This chapter discusses the studies of nucleic acids and their protein interactions, by 19F nuclear magnetic resonance (NMR). Application of 19F NMR spectroscopy for macromolecular complexes is most useful in instances where co-crystal structures are unavailable and where the large size or the complex nature of intermolecular associations severely restricts the application of 1H NMR. Dissection of protein-nucleic acid complexes, by standard 1H NMR methods, has been substantially hampered by overlapping resonances and is only successful when restricted to small proteins (subunit size of about 12 kD) and short or symmetric nucleic acid targets (about 20 base pairs). One would like to extend NMR to extract structural information from larger complexes, with simplified spectra, limited to a preselected local neighborhood of a probe site. The density, distribution, and symmetry of the orbital electrons about a given nucleus determine the sensitivity and the orientation dependence of the resulting chemical shift. A large, intrinsic sensitivity of the covalently bound fluorine atom stems from the anisotropic distribution of the electrons in the three 2-p orbitals. The fluorine nucleus sensitivity to its micro-environment is, therefore, large and highly orientation dependent. The observed chemical shift change, induced by a new chemical environment, is a linear combination of shielding contributions from: (a) van der Waals interactions, (b) ring current shielding, (c) electronically anisotropic groups, (d) dipoles, and (e) fluorine hydrogen bonding.
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