dA)-poly(dT) DNA homopolymer dissolved in aqueous solution have been theoretically studied within the recently developed effective-field model, including longitudinal as well as radial fields, and a properly frequency-dependent dielectric constant for the surrounding water. We have analyzed the vibrational eigenvectors to characterize two types of motions involving hydrogen bonds, namely, propeller twist and hydrogen-bond breathing. We ran our analysis for five different sets of partial atomic charges, and found that the major mode frequencies are essentially independent of the choice of partial charges. Since hydrogen-bond strength changes with temperature, we simulated the effect of temperature on the hydrogen bonds by varying the hydrogen-bond force constants. Our calculations indicate that a mode near 42 cm - 1 with strong propeller twist motion is to be expected. Around 63 cm - 1 , another mode with strong hydrogen-bond breathing character should be found. We discuss the expected variations of these resonances with temperature as a guide to spectral identification.

Journal

Physical Review A – American Physical Society (APS)

Published: Apr 15, 1991

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