Raman and Infrared Spectra of (2‘S)-[2‘-²H]Thymidine:  Vibrational Coupling between Deoxyribosyl and Thymine Moieties and Structural Implications

Abstract

The thymidine stereoisotopomer, (2′S)-[2′-2 H]thymidine, which incorporates deuterium in the S configuration at the furanosyl 2′ carbon, has been synthesized and its vibrational spectra have been recorded and compared with those of normal thymidine. Infrared and Raman spectra were collected from crystalline powders, the latter using 1063-and 514.5-nm excitations; ultraviolet resonance-Raman spectra were collected from aqueous solutions using 244-nm excitation. The results show, remarkably, that virtually all normal modes of thymidine involve some degree of vibrational coupling between the thymine base residue and the deoxyribose moiety. Nevertheless, systematic assignments and correlation of the spectral frequencies of thymidine and (2′S)-[2′-2 H]thymidine have been accomplished. A finding of importance for nucleic acid structure applications is that many prominent Raman marker bands of thymidine, assigned previously as thymine ring vibrations, in fact involve appreciable coupling with the C2′ methylene group of the attached sugar. Vibrational coupling between the base and sugar groups implies frequency dependence upon sugar conformation and allows the bands in question to be exploited as markers of deoxyribose ring pucker and glycosyl orientation in Raman spectra of DNA, antiviral drugs, and other thymine-containing nucleoside analogues. The present results also enable unambiguous and novel assignment of spectral bands to specific vibrational modes of the C2′ methylene group of thymidine as follows: C2′H 2 antisymmetric stretching (2995 cm -1 ), symmetric stretching (2956 cm -1 ), scissoring (1404 cm -1 ), and wagging (1174 cm -1 ). Additionally, probable assignments are deduced for the C2′H 2 twisting (1103 cm -1 ) and rocking modes (898 cm -1 ). Normal mode assignments are also proposed for many other vibrational bands of thymidine.

Dependence of the Raman signature of genomicB-DNA on nucleotide base sequence

“…The parent band has been assigned to a skeletal deformation of the pyrimidine ring that is coupled with both in-phase bending of the C2AO and C4AO carbonyl groups and distortion of the furanose ring. 36 The observed difference band near 665 cm Ϫ1 may reflect the greater propeller twist noted above for base pairs of poly(dA-dT)⅐poly(dA-dT) than for AT pairs in genomic DNA. It has also been demonstrated previously that a change in deoxynucleoside conformation can have a dramatic effect on the intensity of this band.…”

“…The carbonyl group stretching vibrations of thymine (C2AO and C4AO), guanine (C6AO), and cytosine (C2AO) are expected to give strong Raman bands in the 1600 -1750 cm Ϫ1 region and unambiguous assignments have been developed from studies of model compounds. 28,[33][34][35][36] Figure 2 shows that thymine carbonyls produce intense bands at 1652 and 1672 cm Ϫ1 , whereas the guanine C6AO mode at 1713 cm Ϫ1 is only moderately intense. Conversely, the cytosine C2AO mode near 1680 cm Ϫ1 is extremely weak.…”

Structural Analysis of DNA Interactions with Magnesium Ion Studied by Raman Spectroscopy

“…The cytosine vibration is sensitive to deputation exocyclic substitution while the phosphodiester vibration is less sensitive to deputation. The thymidine vibration, which involves both significant contribution from deoxyribose ring and dominant contribution from the thymine vibration, is sensitive to C2' deuteration (Tsuboi et al, 1997). The appearance of the cytosine vibration at higher frequency at 790 cm…”

A systematic approach toward the analysis of drug–DNA interactions using Raman spectroscopy: The binding of metal‐free bleomycins A 2 and B 2 to calf thymus DNA

“…Tsuboi et al have observed similar behavior for this mode in both IR and Raman studies in which the C2Ј of the deoxyribose moiety was deuterated, thereby uncoupling these two vibrations. 39 Another deoxyribose band at 1323 cm Ϫ1 in ct-DNA (Figure 4, 30°C) or 1321 cm Ϫ1 (Figure 6, 19°C) shifts up to its uncoupled frequency of ϳ1325 cm Ϫ1 . 17,22 There is no change in bandwidth and the intensity increase for this mode occurs only at 30°C.…”

“…21,22,38,39 The band at 1274 cm Ϫ1 in ct-DNA is assigned to a deoxyribose mode and is normally relatively weak when coupled to T. 39 Upon binding of Blm this mode becomes almost 50% more intense, becomes broader and this band shifts to a frequency of ϳ1270 cm Ϫ1 . 17,39 This is a pattern seen not only at 30 but at 19°C (Figure 6). Tsuboi et al have observed similar behavior for this mode in both IR and Raman studies in which the C2Ј of the deoxyribose moiety was deuterated, thereby uncoupling these two vibrations.…”