title: The significance of the 2' OH group and the influence of cations on the secondary structure of the RNA backbone.
abstract: In the IR spectra, the coupling of vibrations leads to band splitting and/or bands shifting in opposite directions which provides information on the mutual orientation of groupings. From such band shifts in the range 1800 to 1500 cm-1 one can draw conclusions on the double helix formation of polynucleotides. These band shifts are caused either by vibrational coupling of stretching vibrations within pairs of base residues or by coupling of stretching vibrations with the bending (scissor) vibration of the -NH2 groups; the latter is indicated by band shifts after deuterium substitution within the amino groups. Couplings of phosphate and 1 ibose vibrations in the range 1300 to 1000 cm-1 provide information on the secondary structure of the backbone. In order to obtain information of the structure of the RNA backbone, the IR spectra of poly(ribonucleotides) were studied in neutral media in which they were single-stranded. The shift due to coupling of the band of the 2'OD bending vibration and that of the antisymmetric stretching vibration of the ether group of the ribose residue proves that ribose residues of the backbone are cross-linked via hydrogen bonds. These are formed between the 2'OD or 2'OH groups, respectively, and the O atoms of the ether group of the neighboring ribose residues. This is the reason for the difference between DNA and RNA as regards the 2'OH group. The structure formation caused by these hydrogen bonds results in a stiffening of the RNA backbone. The tendency to form these hydrogen bonds increases in the order poly (U), poly(C), poly (A). This order of secondary structure stabilization is due to an interplay between the influences of (1) the 2'OH hydrogen bonds and (2) the base residues' stacking. Furthermore, the coupling of the antisymmetric stretching vibration of the greater than PO2- groups with a vibration involving the 2'OH group can result in a doublet structure of the band at about 1240 cm-1 if cations with strong fields are present. This probably shows that these cations can turn the greater than PO2-groups-which are usually turned outward at the backbone, as shown by construction of molecular models- towards the basic residues. Thus they cause stiff monohelices which are right-handed screws.
mesh_terms: D001718:Birefringence; D002413:Cations, Divalent; D002414:Cations, Monovalent; D003903:Deuterium; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009943:Organophosphorus Compounds; D011131:Polyribonucleotides; D012313:RNA; D013055:Spectrophotometry, Infrared; D014867:Water; D014961:X-Ray Diffraction
chemical_list: D002413:Cations, Divalent; D002414:Cations, Monovalent; D009943:Organophosphorus Compounds; D011131:Polyribonucleotides; D014867:Water; D012313:RNA; D003903:Deuterium