Phosphodiester group, conformation

Figure 6. Qualitative confonnational analysis of the homo-DNA single strand backbone based on idealized conformations. Three simple criteria predict one single pairing conformation of a nucleotide uniL provided that the phosphodiester groups have a synclinal/ synclinal bond arrangement [2].

This paper attempts to conform to the terminology recommended by the lUPAC-IUB Commission on Biochemical Nomenclature. Bases are generally symbolized by Ade, Gua, etc., while mono-, di-, and triphosphates of 5 nucleosides are given by NMP, NDP, and NTP. A few exceptions are made in the text for example for the sake of brevity and clairity on diagrams. The symbol for the phosphodiester group represents a 3 -5 link in accordance with standard lUPAC rules unless otherwise indicated. In naming enzymes the recommendations of the lUB Commission on Biochemical Nomenclature is used where ever practical. The abbreviations which are important and may not be standard or may not be familiar or to the reader are outlined below. 

The B - Z transition is Na -dependent and the endpoint corresponds to 2 positive charges per phosphodiester group. The ability to induce this transition is remarkable in view of the fact that normal methods of induction involve high concentrations of salt (2.5M Na ) or ethanol (60% vol/vol). The complex is now used routinely to induce the Z-conformation and as a probe for DNA structure. 

The Raman vibration of the symmetric stretching of the phosphodiester group -5 -CH2-O-PO2-O- appears at 814 cm and is slightly altered on fixation of a metal to the phosphate group.lt has been shown (8) that the intensity of the Raman line at 814 cm is a measure of the conformation in the tRNA backbone.The intensity of the above line undergoes a decrease of about 20% when the Mg " ions are extracted with a chelating agent (EDTA) and suitable dialysis. The backbone structure is... 

The other important feature of the primary stmcture of RNA is the presence of the 2 -hydroxyl group in ribose. Although this hydroxyl group is never involved in phosphodiester linkages, it does impose restrictions on the heHcal conformations accessible to double-stranded RNA. 

DNA is a structurally polymorphic macromolecule which, depending on nucleotide sequence and environmental conditions, can adopt a variety of conformations. The double helical structure of DNA (dsDNA) consists of two strands, each of them on the outside of the double helix and formed by alternating phosphate and pentose groups in which phosphodiester bridges provide the covalent continuity. The two chains of the double helix are held... 

Nucleic acids have a phosphodiester backbone that includes a ribose or deoxyri-bose group that is bound to a base (G, A, C, U, or T). The furanose sugar can adopt different conformations, and the link of the sugar to the base may have various torsion angles. 

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