Determination of the Backbone Structure of Nucleic Acids and Nucleic Acid Oligomers by Laser Raman Scattering

Abstract

Raman spectra of fibers of DNA that have been prepared in the A, B, and C forms are presented and compared with Raman spectra of DNA and RNA in dilute solution. It is shown that the phosphate vibrations in the region 750-850 cm-' are very sensitive to the specific conformation of the phosphate group in the backbone chain and are virtually independent of all other factors. Thus, a very simple method for the determination of the specific conformation of the backbone chain of nucleic acids, at least so far as the sugar-phosphate chain is concerned, appears available. The method is applied to short oligomers and dimers of ribonucleosides. It is found that at low temperatures, at pH 7, the phosphate group goes into the geometry of the A conformation when the stacking forces between the bases are sufficiently strong.The most reliable method for the determination of the structure of nucleic acids and polynucleotide helical chains appears to be that of x-ray diffraction (1, 2). However, this method is only applicable to nucleic acids in highly concentrated fibrous form. In general, it is not applicable to dilute nucleic acid solutions, although meaningful progress in the interpretation of x-ray scattering from fairly concentrated solutions has recently been reported (3). Thus, it would seem helpful to have available a method that could be used to obtain structural information, both on fibers and on dilute solutions, where these materials naturally occur. In this paper, we wish to report the observation of several Raman bands that arise from the vibration of the sugarphosphate backbone, in both ribonucleic acids (RNA) and deoxyribonucleic acids (DNA) whose frequencies and intensities are directly related to whether or not the material is in the A, B, or C form, as designated by the x-ray crystallographers (1, 2), and are virtually independent of all other parameters, such as the base composition, the presence or absence of the 2'-hydroxyl, etc. Furthermore, these bands can be observed in single-chain structures and oligomers, so that the geometry of the phosphate group in these substances can, under favorable circumstances, be determined.Recently, work in several laboratories has shown the existence of a Raman band at about 810-814 cm-' that is always present in ribonucleic acid structures, when these structures are in an ordered or partially ordered form (4-6). This band is plainly evident in the Raman spectrum of yeast transfer RNA shown in Fig. 1, and has also been observed in ribosomal RNA (5). Upon raising the temperature of the solution, so that the secondary structure vanishes, this band at 814 cm-' inevitably vanishes (4, 5). Since this band is completely independent of base composition and is present in all ordered ribo-structures, it may be due to the sugarphosphate diestersymmetric (4, 5) stretch or antisymmetric (6) stretch. The band at 814 cm-' is highly polarized, so that the former assignment seems somewhat more reasonable. Recent work in this laboratory (4) has shown that in aqueous solution, deox...

Junction between Z and B conformations in a DNA restriction fragment: evaluation by Raman spectroscopy.

“…3. The low salt spectrum has bands characteristic of DNAs in the B conformation (16,17). In particular, one observes a band at 832 cm1-~assigned to a ribose phosphate vibration (18)-and the 682-cm-1 peak-associated with the guanine ring (22)(23)(24).…”

“…Intensity predicted at 835 cm-1 is not observed. The latterband has been correlated with a ribose phosphate vibration in the E conformation (16)(17)(18) (14,15,20). DNA samples were prepared for Raman spectroscopy by precipitating 1-2 mg of DNA with ethanol in a 1.5-ml tube.…”

Nucleosome conformation: pH and organic solvent effects

“…Among these are the line at 832 cm I which is assigned to a vibration of the phosphodiester group, and the line near 675 cm 1which is actually composed of an overlapping pair (doublet) of lines at 671 and 681 cm 1, due, respectively, to ring vibrations of thymine and guanine residues (10,(15)(16)(17)(18). At higher spectral resolution than employed for the present study, the doublet is more clearly resolved into its two components (see, for example, refs.…”

Escherichia coli ribosome unfolding in low Mg2+solutions observed by laser Raman spectroscopy and electron microscopy

“…(The intensity of the 813 peak is therefore expected to be proportional to the number of nucleotides in the 3' endo conformation.) If the ribose moieties of a polynucleotide are perturbed from the rigid 3' endo conformation, the 0-P-0 symmetric stretch vibration is shifted to lower wave numbers (12). As a result, the intensity at 813 cm-1 is diminished.…”