Subpicosecond dynamics in nucleotides measured by spontaneous Raman spectroscopy

Abstract

The band widths in Raman spectra are sensitive to dynamics active on a time scale from 0.1 to 10 ps. The band widths of nucleotide vibrations and their dependence on temperature, concentration, and structure are reported. From the experimental band widths and second moments, it is derived that the adenine vibrations at 725, 1336, 1480, and 1575 cm−1, and the uracil vibration at 787 cm−1, are in the fast modulation limit. The correlation times of the perturbations are faster than 0.4 ps. Thermal melting of the helical structure in polynucleotides results in larger band widths, due to an increase in vibrational dephasing and energy relaxation as a consequence of the increased interaction of the base moieties with the solvent molecules. The band width of the 725 cm−1 adenine vibration is dependent on the type and structure of the backbone. It is found to be perturbed by movements of the sugar‐phosphate moiety relative to the base. The band width of the 1575 cm−1 adenine vibration is found to be sensitive to the base‐pairing interaction. From a comparison of the band widths in polynucleotides with a different base sequence (homopolymer vs alternating purine‐pyrimidine sequence), it is concluded that resonant vibrational energy transfer between the base molecules is not important as a relaxation process for the vibrational band widths of nucleotides. Several theoretical models for the interpretation of band widths are discussed. The theory does not take into account the strong hydrogen‐bonding nature water and hence fails to describe the observations in nucleotide‐water systems. The bands of the carbonyl stretching vibrations are inhomogeneously broadened. The carbonyl groups have a strong dipolar interaction with the polar water molecules and are therefore strongly perturbed by coupling to the heatbath via hydrogen bonds. © 1997 John Wiley & Sons, Inc. Biopoly 41: 751–763, 1997

Subpicosecond dynamics in DNA from leaves ofin vitro-grown apple plants: A SERS study

“…The development of fast and accurate curve fitting programs allows the analysis of the vibrational spectra of complicated biological molecules, containing often more than 40 vibrational bands ( [9,19] and references therein).…”

“…The values of the global relaxation time suggest also the existence of a vibrational relaxation time, because the reorientational movement is much more slower for the DNA macromolecule in aqueous solution [7,9]. Particularly, the absence of reorientational broadening in polynucleotides indicates that the bases in polynucleotides reorient through an angle of 41 • in times slower than 21 ps ( [8,19] and references therein).…”

“…As a general rule, the bandwidths in the Raman spectra are sensitive to a dynamics active on a time scale from 0.1 to 10 ps [7,19].…”

“…A number of dynamical processes which have been considered to broaden the vibrational bands of nucleic acids in the frequency domain, are: vibrational resonance coupling, vibrational energy exchange, vibrational dephasing and rotational broadening ( [7,19] and references therein).…”

Molecular relaxation processes in calf-thymus DNA, in the presence of Mn2+and Na+ions: A Raman spectroscopic study

“…The bandwidths in the Raman spectra are sensitive to a dynamics active on a time scale from 0.1 to 10 ps [4]. The macromolecular motion in fluids is generally too slow to be observed in the Raman time window that is accessible in the frequency domain.…”