Vibrational Relaxation of the Backbone and Base Modes in LacDNA Complexes by UV Resonance Raman Spectroscopy

Abstract

Vibrational band shape analysis through time correlation function concept is widely used to obtain experimental information on the molecular dynamics of medium-size molecules in different environments. Interesting details are revealed by extending this technique to biomolecules such as functional groups of the nucleic acids in media approaching the physiological conditions. In this work a study into the UV resonance Raman (UVRR) vibrational half bandwidths of functional groups in LacDNA, upon lowering the pH (pH 6.4, pH 3.45) and in the presence of Mn and Ca ions, respectively, was of interest. The corresponding global relaxation times have been derived. Also, the 793 cm UVRR band, corresponding to ν (backbone O-P-O, dT) oscillator of LacDNA in aqueous solutions, was selected for band shape-analysis. Vibrational relaxation appears as the dominant relaxation process for this mode, with vibrational dephasing being the most efficient for this oscillator. Current theories developed for vibrational dephasing have been applied to this profile, and relevant relaxation parameters have been obtained and discussed. To our knowledge this is the first study on DNA oligomers vibrational band shape analysis through time correlation function concept.

Molecular understanding of label-free second harmonic imaging of microtubules

“…The experimental set-up used for HRS was already described elsewhere 58 . The laser system (Supplementary Fig.…”

Vibrational Relaxation of Functional Groups in dAMP Molecules Probed with UV Resonance Raman Spectroscopy

“…Studies on the fwhm's of calf-thymus DNA Raman bands revealed their sensitivity to pH, as well as to the presence and concentration of different metal cations [13]. Besides, our group investigated the vibrational relaxation of a 22-mer duplex DNA, as probed with UVRR spectroscopy [14]. Resonance Raman spectroscopy (RRS) is a useful technique employed to obtain experimental data on molecular relaxation dynamics [15].…”

“…The UV resonance Raman measurements were done at the University of Osnabrück, Osnabrück, Germany. Continuous wave Raman equipment described in detail elsewhere [14,21] was employed for recording the UVRR spectra. All UV resonance Raman profiles of dAMP molecules were registered in the same experimental conditions.…”

“…As seen in this figure, the experimental profile fits well with a Gauss one, with Lorentz (or Cauchy) corrections in its wings. Some models have been developed for vibrational dephasing, as one of the most important contribution to vibrational relaxation, based on Gaussian-Markovian theory [9,14,[26][27][28][29][30]. According to Kubo-Rothschild's model the logarithm of the vibrational correlation function [Gv(t)] is expressed by:…”