Torsion angles nucleic acid backbones

Several mathematical techniques have been used to obtain atomic coordinates for nucleic acid structures. They incorporate several different approaches. (a) Systematic rotations about all backbone torsional angles are performed and those conformations which form helicies and have adjacent bases parallel or in a given orientation are selected (59 6o). (b) Least squares techniques are used to re-... 

Torsion angles are important in the description and characterization of portions of proteins and nucleic acids. A Ramachandran plot of the torsion angles of the peptide backbone provides a graphical description of the protein. 

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. 

The Karplus-like relationship between HCOP and CCOP dihedral angles and and three-bond coupling constants, respectively, has been used to determine the conformation about the ribose-phosphate backbone of nucleic acids in solution. Torsional angles about both the C3 -03 and C5 -05 bonds in 3, 5 -phosphodiester linkages have been determined from the coupled and P NMR spectra. 

As described in Chapters 1 and 8, P-NMR chemical shifts in nucleic acids have been shown to provide a direct probe of P—O ester bond torsional angles. The interaction of drugs with nucleic acids is believed to perturb the conformation of the sugar-phosphate backbone, and hence structural and dynamic information on these complexes is potentially readily accessible through 3 P-NMR spectroscopy. 

Rather large changes in local conformation can be obtained by concerted alterations in the torsion angles about some of the bonds (illustrated in Fig. 7) without significant effect on the overall conformational energy (Keepers et al., 1982 Olson, 1982). For example, it is possible that one member of a base pair could temporarily move away from the other or, even more moderate, that crankshaft motions could take place along the backbone of the nucleic acid (Keepers and James, 1982). 

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