Observation of internucleotide NH...N hydrogen bonds in the absence of directly detectable protons

J Biomol NMR. 1999 Nov;15(3):207-11. doi: 10.1023/a:1008357304708.

Abstract

Several structural motifs found in nucleic acids involve N-H...N hydrogen bonds in which the donor hydrogens are broadened to extinction due to chemical or conformational exchange. In such situations, it is impossible to use the well-established HNN-COSY or soft HNN-COSY experiments, which report the presence of the hydrogen bond directly on the donor proton(s). We present a pulse sequence, H(CN)N(H), for alleviating this problem in hydrogen bonds of the type NdH...Na-CH, in which the donor Nd nitrogen is correlated with the corresponding non-exchangeable C-H proton associated with the acceptor Na nitrogen. In this way, missing NdH...Na correlations in an HNN-COSY spectrum may be recovered from CH-Nd correlations in the H(CN)N(H) spectrum. By correlating a different set of nuclei relative to the HNN-COSY class of experiments, the H(CN)N(H) experiment also serves to remove ambiguities associated with degeneracies in HNN-COSY spectra. The technique is demonstrated on d(GGAGGAG)4,a quadruplex containing a novel A. (G.G.G.G). A hexad and on d(GGGCAGGT)4, containing a G.G.G.C tetrad, in which missing NH2...N7 correlations are retrieved via H8-(N2,N6) correlations in the H(CN)N(H) spectrum.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenine / chemistry
  • Base Pairing*
  • Guanine / chemistry
  • Hydrogen Bonding
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation
  • Protons

Substances

  • Protons
  • Guanine
  • Adenine