Terahertz Absorption of DNA Decamer Duplex

This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5′-CCGGCGCCGG-3′. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identifica...

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Bibliographic Details
Published in:The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory Molecules, spectroscopy, kinetics, environment, & general theory, 2008-11, Vol.112 (47), p.12090-12096
Main Authors: Li, Xiaowei, Globus, Tatiana, Gelmont, Boris, Salay, Luiz C, Bykhovski, Alexei
Format: Article
Language:English
Subjects:
A: Kinetics, Spectroscopy
Absorption
Base Sequence
Circular Dichroism
Computer Simulation
DNA - chemistry
DNA - genetics
Models, Molecular
Nucleic Acid Conformation
Oligodeoxyribonucleotides - chemistry
Oligodeoxyribonucleotides - genetics
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Summary:This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5′-CCGGCGCCGG-3′. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10−25 cm−1 using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.
ISSN:1089-5639
1520-5215
DOI:10.1021/jp806630w