Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Chewook Lee, Kwang Hee Park, Minhaeng Cho

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm-1. These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.

Original languageEnglish
Article number114508
JournalJournal of Chemical Physics
Volume125
Issue number11
DOIs
Publication statusPublished - 2006 Oct 3

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Multilayers
deoxyribonucleic acid
DNA
Thymine
Cytosine
Guanine
Adenine
Propellers
Density functional theory
Conformations
Absorption spectra
Hydrogen bonds
Derivatives
Hessian matrices
propellers
thymine
guanines
adenines
interlayers
interactions

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings. / Lee, Chewook; Park, Kwang Hee; Cho, Minhaeng.

In: Journal of Chemical Physics, Vol. 125, No. 11, 114508, 03.10.2006.

Research output: Contribution to journalArticle

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