Discrimination between UV radiation‐induced and thermally induced spectral changes in AT‐paired DNA oligomers using UV resonance Raman spectroscopy

Abstract

Ultraviolet resonance Raman spectroscopy (UVRRS) was used to monitor UV radiation and thermal energy deposition in 12-and 18-mer AT oligomers. Difference spectroscopy and two-dimensional correlation spectroscopy (2DCOS) were used to characterize the distinct spectral responses manifested by the two processes, and to examine their potential cooperative and/or independent effects on the ensemble spectrum. Experiments utilizing incremental doses of 257-nm radiation revealed that the most affected bands are those involving double bonds when the sample temperature was held constant. Complementary experiments utilizing sample heating indicated that the most affected bands were those involving hydrogen-bond disruption. Finally, it is shown that bands associated with Watson-Crick hydrogen-bond disruption are the most affected in rapidly heat-cycled samples. The results also suggest that both radiation and thermal effects produce independent structural changes in AT oligomers and, furthermore, that these effects are complementary when the experiments involve single-strand DNA fragments. When using UVRRS to study one of these perturbations (e.g. thermal stability of DNA), the concurrent perturbation (e.g. UV exposure) must not be neglected, since UV exposure is inherent in the UVRR process. These findings thus have implications for the use of UVRRS in the study of DNA dynamics.

Two‐dimensional correlation Raman spectroscopy for characterizing protein structure and dynamics

“…Furthermore, the effect of Ca 2+ on the rate of β-sheet formation has been studied. [30] A later study [31] investigates the effect of potassium ions on the folding of silk fibroin using a combination of C [13] NMR and Raman techniques. Raman spectroscopy was utilized to probe the hydrogen bonding of the tyrosine phenolic-OH moiety over the course of the silk fibroin structural rearrangements.…”

Recent Advances in linear and nonlinear Raman spectroscopy I

“…Benevides et al 151 reviewed in detail how visible and UV resonance Raman spectroscopy has been applied to exploring the local structure, global conformation, and molecular dynamics of DNA and RNA. UV radiation effects on calf thymus DNA were discussed by Ke et al 152 Using UV resonance Raman spectroscopy, Jirasek et al 153 investigated the discrimination between UV radiation-induced and thermally induced spectral changes in AT-paired DNA oligomers. A Raman study of DNA structure at low pH in the presence of Mn 2C was performed by Muntean et al 154 The diversity of porphyrin structures results in various porphyrin-binding modes to nucleic acids.…”

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“…2D-correlation IR spectroscopy has been applied to study water absorption into polymer films [50,51], adsorption of small molecules at interfaces [52], and diffusion of small molecules inside polymers [53,54], but has not been applied to the types of ATR-IR sensors mentioned above. 2D-correlation Raman analysis has been used to study a wide range of compounds including small molecules, polymers, proteins, lipids, and DNA [48,[55][56][57][58][59]. However, to the best of our knowledge, there have been no previous Sensor optics: ray tracing scheme (top) and actual system (bottom).…”