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Nucleic Acids Research, 2000, Vol. 28, No. 7 1585-1593
© 2000 Oxford University Press

Detection of N-H···N hydrogen bonding in RNA via scalar couplings in the absence of observable imino proton resonances

Mirko Hennig and James R. Williamson*

Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, MB 33, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA

Hydrogen bond networks stabilize RNA secondary and tertiary structure and are thus essentially important for protein recognition. During structure refinements using either NMR or X-ray techniques, hydrogen bonds were usually inferred indirectly from the proximity of donor and acceptor functional groups. Recently, quantitative heteronuclear J(N,N)-HNN COSY NMR experiments were introduced that allowed the direct identification of donor and acceptor nitrogen atoms involved in hydrogen bonds. However, protons involved in base pairing interactions in nucleic acids are often not observable due to exchange processes. The application of a modified quantitative J(N,N)-HNN COSY pulse scheme permits observation of 2hJ(N,N) couplings via non-exchangeable protons. This approach allowed the unambiguous identification of the A27·U23 reverse Hoogsteen base pair involved in a U-A·U base triple in the HIV-2 transactivation response element–argininamide complex. Despite a wealth of NOE information, direct evidence for this interaction was lacking due to the rapid exchange of the U23 imino proton. The ability to directly observe hydrogen bonds, even in D2O and in the presence of rapid exchange, should facilitate structural studies of RNA.

* To whom correspondence should be addressed. Tel: +1 858 784 8740; Fax: +1 858 784 2199; Email: jrwill@scripps.edu


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