Phosphorus relaxation methods

Chi-Wan Chen and Jack S. Cohen introduce the application of - P NMR to DNA and RNA conformations. High-resolution P NMR of transfer ribonucleic acids and P studies on drug-nucleic acid complexes (prepared by the editor with Evelyn M. Goldfield) are then presented. Phillip A. Hart introduces phosphorus relaxation methods, which are shown to provide important information on the conformation and dynamics of nucleic acids and phosphoproteins. Thomas L. James delves further into relaxation behavior of solution-state nucleic acids, and Heisaburo Shindo completes this section by describing solid-state " P NMR of nucleic acids. 

Phosphorus Relaxation Methods Conformation and Dynamics of Nucleic Acids and Phosphoproteins... 

A large body of work reports experimental probes of most of the torsion angles of Table I. This work is far too extensive to quote here. Lee et al. (1976 Lee and Tinoco, 1977), Alderfer and T so (1977), Davies (1978), and Sarma (1980) have summarized most of it. Those bonds that involve phosphorus are the salient ones for the purposes of this volume. Those cases where phosphorus relaxation methods have been useful or show promise are emphasized in this chapter. 

The phosphorus relaxation methods that are routinely available are the phosphorus-hydrogen nuclear Overhauser effect (NOE) and the various relaxation times, the spin-lattice relaxation time T, the spin-spin relaxation time T2, and the spin - lattice relaxation time in the rotating frame Under ideal circumstances for interpretation, both geometric and dynamic information can be gotten from these experimental values however, it is almost inevitable that the ideal is seldom encountered. Instead, various assumptions and approximations are required before any interpretation can be made. 1 partition the following discussion along the lines of the relaxation methods listed here and I show what interpretation can be placed on the data. As well, I try to clarify directions for further work that I consider potentially fruitful. 

Section III establishes how the NOE method could be used to analyze the rotamer distribution about the a,S,e bonds (and to some extent, the bonds of the sugar ring), but that the method is not at all applicable to )ff,y-bond analysis in oligonucleotides. In this section, I show how it is possible to approach the p,y distribution problem by interpretation of phosphorus relaxation times, and I show how this method can be used in conjunction with the phosphorus chemical-shift correlations of Gorenstein (1981). 

Selected entries from Methods in Enzymology [vol, page(s)] Anisotropy effects, 261, 427-430 determination by dynamic laser light scattering (quasi-elastic light scattering), 261, 432-433 determination for nucleic acids by NMR [accuracy, 261, 432-433 algorithms, 261, 11-13, 425, 430 carbon-13 relaxation, 261, 11-12, 422-426, 431, 434-435 cross-relaxation rates, 261,419-422, 435 error sources, 261, 430-432 phosphorus-31 relaxation, 261, 426-427, 431 proton relaxation, 261,51,418-422 relaxation matrix calculations, 261,12] deuterium solvent viscosity effects, 261,433 effect... 

General discussion of intra- and intermolecular interactions 3 van der Waals interactions 3 Coulombic interactions 5 Medium effects on conformational equilibria 5 Quantum mechanical interpretations of intramolecular interactions 7 Methods of study 8 Introduction 8 Nmr and esr spectroscopy 8 Microwave spectroscopy (MW) 12 Gas-phase electron diffraction (ED) 12 X-ray crystallographic methods 13 Circular-dichroism spectroscopy and optical rotation 14 Infrared and Raman spectroscopy 18 Supersonic molecular jet technique 20 Ultrasonic relaxation 22 Dipole moments and Kerr constants 22 Molecular mechanic calculations 23 Quantum mechanical calculations 25 Conformations with respect to rotation about sp —sp bonds 27 Carbon-carbon and carbon-silicon bonds 28 Carbon-nitrogen and carbon-phosphorus bonds 42 Carbon-oxygen and carbon-sulphur bonds 48 Conformations with respect to rotation about sp —sp bonds Alkenes and carbonyl derivatives 53 Aromatic and heteroaromatic compounds 60 Amides, thioamides and analogues 75 Conclusions 83 References 84... 

NMR is a useful alternative to proton NMR. It is a reasonably sensitive nucleus which does not suffer from the relaxation problems associated with NMR. Phosphorus trichloride can be used as a reagent for self-recognition by a chiral substrate. Two molecules of an enantiomerically enriched alcohol react with each PCI3 molecule to form a phosphonate. Four stereochemically distinct species are possible (R,R) and (5, S) (a pair of enantiomers), (R,S) and (5, R) which are meso compounds. There are consequently three resonances in the 3ip NMR spectrum, whose non-equivalence is typically 0.5 ppm and integration gives results within 2% of those obtained by chiral GC methods. Subsequently methyl phosphoryl chloride has been employed in the same way giving improved chemical shift non-equivalences, A5 = 1 ppm (Scheme 3.3). 

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