This Protocol is listed in the following Categories:
Biochemistry and protein analysis, Spectroscopy and structural analysis

Author(s): Andrew J. Dingley, Lydia Nisius, Florence Cordier and Stephan Grzesiek
Affiliation(s): Department of Chemistry and School of Biological Sciences, The University of Auckland, Private Bag 92019
DOI: 10.1038/nprot.2007.497

Direct detection of N−H⋯N hydrogen bonds in biomolecules by NMR spectroscopy

A nuclear magnetic resonance (NMR) experiment is described for the direct detection of N–H⋯N hydrogen bonds (H-bonds) in 15N isotope-labeled biomolecules. This quantitative HNN-COSY (correlation spectroscopy) experiment detects and quantifies electron-mediated scalar couplings across the H-bond (H-bond scalar couplings), which connect magnetically active 15N nuclei of the H-bond donor and acceptor. Detectable H-bonds comprise the imino H-bonds in canonical Watson–Crick base pairs, many H-bonds in unusual nucleic acid base pairs and H-bonds between protein backbone or side-chain N–H donor and N acceptor moieties. Unlike other NMR observables, which provide only indirect evidence of the presence of H-bonds, the H-bond scalar couplings identify all partners of the H-bond, the donor, the donor proton and the acceptor in a single experiment. The size of the scalar couplings can be related to H-bond geometries and as a time average to H-bond dynamics. The time required to detect the H-bonds is typically less than 1 d at millimolar concentrations for samples of molecular weight ≈25 kDa. A 15N/13C-labeled potato spindle tuber viroid T1 RNA domain is used as an example to illustrate this procedure.

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