Terahertz absorption of DNA decamer duplex

J Phys Chem A. 2008 Nov 27;112(47):12090-6. doi: 10.1021/jp806630w.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Absorption
  • Base Sequence
  • Circular Dichroism
  • Computer Simulation
  • DNA / chemistry*
  • DNA / genetics
  • Models, Molecular
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides / chemistry*
  • Oligodeoxyribonucleotides / genetics

Substances

  • Oligodeoxyribonucleotides
  • DNA