Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes

Abstract

Applications of Raman spectroscopy to investigate the molecular constituents of nucleic acids were initiated in the late 1960s and soon thereafter progressed to studies of synthetic and native nucleic acids and complex biological assemblies containing either DNA or RNA. Raman applications to nucleic acids have continued to increase in number and diversity up to the present time. This paper attempts to provide an overview of this large body of work, with emphasis on studies carried out during the past decade and focusing on problems of biological interest and significance. The specific Raman methodologies included in this review of nucleic acid applications are (i) conventional Raman spectroscopy (i.e. off-resonance Raman excitation), (ii) ultraviolet resonance Raman (UVRR) spectroscopy, and (iii) polarized Raman microspectroscopy. For each methodology, the experimentally obtained nucleic acid spectrum consists of a number of discrete vibrational bands, most of which can be assigned confidently to a base, sugar or phosphate constituent of the macromolecule and many of which can be employed as sensitive indicators or fingerprints of either local structure, global conformation, intermolecular interaction or molecular dynamics. The applications selected for review include numerous examples from the authors' laboratories. The topics addressed include the influences of base composition, base sequence, superhelical stress and drug ligation on nucleic acid structure and polymorphism, the thermodynamic parameters governing nucleic acid premelting and melting phenomena, the molecular mechanisms and determinants of protein/nucleic acid recognition and the structures and dynamics of nucleic acids in virus assemblies.

Simplified Sum-Over-States Approach for Predicting Resonance Raman Spectra. Application to Nucleic Acid Bases

“…absorbing chemical constituents such as nucleic acid bases, aromatic aminoacids, and heme chromophores [3][4][5] Another important manifestation of resonance enhancement emerges in surface-enhanced Raman scattering (SERS). [6][7][8] The surface enhancement of Raman scattering is observed in molecules adsorbed on rough or nanostructured noble-metal surfaces and comprises an electromagnetic and a chemical contribution.…”

A micro-Raman spectroscopic investigation of leukemic U-937 cells treated with Crotalaria agatiflora Schweinf and the isolated compound madurensine

“…The weak band at ∼1580 cm −1 is assigned to nucleic acid ring stretches of guanine and adenine. The peak ∼1096 cm −1 is associated with O-P-O backbone vibrations of DNA and the peak at 783 cm −1 suggests that the DNA is B-form [6], [10], [11] and [12]. However, as the B-form of DNA has only been observed when cells are in the hydrated state this assignment should be verified with FTIR measurements.…”

“…1003 sn Phenylalanine (ring breathing mode) [5], [6] and [10] 1031 mn Cell culture medium [7] 1096 mb DNA (O-P-O-stretch) [7] and [10] 1125 mn C-C stretching [5] 1172 wn Tyrosine, Phenylalanine [5] and [7] 1193-1207 mn Tyrosine, Phenylalanine [6] and [7] 1255-1268 wn Amide III [6] and [7] 1309 wn Adenine [14] 1340 wn C-H deformation, Tryptophan [6] and [7] Polynucleotide chain (DNA purine bases, specially Adenine) [5] and [10] 1361 mn Thymine and adenine [7] 1447 sb CH 2 stretching [6] and [7] CH 2 stretching [6] and [7] 1490 wn Adenine [11] 1555 mn Amide III (C-N stretching mode) [15] 1573-1580 mn Guanine, Adenine ring stretch [8] and [10] 1607 wn Phenylalanine and tyrosine [5] 1657 sb Amide I [16] C C stretch [6] Abbreviations regarding Raman peaks: s, strong; m, medium; w, weak; n, narrow; b, broad.…”

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

“…In addition, water absorbs in the IR range but is not observed in Raman spectra. Thus, the two methods can yield useful complementary information on a fast timescale and in all physical states [175,176]. Discrete vibrational bands for base, sugar and phosphate groups can be observed, albeit only as an average signal of all conformational states in the sample.…”