Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations

Abstract

Polarized Raman spectra of oriented fibers of calf thymus DNA in the A and B conformations have been obtained by use of a Raman microscope operating in the 180 degrees back-scattering geometry. The following polarized Raman intensities in the spectral interval 200-1800 cm-1 were measured with both 514.5 and 488.0 nm laser excitations: (1) Icc, in which the incident and scattered light are polarized parallel to the DNA helical axis (c axis); (2) Ibb, in which the incident and scattered light are polarized perpendicular to c; and (3) Ibc and Icb, in which the incident and scattered light are polarized in mutually perpendicular directions. High degrees of structural homogeneity and unidirectional orientation were confirmed for both the A and B form fibers, as judged by comparison of the observed Raman markers and intensity anisotropies with measurements reported previously for oligonucleotide single crystals of known three-dimensional structures. The fiber Raman anisotropies have been combined with solution Raman depolarization ratios to evaluate the local tensors corresponding to key conformation-sensitive Raman bands of the DNA bases and sugar-phosphate backbone. The present study yields novel vibrational assignments for both A DNA and BDNA conformers and also confirms many previously proposed Raman vibrational assignments. Among the significant new findings are the demonstration of complex patterns of A form and B form indicator bands in the spectral intervals 750-900 and 1050-1100 cm-1, the identification of highly anisotropic tensors corresponding to vibrations of base, deoxyribose, and phosphate moieties, and the determination of relatively isotropic Raman tensors for the symmetrical stretching mode of phosphodioxy groups in A and B DNA. The present fiber results provide a basis for exploitation of polarized Raman spectroscopy to determine DNA helix orientation as well as to probe specific nucleotide residue orientations in nucleoproteins, viruses, and other complex biological assemblies.

Single DNA molecule detection in an optical trap using surface-enhanced Raman scattering

“…The peak at 1140 cm −1 is attributed to the deoxyribose-phosphate backbone and the C-O stretching in the deoxyribose gives the Raman peak at 1000 cm −1 . 16,17 These peaks have previously been observed to be strongly enhanced through interaction with Ag colloids. 12,18 We must point out the absence of the highly SERS active adenine modes which have been observed in single stranded DNA 10 and at single molecule concentrations in solution 9 with silver particles.…”

Photons and particles emitted from cold atmospheric-pressure plasma inactivate bacteria and biomolecules independently and synergistically

“…Raman spectra of dried dG 18 were taken after a 30 min treatment with the different jets. By comparing the spectra taken before plasma treatment, we identified a number of chemical modifications (figure 7a) that were assigned using annotations of structural peaks taken from references [32][33][34]. The peak at 920 cm 21 is generated by vibrations of coupled nucleobases: a massive loss of relative intensity after treatment with the complete-jet was observed.…”

Raman micro spectroscopy study of the interaction of vincristine with A549 cells supported by expression analysis of bcl-2 protein

“…Conversely, 21 have reported an increase in the intensities ), due to the action of vincristine, provides evidence of intracellular intercalation of vincristine into the DNA. Moreover, in the 30 control spectra of the nucleus of A549 cells, the CH 2 scissoring mode, observed as a sharp band at 1422 cm -1 , is considered as an important Raman marker of the B-form DNA and is found to be much more broader and lower in peak intensity in the A-form DNA 34 . This trend is clearly 35 observable in the decreased contributions of this band in exposed samples in Figure 2, again indicating conformational changes in the B-form DNA in favour of the A-form.…”